From a.janke at gmail.com  Thu Aug  8 02:43:58 2013
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 8 Aug 2013 16:43:58 +1000
Subject: [MINC-development] Updated nii2mnc courtesy of Claude
Message-ID: <CAG0CB23drVVtxhwUto-oyUS0OmQ9OEUK8=+3_qvYs-OWmNoEjA@mail.gmail.com>

Hi all,

Claude has sent me some changes to nii2mnc that takes care of the
s-form + q-form issues plus some of the large data issues. This is
somewhat topical given the recent number of NIfti->MINC conversion
topics on MINC-users.

   https://github.com/BIC-MNI/minc-tools/commit/c1e12dcc45b068cb90c367af68e34b04e3375f1f

I have put it through some testing so far but would appreciate if
others could too. Ideally this should all be converted to use niftilib
but that's probably a job for another day.

ta


a

From steve at sumost.ca  Fri Aug 16 11:35:19 2013
From: steve at sumost.ca (Steve M. Robbins)
Date: Fri, 16 Aug 2013 10:35:19 -0500
Subject: [MINC-development] Fwd: Bug#719502: minc: FTBFS with perl 5.18: POD
	errors
Message-ID: <21872290.maTStMNO8S@riemann>

Hi MINC developers,

FYI: new perl causes problems.  

Regards,
-Steve
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From: Dominic Hargreaves <dom at earth.li>
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From a.janke at gmail.com  Mon Aug 19 17:11:39 2013
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 20 Aug 2013 07:11:39 +1000
Subject: [MINC-development] Fwd: Bug#719502: minc: FTBFS with perl 5.18:
 POD errors
In-Reply-To: <21872290.maTStMNO8S@riemann>
References: <21872290.maTStMNO8S@riemann>
Message-ID: <CAG0CB22Tv_fkxVXP9nK5Yz=svi62-qRFnmqDjhw_PWwSLyP-PA@mail.gmail.com>

Thanks Steve,

See:


https://github.com/BIC-MNI/minc-tools/commit/575e6846768a67964b00ac995380270e10ca0529

While you are here 2 things:

1. You may or may not have noticed that MINC is now libminc and minc-tools,
this was for integration into ITK.

2. As part of the ITK thing, there is now a parallel cmake build of
MINC/minc-tools. I have been reading up what I can on this and it would
seem that this is now OK to build for Debian. Given that you are the MINC
debian package maintainer, what's your thoughts on us shifting to cmake for
build?


a



On 17 August 2013 01:35, Steve M. Robbins <steve at sumost.ca> wrote:

> Hi MINC developers,
>
> FYI: new perl causes problems.
>
> Regards,
> -Steve
>
>
> ---------- Forwarded message ----------
> From: Dominic Hargreaves <dom at earth.li>
> To: submit at bugs.debian.org
> Cc:
> Date: Mon, 12 Aug 2013 17:35:22 +0200
> Subject: Bug#719502: minc: FTBFS with perl 5.18: POD errors
> Source: minc
> Version: 2.2.00-1
> Severity: important
> User: debian-perl at lists.debian.org
> Usertags: perl-5.18-transition
>
> This package FTBFS with perl 5.18 (which will soon be uploaded to
> unstable) owing to a stricter pod2man:
>
> /usr/bin/pod2man --section=1 progs/mincpik/mincpik >
> progs/mincpik/mincpik.man1
> progs/mincpik/mincpik around line 580: You forgot a '=back' before '=head3'
> progs/mincpik/mincpik around line 582: '=item' outside of any '=over'
> progs/mincpik/mincpik around line 599: You forgot a '=back' before '=head3'
> progs/mincpik/mincpik around line 601: '=item' outside of any '=over'
> progs/mincpik/mincpik around line 618: You forgot a '=back' before '=head3'
> progs/mincpik/mincpik around line 620: '=item' outside of any '=over'
> POD document had syntax errors at /usr/bin/pod2man line 71.
>
> This is also the lintian warning:
> <http://lintian.debian.org/tags/manpage-has-errors-from-pod2man.html>
>
> Thanks,
> Dominic.
>
>
>
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>
>
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From steve at sumost.ca  Sat Aug 24 23:35:53 2013
From: steve at sumost.ca (Steve M. Robbins)
Date: Sat, 24 Aug 2013 22:35:53 -0500
Subject: [MINC-development] Fwd: Bug#719502: minc: FTBFS with perl 5.18:
	POD errors
In-Reply-To: <CAG0CB22Tv_fkxVXP9nK5Yz=svi62-qRFnmqDjhw_PWwSLyP-PA@mail.gmail.com>
References: <21872290.maTStMNO8S@riemann>
	<CAG0CB22Tv_fkxVXP9nK5Yz=svi62-qRFnmqDjhw_PWwSLyP-PA@mail.gmail.com>
Message-ID: <2378952.H3NEBngYp7@riemann>

On August 20, 2013 07:11:39 AM Andrew Janke wrote:

> See:
> https://github.com/BIC-MNI/minc-tools/commit/575e6846768a67964b00ac995380270
> e10ca0529

Great!  Thanks!!

 
> While you are here 2 things:
> 
> 1. You may or may not have noticed that MINC is now libminc and minc-tools,
> this was for integration into ITK.

OK, I can see that in the github.  What does this mean for releases?  Have any 
been made since MINC 2.2.00?


> 2. As part of the ITK thing, there is now a parallel cmake build of
> MINC/minc-tools. I have been reading up what I can on this and it would
> seem that this is now OK to build for Debian. Given that you are the MINC
> debian package maintainer, what's your thoughts on us shifting to cmake for
> build?

CMake certainly has the advantage of being cross-platform.  If the concensus 
is to shift, I have no objection.

-Steve

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From a.janke at gmail.com  Mon Aug 26 03:15:53 2013
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 26 Aug 2013 09:15:53 +0200
Subject: [MINC-development] Fwd: Bug#719502: minc: FTBFS with perl 5.18:
 POD errors
In-Reply-To: <2378952.H3NEBngYp7@riemann>
References: <21872290.maTStMNO8S@riemann>
	<CAG0CB22Tv_fkxVXP9nK5Yz=svi62-qRFnmqDjhw_PWwSLyP-PA@mail.gmail.com>
	<2378952.H3NEBngYp7@riemann>
Message-ID: <CAG0CB20Jj23ij0xCKorPSsdy1RsDDVaFtGpM_ZSZdBbZjbP1ag@mail.gmail.com>

> > While you are here 2 things:
> >
> > 1. You may or may not have noticed that MINC is now libminc and
> minc-tools,
> > this was for integration into ITK.
>
> OK, I can see that in the github.  What does this mean for releases?  Have
> any
> been made since MINC 2.2.00?


No release has been made since 2.2.00 but one is imminent. I have been
doing a lot of testing on the new build and changes that have been made
since splitting the package.


> > 2. As part of the ITK thing, there is now a parallel cmake build of
> > MINC/minc-tools. I have been reading up what I can on this and it would
> > seem that this is now OK to build for Debian. Given that you are the MINC
> > debian package maintainer, what's your thoughts on us shifting to cmake
> for
> > build?
>
> CMake certainly has the advantage of being cross-platform.  If the
> concensus
> is to shift, I have no objection.


OK, in the absence of others input then I say we dump automake/autoconf and
go with CMake given all the work that Vladimir has put into this. You will
also note that volume_io is now merged into minc itself as part of a larger
effort of rationalisation.

Steve, do you happen to know of any implications of using CMake with
libtool and release versioning of libraries?

Thanks


a
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From steve at sumost.ca  Mon Aug 26 22:22:32 2013
From: steve at sumost.ca (Steve M. Robbins)
Date: Mon, 26 Aug 2013 21:22:32 -0500
Subject: [MINC-development] Fwd: Bug#719502: minc: FTBFS with perl 5.18:
	POD errors
In-Reply-To: <CAG0CB20Jj23ij0xCKorPSsdy1RsDDVaFtGpM_ZSZdBbZjbP1ag@mail.gmail.com>
References: <21872290.maTStMNO8S@riemann> <2378952.H3NEBngYp7@riemann>
	<CAG0CB20Jj23ij0xCKorPSsdy1RsDDVaFtGpM_ZSZdBbZjbP1ag@mail.gmail.com>
Message-ID: <1581218.zBTiWnxpd6@riemann>

On August 26, 2013 09:15:53 AM Andrew Janke wrote:

> Steve, do you happen to know of any implications of using CMake with
> libtool and release versioning of libraries?

Sorry, I don't actually develop libraries so I haven't looked into it.  A 
quick google suggests you need to use set_target_properties(); c.f. 
http://code.google.com/p/pugixml/source/diff?spec=svn812&r=812&format=side&path=/trunk/scripts/CMakeLists.txt

-Steve
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From a.janke at gmail.com  Mon Aug 26 22:28:46 2013
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 27 Aug 2013 04:28:46 +0200
Subject: [MINC-development] Fwd: Bug#719502: minc: FTBFS with perl 5.18:
 POD errors
In-Reply-To: <1581218.zBTiWnxpd6@riemann>
References: <21872290.maTStMNO8S@riemann> <2378952.H3NEBngYp7@riemann>
	<CAG0CB20Jj23ij0xCKorPSsdy1RsDDVaFtGpM_ZSZdBbZjbP1ag@mail.gmail.com>
	<1581218.zBTiWnxpd6@riemann>
Message-ID: <CAG0CB237SnvN46hx4ixE6xY5D0iboN0VEZ2+DZ0y3d6nLGJVZw@mail.gmail.com>

On 27 August 2013 04:22, Steve M. Robbins <steve at sumost.ca> wrote:

>
> Sorry, I don't actually develop libraries so I haven't looked into it.  A
> quick google suggests you need to use set_target_properties(); c.f.
>
> http://code.google.com/p/pugixml/source/diff?spec=svn812&r=812&format=side&path=/trunk/scripts/CMakeLists.txt



OK,

A bit of searching on this leads me here:


http://cmake.org/cmake/help/v2.8.8/cmake.html#command:set_target_properties

Vladimir, can you please have a look at this and add this into the libminc
cmake build? With this done we can ditch automake/autoconf.

Thanks



a
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From vladimir.fonov at gmail.com  Tue Aug 27 00:42:29 2013
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Tue, 27 Aug 2013 00:42:29 -0400
Subject: [MINC-development] Fwd: Bug#719502: minc: FTBFS with perl 5.18:
 POD errors
In-Reply-To: <CAG0CB237SnvN46hx4ixE6xY5D0iboN0VEZ2+DZ0y3d6nLGJVZw@mail.gmail.com>
References: <21872290.maTStMNO8S@riemann> <2378952.H3NEBngYp7@riemann>
	<CAG0CB20Jj23ij0xCKorPSsdy1RsDDVaFtGpM_ZSZdBbZjbP1ag@mail.gmail.com>
	<1581218.zBTiWnxpd6@riemann>
	<CAG0CB237SnvN46hx4ixE6xY5D0iboN0VEZ2+DZ0y3d6nLGJVZw@mail.gmail.com>
Message-ID: <CAMCwi7OVvCng6dQXPXcfhj=EBnUL63B=ZeouwHLtnfHLkSP5Dg@mail.gmail.com>

I think it's already there:
https://github.com/BIC-MNI/libminc/blob/develop/CMakeLists.txt#L336

On Mon, Aug 26, 2013 at 10:28 PM, Andrew Janke <a.janke at gmail.com> wrote:
>
> On 27 August 2013 04:22, Steve M. Robbins <steve at sumost.ca> wrote:
>>
>>
>> Sorry, I don't actually develop libraries so I haven't looked into it.  A
>> quick google suggests you need to use set_target_properties(); c.f.
>>
>> http://code.google.com/p/pugixml/source/diff?spec=svn812&r=812&format=side&path=/trunk/scripts/CMakeLists.txt
>
>
>
> OK,
>
> A bit of searching on this leads me here:
>
>
> http://cmake.org/cmake/help/v2.8.8/cmake.html#command:set_target_properties
>
> Vladimir, can you please have a look at this and add this into the libminc
> cmake build? With this done we can ditch automake/autoconf.
>
> Thanks
>
>
>
> a



-- 
Best regards,

 Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com

From a.janke at gmail.com  Tue Aug 27 02:52:12 2013
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 27 Aug 2013 08:52:12 +0200
Subject: [MINC-development] Fwd: Bug#719502: minc: FTBFS with perl 5.18:
 POD errors
In-Reply-To: <CAMCwi7OVvCng6dQXPXcfhj=EBnUL63B=ZeouwHLtnfHLkSP5Dg@mail.gmail.com>
References: <21872290.maTStMNO8S@riemann> <2378952.H3NEBngYp7@riemann>
	<CAG0CB20Jj23ij0xCKorPSsdy1RsDDVaFtGpM_ZSZdBbZjbP1ag@mail.gmail.com>
	<1581218.zBTiWnxpd6@riemann>
	<CAG0CB237SnvN46hx4ixE6xY5D0iboN0VEZ2+DZ0y3d6nLGJVZw@mail.gmail.com>
	<CAMCwi7OVvCng6dQXPXcfhj=EBnUL63B=ZeouwHLtnfHLkSP5Dg@mail.gmail.com>
Message-ID: <CAG0CB20v5ZSNbG0c24+6Gh4i1-eB17JCLf7n-yRtaDe0j5J_uw@mail.gmail.com>

Hi Vladimir,

The library version (libtool) does not and in most cases should not match
the code release version. Confusing I know but required. See this:

   https://github.com/BIC-MNI/libminc/blob/develop/README.release

For more detail. This is what allows libtool to work and sort out
incompatible and compatible shared library changes.

So yes, it is in there but we will have to update the cmake stuff to better
match this. We need to keep the libtool version info correct or else we
will hit all sorts of libtool problems in the future.


a



On 27 August 2013 06:42, Vladimir S. FONOV <vladimir.fonov at gmail.com> wrote:

> I think it's already there:
> https://github.com/BIC-MNI/libminc/blob/develop/CMakeLists.txt#L336
>
> On Mon, Aug 26, 2013 at 10:28 PM, Andrew Janke <a.janke at gmail.com> wrote:
> >
> > On 27 August 2013 04:22, Steve M. Robbins <steve at sumost.ca> wrote:
> >>
> >>
> >> Sorry, I don't actually develop libraries so I haven't looked into it.
>  A
> >> quick google suggests you need to use set_target_properties(); c.f.
> >>
> >>
> http://code.google.com/p/pugixml/source/diff?spec=svn812&r=812&format=side&path=/trunk/scripts/CMakeLists.txt
> >
> >
> >
> > OK,
> >
> > A bit of searching on this leads me here:
> >
> >
> >
> http://cmake.org/cmake/help/v2.8.8/cmake.html#command:set_target_properties
> >
> > Vladimir, can you please have a look at this and add this into the
> libminc
> > cmake build? With this done we can ditch automake/autoconf.
> >
> > Thanks
> >
> >
> >
> > a
>
>
>
> --
> Best regards,
>
>  Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
>
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