Re: Status of ITK 4.8 packaging

2015-07-26 Thread Paul Novotny
On Sat, 2015-07-25 at 14:01 -0500, Steve M. Robbins wrote: > Paul: thanks for this! > > > On July 25, 2015 01:21:33 PM Paul Novotny wrote: > > On Fri, 2015-07-24 at 19:34 -0500, Steve Robbins wrote: > > > Sure! Commit away. > > > > K, I commited it. I m

Re: Status of ITK 4.8 packaging

2015-07-25 Thread Paul Novotny
On Fri, 2015-07-24 at 19:34 -0500, Steve Robbins wrote: > Sure! Commit away. K, I commited it. I moved the code I had in debian/update.sh to get -orig-source in debian/rules. That seems to follow more what I have seen in debian-med. Also, I renamed the ExternalData directory to data. Just so th

Re: Status of ITK 4.8 packaging

2015-07-24 Thread Paul Novotny
On Fri, 2015-07-24 at 17:45 -0500, Steve M. Robbins wrote: > On July 21, 2015 04:46:40 PM Paul Novotny wrote: > > On Mon, 2015-07-20 at 11:34 -0500, Steve M. Robbins wrote: > > > 1. Upstream now separates the test data from the source tarball. > > > I > > > w

Re: Status of ITK 4.8 packaging

2015-07-21 Thread Paul Novotny
On Mon, 2015-07-20 at 11:34 -0500, Steve M. Robbins wrote: > 1. Upstream now separates the test data from the source tarball. I > would like > to keep the tests so I planned to use the "multiple orig tarball" > feature. I > believe I've done it before with ITK but last week "svn buildpackage"

Re: Status of ITK 4.8 packaging

2015-07-21 Thread Paul Novotny
On Tue, 2015-07-21 at 13:07 -0500, Steve M. Robbins wrote: > On July 20, 2015 04:09:24 PM Paul Novotny wrote: > > On Mon, 2015-07-20 at 11:34 -0500, Steve M. Robbins wrote: > > > 2. I disabled patches/0005-make-gdcm-helper-library-static.patch > > > because it > >

Re: Status of ITK 4.8 packaging

2015-07-20 Thread Paul Novotny
On Mon, 2015-07-20 at 11:34 -0500, Steve M. Robbins wrote: > 2. I disabled patches/0005-make-gdcm-helper-library-static.patch > because it > did not apply cleanly. I did not spend time investigating how to fix > it or > whether it is even needed. I just tried this, and the patch appears to ap

Breaking ABI in shlibs (yaml-cpp)

2015-05-18 Thread Paul Novotny
I recently updated yaml-cpp from 0.5.1 to 0.5.2. This caused a bug in a dependent package [1]. It turns out, 0.5.2 is not binary compatible with 0.5.1 (abi-compliance-checker confirms this) and is probably the source of the bug. Does anyone have advice? What should I do to resolve this? Thanks, -P

Re: Updates to yaml-cpp and opensurgsim

2015-04-30 Thread Paul Novotny
On Thu, 2015-04-30 at 16:47 +0200, Andreas Tille wrote: > On Tue, Apr 28, 2015 at 08:03:58PM -0400, Paul Novotny wrote: > > > Uploaded to unstable. Thanks for your preparation. > > > > I noticed that only amd64 seems to be available. I can't figure out >

Re: Updates to yaml-cpp and opensurgsim

2015-04-28 Thread Paul Novotny
On Sun, Apr 26, 2015, at 03:54 PM, Andreas Tille wrote: > On Sun, Apr 26, 2015 at 12:37:13PM -0400, Paul Novotny wrote: > > Hello, I just updated two packages I worked on for a MoM in February. > > Yaml-cpp released a new version (0.5.2) so I updated the packaging in > > col

Updates to yaml-cpp and opensurgsim

2015-04-26 Thread Paul Novotny
Hello, I just updated two packages I worked on for a MoM in February. Yaml-cpp released a new version (0.5.2) so I updated the packaging in collab-maint [1]. I also updated opensurgsim to use this new version of yaml-cpp [2]. During the MoM, Andreas sponsered my changes and pushed out a new version

Re: [MoM] Packaging OpenSurgSim

2015-03-04 Thread Paul Novotny
On Mon, 2015-03-02 at 15:16 +0100, Andreas Tille wrote: > > Finally, I would like to stay involved with debian-med, to keep > > OpenSurgSim (and yaml-cpp) up to date and help out where I can. > Would > > you consider being an advocate for me? I would like to apply to be a > > Debian Maintainer [1],

Re: [MoM] Packaging OpenSurgSim

2015-03-02 Thread Paul Novotny
On Fri, 2015-02-27 at 12:27 +0100, Andreas Tille wrote: > I'm not sure when I will be able to have a (possibly final) look. I'm > a > bit busy with real life this weekend but I'll see what I can do. I > think > we are so cloes to the final upload that our goal to get the package > until > end of

Re: [MoM] Packaging OpenSurgSim

2015-02-26 Thread Paul Novotny
On Wed, 2015-02-25 at 16:28 +0100, Andreas Tille wrote: > Hi Paul, > > On Tue, Feb 24, 2015 at 09:45:07AM +0100, Andreas Tille wrote: > > Hi Paul, > > > > On Mon, Feb 23, 2015 at 09:51:11PM -0500, Paul Novotny wrote: > > > I am back to packaging OpenSurgSim,

Re: [MoM] Packaging OpenSurgSim

2015-02-23 Thread Paul Novotny
Andreas, I am back to packaging OpenSurgSim, now that yaml-cpp has been added to experimental. I just pushed changes that add yaml-cpp as a build-depends, fixes the naming of the shared libraries to include the version number, and adds DEP3 headers to the patches. The packaging now runs completely

Re: camitk vs. mitk vs. slicer?

2015-02-23 Thread Paul Novotny
I have not used mitk or camitk, so I can't answer your question directly. But I have had luck prototyping applications using itk and vtk in python. It gives you a Matlab-y way to try things out in ITK, and visualize in VTK (or matplotlib). There are some rough parts, like remembering how to move da

Re: Yaml-cpp now in collab-maint git (Was: Maintaining yaml-cpp in collab-maint? (Was: [MoM] Packaging OpenSurgSim))

2015-02-21 Thread Paul Novotny
On Fri, Feb 20, 2015, at 01:59 AM, Andreas Tille wrote: > Technically yes, but I would like you to add DEP3[1] headers at least to > the patches you added / changed. Lintian -i -I will tell you that the > headers are missing. I consider them important for other Debian > maintainers who joing the

Re: Yaml-cpp now in collab-maint git (Was: Maintaining yaml-cpp in collab-maint? (Was: [MoM] Packaging OpenSurgSim))

2015-02-19 Thread Paul Novotny
On Wed, Feb 18, 2015, at 08:57 AM, Andreas Tille wrote: > > I also fixed a couple bugs in yaml-cpp that caused build failures and > > added them as quilt patches. > > It might make sense to forward these upstream before they release. Will do. > If you consider the current status of yaml-cpp as f

Re: Yaml-cpp now in collab-maint git (Was: Maintaining yaml-cpp in collab-maint? (Was: [MoM] Packaging OpenSurgSim))

2015-02-17 Thread Paul Novotny
On Tue, Feb 17, 2015, at 09:50 AM, Andreas Tille wrote: > Hi Paul, > > On Mon, Feb 09, 2015 at 08:07:37PM -0500, p...@paulnovo.us wrote: > > > > Please grant access for Paul Novotny (paulnovo-guest) to > > collab-maint. We are going to work together on project y

Re: [MoM] Packaging OpenSurgSim

2015-01-29 Thread Paul Novotny
On Mon, 2015-01-26 at 17:36 +0100, Andreas Tille wrote: > > Should I get in touch with the maintainer of Debian > > yaml-cpp to see if I can help getting the new version packaged? > > This sounds sensible. Considering the old debhelper and Standards-Version > > $ apt-cache showsrc yaml-cpp > Pac

Re: [MoM] Packaging OpenSurgSim

2015-01-26 Thread Paul Novotny
On Fri, 2015-01-23 at 16:24 +0100, Andreas Tille wrote: > > > I think this is actually a *related* note. Does this > "unsuccessful so > > > far" mean upstream has a problem to integrate the changes or did > not yet > > > released a version which does contain the changes? Its Debian > policy do >

Re: [MoM] Packaging OpenSurgSim

2015-01-23 Thread Paul Novotny
On Fri, 2015-01-23 at 12:34 +0100, Andreas Tille wrote: > Hi Paul, > > On Thu, Jan 22, 2015 at 07:58:43PM -0500, p...@paulnovo.us wrote: > > Ok, so I have created the git repository for packaging OpenSurgSim: > > > > git://anonscm.debian.org/debian-med/opensurgsim.git > > > > And put up an ini

Re: [Fwd: Bug#775753: ITP: opensurgsim -- A free platform for surgical simulation]

2015-01-20 Thread Paul Novotny
On Mon, 2015-01-19 at 22:52 +0100, Andreas Tille wrote: > Hi Paul, > > On Mon, Jan 19, 2015 at 11:27:42AM -0500, Paul Novotny wrote: > > First of, does this project fit debian-med? It is similar to SOFA, which > > I see is a currently a debian-med package, in the Imagin

[Fwd: Bug#775753: ITP: opensurgsim -- A free platform for surgical simulation]

2015-01-19 Thread Paul Novotny
t the documentation has instructions for running "setup-repository" on git.debian.org. I have an Alioth account, is this what I should do? Finally, would this effort be a good candidate for a MoM? -Paul Forwarded Message ---- > From: Paul Novotny > Reply-to: Paul Novotny , 7

Bug#775753: ITP: opensurgsim -- A free platform for surgical simulation

2015-01-19 Thread Paul Novotny
Package: wnpp Severity: wishlist Owner: Paul Novotny * Package name: opensurgsim Version : 0.6.0 Upstream Author : Paul Novotny * URL : http://www.opensurgsim.org/ * License : Apache 2.0 Programming Lang: C++ Description : A free platform for surgical

Re: itk-4.5 and python

2014-03-26 Thread Paul Novotny
On Wed, 2014-03-26 at 12:10 +0100, Gert Wollny wrote: >"-Wall -Wextra -Wdeprecated-declarations -O2 -g -funroll-loops > -ftree-vectorize -pthread -march=native -mtune=native" > > in the shell, and when I don't undefine these before running > svn-buildpackage they are actually used, resulting

Re: itk and big endian arcitectures

2014-03-09 Thread Paul Novotny
On Sat, 2014-03-08 at 09:53 -0600, Steve M. Robbins wrote: > > Can we turn on the other architectures to get an idea of what issues > > still remain? > > You can get an idea of the issues by looking through the older build logs > already present. Thanks. I just found those. Yes, it does look the

itk and big endian arcitectures

2014-03-07 Thread Paul Novotny
Steve, I noticed that itk is only being built on i386 and amd64 at the moment. I haven't been keeping up with itk in debian for a bit, but is this due to the failures we were seeing on big endian machines last summer? Can we turn on the other architectures to get an idea of what issues still rem

Re: itk-4.5 and python

2014-03-07 Thread Paul Novotny
On Fri, 2014-03-07 at 12:08 +0100, Gert Wollny wrote: > Hello, > > >> I haven't tested to build it in a pbuilder environment yet. I'll get > >> back to you when this is done in for i386 and amd64, Just running these > >> which will probably take two more days. > > amd64 run fine, but i386 hit a

Hiring for Open Source Surgical Simulator Project

2013-08-28 Thread Paul Novotny
Hello debian-med, I don't know if this is the best place to post this, but my company, SimQuest [1], is looking to hire software engineers to work on an open source surgical simulation platform [2]. BTW, it is multi-platform and we are targeting and developing on Debian. So sometime soon, I'll be b

Re: itk and tiff

2013-03-20 Thread Paul Novotny
On Wed, 2013-03-20 at 08:50 +0100, Mathieu Malaterre wrote: > >> Anyway I should probably summarize what I have been trying to do lately. > >> Basically, I have been trying to get all the tests to pass on a sparc > >> machine. From what I can tell, most of them have to do with gdcm, and it > >> not

Re: itk and tiff

2013-03-19 Thread Paul Novotny
On Mon, 2013-03-18 at 00:56 -0500, Steve M. Robbins wrote: > Hi Paul, > > Just getting back to some ITK work... > > On February 13, 2013 08:21:52 AM Paul Novotny wrote: > > > So, long story short, we should use system tiff > > (-DITK_USE_SYSTEM_TIFF:BOOL=ON) an

itk and tiff

2013-02-13 Thread Paul Novotny
Ok, so itk is failing to build on big endian systems because of the TIFF that is included with itk. I fixed this before, but it has come back. I sent a patch upstream [1], and it has been merged and will probably be in the next release. However, we should probably use the system TIFF. The reason

Re: ITK 4 and Python

2013-01-04 Thread Paul Novotny
On Thu, 2013-01-03 at 14:37 -0500, Paul Novotny wrote: > On Thu, 2013-01-03 at 13:15 +0100, Gert Wollny wrote: > > On 01/02/13 23:57, Steve M. Robbins wrote: > > > On December 29, 2012 04:20:57 PM Paul Novotny wrote: > > >> On Thu, 2012-12-27 at 10:26 -0600, Steve M.

Re: ITK 4 and Python

2013-01-03 Thread Paul Novotny
On Thu, 2013-01-03 at 09:02 -0500, Yaroslav Halchenko wrote: > On Wed, 02 Jan 2013, Steve M. Robbins wrote: > > > > Any chance I could get access to non i386/amd64 machines? I thought > > > someone mentioned there was a way to test things on the other > > > architectures, but i can't remember the

Re: ITK 4 and Python

2013-01-03 Thread Paul Novotny
On Thu, 2013-01-03 at 13:15 +0100, Gert Wollny wrote: > On 01/02/13 23:57, Steve M. Robbins wrote: > > On December 29, 2012 04:20:57 PM Paul Novotny wrote: > >> On Thu, 2012-12-27 at 10:26 -0600, Steve M. Robbins wrote: > > > >>> I haven't yet succeeded at

Re: ITK 4 and Python

2013-01-03 Thread Paul Novotny
On Wed, 2013-01-02 at 16:57 -0600, Steve M. Robbins wrote: > > > I haven't yet succeeded at getting the build stable, so help on > that > > > would be appreciated! > > By the way, I have updated the debian subversion repository [1] to the > newest > release ITK 4.3.1. It builds on my x86 and amd

Re: ITK 4 and Python

2012-12-29 Thread Paul Novotny
On Thu, 2012-12-27 at 10:26 -0600, Steve M. Robbins wrote: > On December 24, 2012 11:08:17 AM Paul Novotny wrote: > > I was thinking of taking a crack at enabling the python wrappings for > > insighttoolkit4. Correct me if I am wrong, but this was never enabled > > a

ITK 4 and Python

2012-12-24 Thread Paul Novotny
I was thinking of taking a crack at enabling the python wrappings for insighttoolkit4. Correct me if I am wrong, but this was never enabled after the upgrade from insighttoolkit3 to insighttoolkit4? Has there been any previous progress on this? -Paul -- To UNSUBSCRIBE, email to debian-med-requ.

Re: ITK 4.1 patches for gcc 4.7

2012-06-26 Thread Paul Novotny
On Thu, 2012-06-14 at 15:27 -0400, Paul Novotny wrote: > On Wed, 2012-06-13 at 09:11 -0400, Paul Novotny wrote: > > > > Hopefully these fix some of the errors on the other architectures, > > > > although I think i386 has more failures. > > > > > &g

Re: ITK 4.1 patches for gcc 4.7

2012-06-14 Thread Paul Novotny
On Wed, 2012-06-13 at 09:11 -0400, Paul Novotny wrote: > > > Hopefully these fix some of the errors on the other architectures, > > > although I think i386 has more failures. > > > > Yes, it does: http://open.cdash.org/viewTest.php?onlyfailed&buildid=2355571 >

Re: ITK 4.1 patches for gcc 4.7

2012-06-13 Thread Paul Novotny
On Wed, 2012-06-13 at 02:13 -0500, Steve M. Robbins wrote: > > SpatialObject-Test-Segfaults.patch: Fixes the segfaults, in the spatial > > object tests. > > The comment indicates "not 100% sure why this works. ComputeMatrix > looks fine". This sounds like it could be a work around for gcc bug? >

ITK 4.1 patches for gcc 4.7

2012-06-12 Thread Paul Novotny
no longer on the stack. Author: Paul Novotny --- debian-svn.orig/Modules/Numerics/FEM/test/itkFEMElement2DTest.cxx +++ debian-svn/Modules/Numerics/FEM/test/itkFEMElement2DTest.cxx @@ -90,7 +90,8 @@ femSO->GetFEMObject()->FinalizeMesh(); - double *expectedSolut

Re: [Insight-developers] FEM debian test failures

2012-06-12 Thread Paul Novotny
this link to subscribe/unsubscribe: > > http://www.itk.org/mailman/listinfo/insight-developers > > > > > > > > > > Bradley Lowekamp > > > > Medical Science and Computing for > > > > Of

Re: Plans for ITK version 4

2012-06-08 Thread Paul Novotny
ile the tests were giving the right result, the expectedSolution was wrong. This change just sets expectedSolution directly instead of pointing it to the first element in an array that is no longer on the stack. Author: Paul Novotny --- debian-svn.orig/Modules/Numerics/FEM/test/itkFEMEleme

Re: Plans for ITK version 4

2012-06-06 Thread Paul Novotny
On Tue, 2012-06-05 at 21:33 -0500, Steve M. Robbins wrote: > On Sun, Jun 03, 2012 at 02:17:52PM -0400, Paul Novotny wrote: > > On Sun, 2012-06-03 at 00:11 -0500, Steve M. Robbins wrote: > > > On Sat, Jun 02, 2012 at 06:38:16PM -0400, Paul Novotny wrote: > > > > On

Re: Plans for ITK version 4

2012-06-03 Thread Paul Novotny
On Sun, 2012-06-03 at 00:11 -0500, Steve M. Robbins wrote: > On Sat, Jun 02, 2012 at 06:38:16PM -0400, Paul Novotny wrote: > > On Sat, 2012-06-02 at 16:06 -0500, Steve M. Robbins wrote: > > > First order of business is to go through the buildd logs and get a > > > li

Re: Plans for ITK version 4

2012-06-02 Thread Paul Novotny
On Sat, 2012-06-02 at 16:06 -0500, Steve M. Robbins wrote: > First order of business is to go through the buildd logs and get a > list of the issues. There is only one issue currently filed > (#670609), a trivial missing "Conflicts". Can you push the latest changes to the build servers? I notice

Re: Plans for ITK version 4

2012-06-02 Thread Paul Novotny
What is the status of ITK version 4? I noticed that Wheezy is going to freeze soon, and was wondering what I could do to help get this into testing. Or is it too late? Whether it gets into Wheezy or not, I have some time to work on this. Anyone know what the current issues are? -Paul -- To UNS

Re: Plans for ITK version 4

2012-04-23 Thread Paul Novotny
On Mon, 2012-04-23 at 00:50 -0500, Steve M. Robbins wrote: > On Mon, Mar 19, 2012 at 04:46:42PM -0400, Paul Novotny wrote: > > On Sun, 2012-03-04 at 13:09 -0600, Steve M. Robbins wrote: > > > Other architectures show a regression in that now the libraries don't > > >

Re: Plans for ITK version 4

2012-03-19 Thread Paul Novotny
On Sun, 2012-03-04 at 13:09 -0600, Steve M. Robbins wrote: > Other architectures show a regression in that now the libraries don't > even build whereas before they did build. Still others claim a > dependency installability problem for minc or gdcm. > > [1] > https://buildd.debian.org/status/pac

Re: Change InsightToolkit to use Review/Statistics?

2011-01-25 Thread Paul Novotny
On Sat, 2011-01-22 at 18:03 -0600, Steve M. Robbins wrote: > > * get-orig-source was still deleting the Code/Review directory. This > > directory is needed for WrapITK now. > > Debian's 3.20.0 ".orig.tar.gz" has Code/Review removed, so I have to > keep this in until the next upstream release is

Re: Change InsightToolkit to use Review/Statistics?

2011-01-22 Thread Paul Novotny
nice interface that will display these docs in the shell when you type something like "itk.Image?". I find it handy. Anyway, hope these help. -Paul >From 9ac6d3461862f041ee663b086f7f239090909cbb Mon Sep 17 00:00:00 2001 From: Paul Novotny Date: Tue, 18 Jan 2011 14:32:22 -0500 Subject:

Re: Change InsightToolkit to use Review/Statistics?

2010-11-08 Thread Paul Novotny
On Sun, 2010-11-07 at 12:21 -0600, Steve M. Robbins wrote: > > I am in the middle of packaging 3.20 myself for Ubuntu. I can send you > > the sources when I get it working, if you want. > > Oh! Is there any reason the Debian and Ubuntu packages couldn't > be the same? Rather than duplicate the w

Re: Change InsightToolkit to use Review/Statistics?

2010-11-07 Thread Paul Novotny
On Sat, 2010-11-06 at 16:36 -0500, Steve M. Robbins wrote: > Hello, > > On Fri, Oct 22, 2010 at 12:43:03PM -0400, Paul Novotny wrote: > > On Sun, 2010-10-17 at 23:04 -0500, Steve M. Robbins wrote: > > > > I'm considering switching to the new refactored Statistic

Re: Change InsightToolkit to use Review/Statistics?

2010-10-28 Thread Paul Novotny
On Wed, 2010-10-27 at 20:39 -0500, Steve M. Robbins wrote: > On Wed, Oct 27, 2010 at 10:29:50AM -0400, Paul Novotny wrote: > > On Fri, 2010-10-22 at 20:35 -0500, Steve M. Robbins wrote: > > > On Fri, Oct 22, 2010 at 12:43:03PM -0400, Paul Novotny wrote: > > > > >

Re: Change InsightToolkit to use Review/Statistics?

2010-10-27 Thread Paul Novotny
On Fri, 2010-10-22 at 20:35 -0500, Steve M. Robbins wrote: > On Fri, Oct 22, 2010 at 12:43:03PM -0400, Paul Novotny wrote: > > On Sun, 2010-10-17 at 23:04 -0500, Steve M. Robbins wrote: > > > Hi, > > > > > > I'm considering switching to the new refactored

Re: Change InsightToolkit to use Review/Statistics?

2010-10-22 Thread Paul Novotny
On Sun, 2010-10-17 at 23:04 -0500, Steve M. Robbins wrote: > Hi, > > I'm considering switching to the new refactored Statistics classes in > ITK. This is an API-breaking move so I'd like to hear of any concerns > before implementing this. > > The change would be done for version 3.20 of InsightT

Re: Update on WrapITK and debian

2010-05-24 Thread Paul Novotny
> On Mon, Nov 23, 2009 at 06:45:06PM +0100, Mathieu Malaterre wrote: > > Steve, > > > > I thought I should give an update. > > I have been trying for the past weeks to get WrapITK working without > > Review. I have to admit I never succeeded (see all my attempt > > commented out in the patch f