Re: Plans for ITK version 4

2012-04-23 Thread Steve M. Robbins
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 even build whereas before they did build. Still others claim a dependency installability problem

Re: Plans for ITK version 4

2012-04-23 Thread Steve M. Robbins
Hi, To recap: I can build ITK 4.1.0 and run the test suite on Debian/unstable amd64 machine. However, the 32-bit i86 fails on seven FFT tests. Yaroslav provided some output from a Debug run: PlanRigor: FFTW_EXHAUSTIVE (8) ITKFFTTestDriver:

Re: Status of Altree

2012-04-23 Thread Andreas Tille
Hi Vincent, On Mon, Apr 23, 2012 at 02:58:48AM +0200, Vincent Danjean wrote: Sorry for not answering the previous mail. I exchanged a few mails with Claire about it and then I completely forgot about it. Sorry also from my side to push that hard about this. Claire released altree 1.2

Re: Status of Altree

2012-04-23 Thread Vincent Danjean
Le 23/04/2012 08:06, Andreas Tille a écrit : Hi Vincent, On Mon, Apr 23, 2012 at 02:58:48AM +0200, Vincent Danjean wrote: Sorry for not answering the previous mail. I exchanged a few mails with Claire about it and then I completely forgot about it. Sorry also from my side to push that

Build bowtie using gcc-4.7

2012-04-23 Thread Andreas Tille
Hi Ben, as you know the Debian Med team has packaged bowtie for Debian. We also do provide bowtie2 as a separate package because there is some usecase for the old version. Everything I'm writing here applies to bowtie 0.12.7 which was downloaded from:

Re: Plans for ITK version 4

2012-04-23 Thread Yaroslav Halchenko
meanwhile I will blindly try to build/test it against fftw3 in experimental -- who knows, may be it is their bug ;) On Mon, 23 Apr 2012, Steve M. Robbins wrote: I just ran ITKFFTTestDriver itkFFTWF_FFTTest through valgrind with the following results. Any ideas of what to look at next are

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 even build whereas before they did

Fwd: RE: Bug#667156: Bug#667156: epcr: ftbfs with GCC-4.7

2012-04-23 Thread Schuler, Greg (NIH/NLM/NCBI) [E]
Forwarding to the developer. Thanks for the information. -Original Message- From: Andreas Tille [mailto:ti...@debian.org] Sent: Monday, April 23, 2012 2:09 AM To: Debian Med Project List Cc: Schuler, Greg (NIH/NLM/NCBI) [E] Subject: Re: Bug#667156: Bug#667156: epcr: ftbfs with GCC-4.7

Re: Patch for PLink to build using gcc-4.7 - please confirm that it is correct

2012-04-23 Thread Shaun Jackman
Hi Andreas, I'd suggest using a scoped for loop rather than the original while loop. Cheers, Shaun On 2012-04-23, at 1:30 AM, Andreas Tille wrote: Hi Shaun, as you know the Debian Med team has packaged plink for Debian. Recently we received a bug report that the package does not build

Re: Patch for PLink to build using gcc-4.7 - please confirm that it is correct

2012-04-23 Thread Andreas Tille
Hi Shaun, On Mon, Apr 23, 2012 at 08:43:22AM -0700, Shaun Jackman wrote: I'd suggest using a scoped for loop rather than the original while loop. Hi guess for a C++ programmer this hint is perfectly simple to implement however, for me this does not ring a bell without a patch. Thanks for the

RE: RE: Bug#667156: Bug#667156: epcr: ftbfs with GCC-4.7

2012-04-23 Thread Rotmistrovsky, Kirill (NIH/NLM/NCBI) [C]
I've applied the fix. Updated sources are on ftp. -- Thanks, Kirill Rotmistrovsky -Original Message- From: Schuler, Greg (NIH/NLM/NCBI) [E] Sent: Monday, April 23, 2012 9:50 AM To: Rotmistrovsky, Kirill (NIH/NLM/NCBI) [C] Cc: Andreas Tille; Debian Med Project List Subject: Fwd:

Re: Patch for PLink to build using gcc-4.7 - please confirm that it is correct

2012-04-23 Thread Shaun Jackman
No worries, Andreas. It's just a coding style suggestion. Your solution is perfectly fine. Cheers, Shaun On 23 April 2012 11:48, Andreas Tille ti...@debian.org wrote: Hi Shaun, On Mon, Apr 23, 2012 at 08:43:22AM -0700, Shaun Jackman wrote: I'd suggest using a scoped for loop rather than the

Source package names and VCS URLs.

2012-04-23 Thread Charles Plessy
Dear all, for some of the packages in our Subversion or Git repositories, the path (URL) to the repository does not match its source package name. For instance, epcr is in svn://svn.debian.org/debian-med/trunk/packages/ncbi-epcr/. This slightly complicates some automated browsing of our

Re: Plans for ITK version 4

2012-04-23 Thread Steve M. Robbins
On Mon, Apr 23, 2012 at 09:40:28AM -0400, Paul Novotny wrote: SO, in the end, I learned more than I wanted. And the solution is probably to include my patch, changing #if to #ifdef. I agree. It never occurred to me that someone (#cmakedefine) would write #define WORDS_BIGENDIAN rather than