Bug#705495: #705495 tbb_4.1 (experimental)

2013-08-02 Thread Gert Wollny
Hello Mathieu, I installed the tbb version from experimental and can confirm that all test in MIA run through, i.e. this version of tbb fixes the bug. Best regards signature.asc Description: This is a digitally signed message part

Bug#705495: Tests fail to build on powerpc

2013-06-18 Thread Gert Wollny
I tried the new package, and one test fails to build on powerpc (sid, g ++ 4.6.4). The solution could be to replace the __sync_* calls by __atomic_* calls (like in #708929) The packages are build though, and the new version seems to fix #705385. [...] g++ -o test_atomic_compiler_builtins.exe

Bug#713551: 709554 blocks 713551

2013-06-22 Thread Gert Wollny
package src:mialmpick block 713551 by 709554 -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org

Bug#710818: pkg-config files also not installed

2013-06-22 Thread Gert Wollny
The bug most likely does result from switching from the configure based build system to the CMake based build system. As a result, also the pkg-config files (itpp*.pc) are no longer created and therefore, also not installed. Gert -- To UNSUBSCRIBE, email to

Bug#713683: mia: FTBFS: ../mia/3d/libmia3d-2.0.so.8.0.1: undefined reference to `mia::CICAAnalysis::set_row(int, itpp::Vecdouble const, double)'

2013-06-22 Thread Gert Wollny
On Sat, 2013-06-22 at 15:12 +0200, David Suárez wrote: Source: mia Version: 2.0.9-1 Severity: serious Tags: jessie sid User: debian...@lists.debian.org Usertags: qa-ftbfs-20130620 qa-ftbfs Justification: FTBFS on amd64 Hi, During a rebuild of all packages in sid, your package failed

Bug#713683: Fixing this bug

2013-06-27 Thread Gert Wollny
Hello, yes I did rebuild mia yesterday in an updated sid installation successfully. many thanks, Gert signature.asc Description: This is a digitally signed message part

Bug#705385: mia: FTBFS on powerpc: test suite hangs

2013-04-14 Thread Gert Wollny
On Sat, 2013-04-13 at 23:02 -0400, Aaron M. Ucko wrote: 207/228 Test #212: 3d-transform-rotation Passed0.40 sec Start 213: 3d-transform-spline Is this build run on a multi-core machine? The build log somehow suggests it is. I've seen something similar before on my

Bug#705384: mia: FTBFS on architectures such as ia64 lacking SSE or Altivec support

2013-04-14 Thread Gert Wollny
At least one of mia's source files requires SSE (x86) or Altivec (PowerPC) support: .../mia-2.0.8/mia/3d/reg3d/navierasse.cc:387:2: error: #error need SSE or ALTIVEC support I think it is better when I restrict the architectures where the module is build - currently I already do this for

Bug#705383: mia: FTBFS on i386: 3 tests failed out of 228

2013-04-14 Thread Gert Wollny
The fixes are already in the pipeline, but I was told that one should wait with a new upload until the package has been approved by ftpmaster. Best -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org

Bug#705385: mia: FTBFS on powerpc: test suite hangs

2013-04-15 Thread Gert Wollny
I can confirm that the test hangs on powerpc if more then one thread is used. The problem seems to lie somewhere in the thread cleanup routines of TBB, i.e. the parallel code of MIA is run, and then tbb::parallel_reduce/tbb:parallel_for do not return. According to the changelog the TBB release

Bug#705385: mia: FTBFS on powerpc: test suite hangs

2013-04-15 Thread Gert Wollny
The bug does not occur with the latest version of TBB (4.1 Update 2) . -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org

Bug#705495: libtbb2: On powerpc parallel_for and parallel_reduce may hang

2013-04-15 Thread Gert Wollny
Package: libtbb2 Version: 4.0+r233-1 Severity: normal Tags: upstream, patch Dear Maintainer, on PowerPC the functions parallel_for and parallel_reduce may run forever. Specifically, they may hang in the cleanup routines that are called after the user provided callbacks are run. This problem

Bug#705385: mia: FTBFS on powerpc: test suite hangs

2013-04-16 Thread Gert Wollny
I found a very crude fix for teh current version of TBB that needs to be refined and fixes this bug (See blocking bug). -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org

Bug#705495: On powerpc parallel_for and parallel_reduce may hang

2013-04-16 Thread Gert Wollny
The code hangs in a call to atomic_backoff::pause that the main thread initiated from __TBB_FetchAndStoreGeneric because a call to __TBB_CompareAnsdSwapGeneric fails. It seems that by replacing the latter with the new 4.1 version would fix the bug, but it introduces a change of the call

Bug#705495: ibtbb2: On powerpc parallel_for and parallel_reduce may hang

2013-04-17 Thread Gert Wollny
fixes a lockup that may happen in the exit routines of parallel_for and parallel_reduce. . Author: Gert Wollny gw.foss...@gmail.com --- Origin: other Bug-Debian: http://bugs.debian.org/705495 Forwarded: not-needed Last-Update: 2013-04-16 --- tbb-4.0+r233.orig/include/tbb/tbb_machine.h +++ tbb-4.0

Bug#705385: mia: FTBFS on powerpc: test suite hangs

2013-04-17 Thread Gert Wollny
On Mon, 2013-04-15 at 10:29 -0400, Aaron M. Ucko wrote: We're too deep into the wheezy freeze for TBB's maintainers to upload a new upstream version into unstable, but cherry-picked patches might qualify for a freeze exemption. The manageable small fix I found and posted in bug 705495

Bug#695659: libnlopt-dev: The package doesn't install the pkgconfig file 'nlopt.pc'

2012-12-11 Thread Gert Wollny
Package: libnlopt-dev Version: 2.2.4+dfsg-2 Severity: normal Tags: patch Dear Maintainer, upstream provides a nlopt.pc file that should be provided by the devel package. The attached patch against the debian directory fixes this problem. -- System Information: Debian Release: wheezy/sid APT

Bug#694434: ITP: vistaio -- a library for generic data storage

2012-11-26 Thread Gert Wollny
Package: wnpp Severity: wishlist Owner: Gert Wollnygw.foss...@gmail.com * Package name: vistaio Version : 1.2.14 Upstream Author : Gert Wollnygw.foss...@gmail.com, (abandoned by original author Arthur Popep...@cs.ubc.ca) * URL

Bug#694437: ITP: mia - Library and tools for gray scale image processing

2012-11-26 Thread Gert Wollny
Package: wnpp Severity: wishlist Owner: Gert Wollny gw.foss...@gmail.com * Package name: mia Version : 2.0.6 Upstream Author : Gert Wollny gw.foss...@gmail.com, * URL : https://sourceforge.net/projects/mia/files/mia/2.0.6/ DEBs : https://launchpad.net/~gert-die/+archive/ppa

Bug#694436: ITP: mialm - a program to handle 3D landmarks

2012-11-26 Thread Gert Wollny
Package: wnpp Severity: wishlist Owner: Gert Wollny gw.foss...@gmail.com * Package name: mialm Version : 1.0.6 Upstream Author : Gert Wollny gw.foss...@gmail.com, * URL : https://sourceforge.net/projects/mia/files/lmpick/0.2.4/ DEBs : https://launchpad.net/~gert-die/+archive

Bug#694438: ITP: mialmpick - a program to visualize 3D volume data sets and manually pick landmarks

2012-11-26 Thread Gert Wollny
Package: wnpp Severity: wishlist Owner: Gert Wollny gw.foss...@gmail.com * Package name: mialmpick Version : 0.2.4 Upstream Author : Gert Wollny gw.foss...@gmail.com, * URL : https://sourceforge.net/projects/mia/files/lmpick/0.2.4/ DEBs : https://launchpad.net/~gert-die

Bug#694439: IPT: pymia - Python interface for MIA

2012-11-26 Thread Gert Wollny
Package: wnpp Severity: wishlist Owner: Gert Wollny gw.foss...@gmail.com * Package name: pymia Version : 0.1.2 Upstream Author : Gert Wollny gw.foss...@gmail.com, * URL : https://sourceforge.net/projects/mia/files/mia/2.0.6/ DEBs : https://launchpad.net/~gert-die/+archive/ppa

Bug#694442: ITP: viewitgui - visuliaziation tool for MIA

2012-11-26 Thread Gert Wollny
Package: wnpp Severity: wishlist Owner: Gert Wollny gw.foss...@gmail.com * Package name: viewitgui Version : 2.0.2 Upstream Author : Gert Wollny gw.foss...@gmail.com, * URL : https://sourceforge.net/projects/mia/files/mia/2.0.6/ DEBs : https://launchpad.net/~gert-die/+archive

Bug#702882: f2c is simply not added to the linker flags

2013-12-09 Thread Gert Wollny
Hi, here the configure script claims that f2c is added anyway: [AC_MSG_RESULT(not found, trying to use -lf2c anyway.)] but then it does this (and the patch doesn't touch that line): LDFLAGS=${LDFLAGS} which should read (just like the in the BLAS test below) LDFLAGS=${LDFLAGS}

Bug#720681: [Debian-med-packaging] Bug#720681: Help with cmake needed (Was: Bug#720681: (Further) help with C++ needed)

2013-12-13 Thread Gert Wollny
Hello, it seems the attached patch solves the problem (Building at 95% way beyond where it failed before). Actually, it is commit 1e76c9 in the ball git repro https://bitbucket.org/ball/ball Cheers, Gert From 1e76c9cb1920e9176b725269985c7eb43126d188 Mon Sep 17 00:00:00 2001 From: Luis de

Bug#720681: [Debian-med-packaging] Bug#720681: Help with cmake needed (Was: Bug#720681: (Further) help with C++ needed)

2013-12-13 Thread Gert Wollny
Bad news is now compiling fails with: /home/wollny/Debian/ball/build/source/PYTHON/EXTENSIONS/VIEWmodule/sipVIEWpart0.cpp: In member function 'virtual void sipDatasetControl::destroy()': /home/wollny/Debian/ball/build/source/PYTHON/EXTENSIONS/VIEWmodule/sipVIEWpart0.cpp:2981:9: error:

Bug#706486: mialmpick: Link against libm to fix underlinking FTBFS

2013-05-06 Thread Gert Wollny
Thanks for the patch. Since I'm also the upstream author I will incorporated it in the next upstream release. Best Gert -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org

Bug#736172: [Debian-med-packaging] Bug#736172: gdcm: FTBFS on powerpc: _GLIBCXX_LONG_DOUBLE_COMPAT issue?

2014-01-20 Thread Gert Wollny
gdcm FTBFS on powerpc with: | cd /«PKGBUILDDIR»/obj-powerpc-linux-gnu/Utilities/VTK /usr/bin/gccxml ... This is gccxml going boom. gccxml is used as a processing step to create language bindings. | namespace std | { | inline namespace __gnu_cxx_ldbl128 { } | } AFAIK the parser used by

Bug#736172: little mistake

2014-01-20 Thread Gert Wollny
Because the headers that were included I overlooked that the bug is against GDCM and not VTK, so moving to a new version might not be an option. The note on gccxml stands, of course. best Gert -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of

Bug#740296: SimpleITK

2014-03-05 Thread Gert Wollny
Hi, I would look into packaging the software and ask on debian-med for sponsoring, but only after Easter - in case someone else has time and wants to step forward with the packaging. I've seen that the latest versions are 0.7.1.post1 and 0.8rc1. I would ask you to stick to a version

Bug#740296: SimpleITK

2014-03-05 Thread Gert Wollny
Hi, You are referring to versioning of the tar balls found on SourceForge? http://sourceforge.net/projects/simpleitk/files/SimpleITK/ Yes. The numbering is only important for releases, at least I will not package anything else. A typical watch file entry for sourceforge looks like

Bug#742622: ITP: maxflow - a library implementing a minimum cut/maximum flow algorithm

2014-03-25 Thread Gert Wollny
Package: wnpp Severity: wishlist * Package name: maxflow Version : 3.03 Upstream Author : Vladimir Kolmogorov and Yuri Boykov * URL : http://pub.ist.ac.at/~vnk/software.html * License : GPL3+ Programming Lang: C++ Description : This library implements the

Bug#748395: [Debian-med-packaging] Bug#748395: Misaligned array access caused by conflicting declarations

2014-05-16 Thread Gert Wollny
I looked a bit on how the tables are addressed and it seems they only use normal c-array indexing (and not some wired pointer arithmetic). Therefore, I'm quite confident that the element Padding is indeed not more than an explicit way to pad the structure to have a nice size. Given that

Bug#748659: Please add Gert Wollny to the Debian Maintainers keyring

2014-05-19 Thread Gert Wollny
Package: debian-maintainers Severity: normal Please add Gert Wollny to the Debian Maintainers keyring. The jetring changeset is attached. many thanks. Gert -- System Information: Debian Release: jessie/sid APT prefers testing APT policy: (990, 'testing'), (500, 'unstable') Architecture

Bug#748395: [Debian-med-packaging] Bug#748395: Misaligned array access caused by conflicting declarations

2014-05-19 Thread Gert Wollny
Hi, I've uploaded the patch to the debian-med git repository. Since the original version of plplot doesn't contain the padding I'm quite confident that it only needs to be consistent and the actual value is of no further consequence (besides possible optimizations). For the emboss team: the

Bug#746863: [Debian-med-packaging] Bug#746863: insighttoolkit4: ftbfs with GCC-4.9

2014-06-30 Thread Gert Wollny
The significant error is /usr/share/gccxml-0.9/GCC/4.9/bits/stl_algo.h: In function '_OutputIterator std::__unique_copy(_InputIterator, _InputIterator, _OutputIterator, _BinaryPredicate, std::input_iterator_tag, std::output_iterator_tag)': /usr/share/gccxml-0.9/GCC/4.9/bits/stl_algo.h:1086:

Bug#746863: [Debian-med-packaging] Bug#746863: insighttoolkit4: ftbfs with GCC-4.9

2014-07-01 Thread Gert Wollny
Mmm. I think that's wishful thinking on the part of rock-dev. We already have the latest git of gccxml (referenced in the above) packaged and it was used in the build that failed. I see, I've added a note the related upstream bug http://www.gccxml.org/Bug/view.php?id=14912 best, Gert

Bug#759794: [Debian-med-packaging] Bug#759794: insighttoolkit4: FTBFS on amd64 with ENOSPC

2014-08-30 Thread Gert Wollny
insighttoolkit4 repeatedly FTBFS on amd64 [1] because of ENOSPC. A manual build on porterbox barriere.debian.org reported a need of ~44GB while it failed on buildd barber at approx 37GB of disk space. There are two things that could probably help: - change the python-binding dimensions to

Bug#746863: FTBFS src:insighttoolkit4

2014-07-02 Thread Gert Wollny
There must be something wrong with your setup because what is failing is a plain CC compile command /usr/bin/cc that should never include the files from /usr/share/gccxml-0.9/GCC/4.9/ as it does in this build. Besides, from the compiler flags SSE is not enabled, and unless g++-4.9 on i386

Bug#746863: FTBFS src:insighttoolkit4

2014-07-02 Thread Gert Wollny
My bad, I got irritated by the parallel build. The failing command seems to be /usr/bin/gccxml -fxml-start=_cable_ -fxml=/«PKGBUILDDIR»/BUILD/Wrapping/Modules/ITKCommon/vcl_complex.xml --gccxml-gcc-options /«PKGBUILDDIR»/BUILD/Wrapping/Modules/ITKCommon/gcc_xml.inc -DCSWIG

Bug#746863: FTBFS src:insighttoolkit4

2014-07-12 Thread Gert Wollny
Il Mercoledì 2 Luglio 2014 13:15, Gert Wollny gw.foss...@gmail.com The failing command seems to be /usr/bin/gccxml -fxml-start=_cable_ -fxml=/«PKGBUILDDIR»/BUILD/Wrapping/Modules/ITKCommon/vcl_complex.xml --gccxml-gcc-options /«PKGBUILDDIR»/BUILD/Wrapping/Modules/ITKCommon/gcc_xml.inc

Bug#746863: [Debian-med-packaging] Bug#746863: FTBFS src:insighttoolkit4

2014-07-16 Thread Gert Wollny
On Tue, 2014-07-15 at 23:14 +0200, Andreas Tille wrote: [...] I could do the sponsering if needed. Please confirm that debian/makeSource.sh really fetches the source you are working on. I also think *if* I would do the upload and nobody would beat me I would switch to xz compression for the

Bug#748056: systemd and devices from /etc/fstab missing

2014-07-25 Thread Gert Wollny
Today I hit the same problem (after the dist-upgrade introduced systemd). I also had a device listed in /etc/fstab that is not always available and I forgot to add the noauto option. Well, the system does boot, but it drops you into the emergency shell where you can inspect the problem. At

Bug#756480: double-conversion: the package should create and install the *.cmake files

2014-07-30 Thread Gert Wollny
Source: double-conversion Version: Package should generate and install *.cmake files Severity: normal Dear Maintainer, the package is prepared to provide various *.cmake files that can be used by third party libraries using cmake to find the required information about the location of library

Bug#759945: [Debian-med-packaging] Bug#759945: elastix: FTBFS: make[3]: *** No rule to make target '/usr/lib/x86_64-linux-gnu/libhdf5.so', needed by 'bin/elastix'. Stop.

2014-09-09 Thread Gert Wollny
Hello, I guess this is also a transitional problem and will try to rebuild later this week before I'll close the bug. I'm afraid it's more complicated. ITK exposes various libraries via the ITKTargets-none,cmake files, amongst these htf5.so and libfftw3.so - even though these libraries should

Bug#759971: [Debian-med-packaging] Bug#759945: elastix: FTBFS: make[3]: *** No rule to make target '/usr/lib/x86_64-linux-gnu/libhdf5.so', needed by 'bin/elastix'. Stop.

2014-09-09 Thread Gert Wollny
Hello Andreas, It's actually way more simple since it can be explained by me beeing stupid enough to rebuild 4.7-1 (which actually had the fftw3 problem) instead of the current 4.7-2 which builds nicely. Me too, and I saw that as of 4.7-2 elastix has libfftw3-dev as build dependency. Still,

Bug#754249: new driver available from AMD

2014-09-17 Thread Gert Wollny
The new driver 14.9 is out [1] and according to Phoronix it should support xorg-video-abi-18 [2]. [1] http://support.amd.com/en-us/download/embedded?os=Linux +x86rev=13.151 [2] http://www.phoronix.com/scan.php?page=news_itempx=MTc4NTQ best regards, Gert signature.asc Description: This is a

Bug#762094: mate-panel: Applet context menu always on screen 0 also for applets on screen 1

2014-09-18 Thread Gert Wollny
the config menu appeared on screen 0 also for applets running on sereen 1. This patch corrects this by setting the screen apropriately. Author: Gert Wollny gw.foss...@gmail.com Bug: https://github.com/mate-desktop/mate-panel/issues/234 Last-Update: 2014-09-18 --- mate-panel-1.8.0+dfsg1.orig

Bug#698386: Is there a future for ITKSNAP?

2014-10-16 Thread Gert Wollny
Hello Paul, in Debian we are currently at ITK 4.6 and VTK 6.1 and AFAICS this is what will go into Jessie. Hence, if you could get a version released that can be compiled with these two libraries, we could update it, Note however, that the freeze for Jessie is only a few weeks away. Here is

Bug#698386: Is there a future for ITKSNAP?

2014-10-21 Thread Gert Wollny
Hello Paul, On Tue, 2014-10-21 at 04:45 -0400, Paul Yushkevich wrote: I am going to try looking into this problem this week. I have been building on Centos, and there the Qt plugins are being picked up just fine. I suspect the crash is due to the missing plugin, but I am not sure. The crash

Bug#698386: Is there a future for ITKSNAP?

2014-10-21 Thread Gert Wollny
On Tue, 2014-10-21 at 06:31 -0400, Paul Yushkevich wrote: A quick question about the plugins: when you build with Cmake, did you have CMAKE_PREFIX_PATH set to point to the Qt5's lib/cmake directory? I think this is the way the plugins get picked up. No, I didn't. signature.asc

Bug#698386: Is there a future for ITKSNAP?

2014-10-21 Thread Gert Wollny
... Oddly, this happens in Debian but not other OSs. Hope I can find a fix :) On Tue, Oct 21, 2014 at 6:38 AM, Gert Wollny gw.foss...@gmail.com wrote: On Tue, 2014-10-21 at 06:31 -0400, Paul Yushkevich wrote: A quick question about the plugins: when you build with Cmake, did you

Bug#698386: Is there a future for ITKSNAP?

2014-10-21 Thread Gert Wollny
On Tue, 2014-10-21 at 07:49 -0400, Paul Yushkevich wrote: Ok - it was an easy fix. I just checked it into dev32. Gert - could you please confirm that the code runs and builds now? Okay, when I can build it with the patches applied (disabling the search for the plug-ins with cmake and added

Bug#698386: Is there a future for ITKSNAP?

2014-10-23 Thread Gert Wollny
On Thu, 2014-10-23 at 16:50 +0200, Michael Hanke wrote: On Thu, Oct 23, 2014 at 10:43:56AM -0400, Paul Yushkevich wrote: The file is here: /usr/lib/x86_64-linux-gnu/cmake/Qt5/Qt5Config.cmake I'd like to chime in that grep -R QXcb * in the according directory does not yield any

Bug#767138: fftw3: runtime detection of NEON is perhaps broken

2014-10-29 Thread Gert Wollny
A few comments. I'm not sure if the disassembly is the right one. Supposedly it is in a function called fftwf_guru64_kosherp, but it should be in really_have_neon. There I would expect that the actual disassembly results in the the signal SIGILL not being reset and return 1 always being

Bug#767138: fftw3: runtime detection of NEON is perhaps broken

2014-10-29 Thread Gert Wollny
On Wed, 2014-10-29 at 18:36 +0100, Julian Taylor wrote: the flags are only added to files which do the computations, the rest of the program should not have this flag, this should include the file that has the neon runtime check. Makes sense, but then adding an intrinsic should be okay.

Bug#764697: systemd: enable ipv6 by default at least for lo

2014-10-10 Thread Gert Wollny
Package: systemd Version: 215-5+b1 Severity: wishlist Dear Maintainer, currently in /etc/sysctl.d/99-sysctl.conf provided by the systemd package ipv6 seems to be disabled by default i.e. net.ipv6.conf.all.disable_ipv6 = 1 net.ipv6.conf.default.disable_ipv6 = 1 net.ipv6.conf.lo.disable_ipv6 = 1

Bug#776812: usage of -mtune=core2 ? (Was: Bug#776812: vsearch: FTBFS on non-x86: uses non-portable flags)

2015-02-02 Thread Gert Wollny
Hello, On Mon, 2015-02-02 at 07:51 +0100, Andreas Tille wrote: Hi Mentors, It is very important to build vsearch with the maximum optimisation for speed and thus I wonder whether dropping this option is a good idea or whether I should enable it on i386 and amd64 (the question extends also

Bug#698386: Is there a future for ITKSNAP?

2015-01-15 Thread Gert Wollny
Hello, I've now upload the latest changes, with that the package should be okay for upload. Additional changes: * eliminated lintian warning: menu-icon-uses-relative-path * added watch file * corrected dependencies * builds in sid pbuilder amd64 There are still some lintian info

Bug#698386: Is there a future for ITKSNAP?

2015-01-16 Thread Gert Wollny
Hi Michael, They look like they need to be forwarded upstream, but should not hold up an upload. The spelling error needs to be forwarded. Since I had to touch the package anyway, I now corrected the other two. - I'd target experimental not unstable (solely for not causing problems with

Bug#698386: Is there a future for ITKSNAP?

2015-01-14 Thread Gert Wollny
Hello all, now that Paul provided an official upstream tarball I took the liberty to update the itksnap package to version 3.2.0 in the packaging git on alioth. There is still a lintian warning about menu-icon-uses-relative-path and some warnings about NMU, because currently my name is

Bug#776090: [Debian-med-packaging] Bug#776090: please package 4.7 for experimental

2015-01-23 Thread Gert Wollny
Hi, I started with the package. I hope some day next week it will be ready for upload. I'd change the vtk dependency to vtk6, because itksnap already requires this and will link both packages, and I'd add ITK_WRAP_unsigned_long because some filters require it for the python bindings. Best,

Bug#773379: Python specifics in libvtk6-dev

2015-01-09 Thread Gert Wollny
The problem with these files is that they are listed in one of the cmake files installed by vtk6 into /usr/lib/cmake/vtk-6.1, e.g., VTKTargets-none.cmake: IMPORTED_LOCATION_NONE /usr/lib/x86_64-linux-gnu/python2.7/site-packages/vtk/vtkCommonExecutionModelPython.so IMPORTED_SONAME_NONE

Bug#779707: [Debian-med-packaging] Bug#779707: amide: Missing Recommends/Suggests on (x)medcon

2015-03-04 Thread Gert Wollny
The package requires libmdc2, which is the library provided by the xmedcon project, so there is a relation. Considering the suggestion of (x)medcon one might add that amide does also not suggest dcmtk (another set of command line tools for manipulating DICOM files) even though it also has dicom

Bug#795344: [Debian-med-packaging] Bug#795344: libmems-1.6-1: not properly linked to its dependencies

2015-08-17 Thread Gert Wollny
all changes pushed. The new boost.m4 solved my problem, but adding the libraries in the link dependencies was still needed. The package builds and the boost libraries are also linked. BTW it was _LIBS not _LIB, so no AC_SUBST needed. However, building a package I got another error

Bug#795344: libmems-1.6-1: not properly linked to its dependencies

2015-08-16 Thread Gert Wollny
On 13.08.2015 18:17, Andreas Tille wrote: I confirm that this at least has some effect - unfortunately not the wanted one sinde the @BOOST_FILESYSTEM_LIB@ @BOOST_IOSTREAMS_LIB@ @BOOST_SYSTEM_LIB@ placeholders remain unresolved and the $(DEPS_LIBS) variable remains empty. :_( After

Bug#795344: [Debian-med-packaging] Bug#795344: libmems-1.6-1: not properly linked to its dependencies

2015-08-17 Thread Gert Wollny
On 17.08.2015 09:14, Andreas Tille wrote: I wonder whether there is some boost.m4 we could steal somewhere. Kind regards Andreas. Well, there is upstream https://github.com/tsuna/boost.m4 I will now try with this one. Andreas, I you didn't push your changes, right?

Bug#795586: Bug#795586: libfreecontact-perl: FTBFS: Can't load '/tmp/buildd/libfreecontact-perl-0.08/blib/arch/auto/FreeContact/FreeContact.so

2015-08-15 Thread Gert Wollny
On 15.08.2015 16:54, Andreas Tille wrote: This is something I somehow suspected - but *what* dependency? gregor pointed at freecontact, and indeed freecontac.h from libfreecontact0-dev exposes the std::string in the class predictor. Best

Bug#795586: [Debian-med-packaging] Bug#795586: libfreecontact-perl: FTBFS: Can't load '/tmp/buildd/libfreecontact-perl-0.08/blib/arch/auto/FreeContact/FreeContact.so

2015-08-15 Thread Gert Wollny
On 15.08.2015 16:02, Andreas Tille wrote: Hi Perl team, I admit I have no idea how to fix this. It somehow smells like a gcc-5 issue but I'm not sure. Most likely, the missing symbol (below) points to cxx11::std::string which comes from the g++11 dual ABI, which means some dependency needs

Bug#793344: How to inject options only for intel architectures with cmake (Was: Bug#793344: hyphy: FTBFS on non-x86: unrecognized command line option '-msse3')

2015-07-23 Thread Gert Wollny
On Thu, 2015-07-23 at 14:36 +0200, Andreas Tille wrote: Hi, considering the fact that SSE3 optimisation is really wanted on intel architectures how could the option be added only for those architectures that understand -msse3 option? You can do this: ### include(CheckCXXCompilerFlag)

Bug#737915: workaround

2015-07-25 Thread Gert Wollny
Hi, it seems that running Xnest with the -nocursor option is a workaround. I didn't test it extensively, but I was able to open two screens with xterms and copy from one to the other screen. I was not able to debug it on Debian, because there I didn't have debug information available, but on

Bug#793344: How to inject options only for intel architectures with cmake (Was: Bug#793344: hyphy: FTBFS on non-x86: unrecognized command line option '-msse3')

2015-07-23 Thread Gert Wollny
Hello Andreas, On the contrary users want to get the best performance from their recent processors I certainly can understand this ... Is there any better place to help upstream implementing it? This looks quite interesting: https://gcc.gnu.org/wiki/FunctionMultiVersioning It also

Bug#797651: [Debian-med-packaging] Bug#797651: mummy fails to build (libgccxml-dev vs GCC-5)

2015-10-29 Thread Gert Wollny
Hello Daniele, On Thu, 2015-10-29 at 17:30 +0100, Daniele E. Domenichelli wrote: > building the package with > > -DCMAKE_CXX_FLAGS=-D_GLIBCXX_USE_CXX11_ABI=0 > > fixes this issue for me. > > Anyway I'm not sure whether the real issue is in this package or in > libgccxml-dev that is built

Bug#803304: libdcmtk-dev: DCMTKTargets.cmake lists files that are not installed

2015-10-28 Thread Gert Wollny
Package: libdcmtk-dev Version: 3.6.1~20150629-3 Severity: normal The generated files DCMTKTargets*.cmake list executables that are either not installed at all (/usr/bin/*_tests), or moved to another location (/usr/lib/dcmtk/cgi-bin/). However, packages like insighttoolkit4 use the information

Bug#804569: dicomscope: build-depends on libdcmtk2-dev which is no longer built

2015-11-09 Thread Gert Wollny
On Mon, 2015-11-09 at 20:29 +0100, Andreas Tille wrote: > ... > /usr/include/dcmtk/dcmsr/dsrdoc.h:649:25: note: candidate expects 2 > arguments, 0 provided > /build/dicomscope-3.6.0/interface/libsrc/DSRDocument.cpp: In function > '_jstring* Java_J2Ci_jDSRDocument_getAccessionNumber(JNIEnv*, >

Bug#804575: [Debian-med-packaging] Bug#804575: insighttoolkit4: build-depends on libdcmtk2-dev which is no longer built

2015-11-09 Thread Gert Wollny
I'll take on this bug once gdcm (=2.6) - another build dependency of insighttoolkit4 - has cleared NEW. I.e. in the packaging svn I already changed the dependency. Best, Gert

Bug#804569: dicomscope: build-depends on libdcmtk2-dev which is no longer built

2015-11-09 Thread Gert Wollny
I've uploaded a patch to svn, but there are more errors like this. It seems all related methods now uses the OFCondition return value, and pass an OFString& parameter. I'll try to get the complete patch out until tomorrow. Best, Gert

Bug#803304: [Debian-med-packaging] Bug#803304: fixed in dcmtk 3.6.1~20150629-4

2015-11-16 Thread Gert Wollny
On Mon, 2015-11-16 at 16:29 +0100, Michael Onken wrote: > There should already be a clean way in DCMTK to solve the issue > without applying a Debian-specific patch: > > DCMTK offers the CMake option "BUILD_APPS" which is (obviously) > enabled per default. If you disable it, applications (like

Bug#804569: dicomscope: build-depends on libdcmtk2-dev which is no longer built

2015-11-09 Thread Gert Wollny
Uploaded everything to svn, it builds and the dependency was changed to libdcmtk-dev. If you give me upload rights then I will proper checking and uploading tomorrow. Best, Gert

Bug#797738: [Debian-med-packaging] Bug#797738: gdcm: ABI transition needed for libstdc++ v5

2015-10-30 Thread Gert Wollny
On Fri, 2015-10-30 at 15:53 +0100, Emilio Pozuelo Monfort wrote: > This is a friendly ping wrt the libstdc++ ABI transition. Your > package is listed as needing a transition but has seen no action. > It'd be good to get things going > so we can finish the transition soon. Sorry that I forgot to

Bug#803595: waiting for gdcm clearing new

2015-10-31 Thread Gert Wollny
Hello, I'll look into this as soon as gdcm-2.6 has cleared NEW because vtk-dicom depends on gdcm which also needed the transition to vtk6. Best, Gert

Bug#751395: approach to fix "vtk6: Do not compress perl scripts"

2015-10-19 Thread Gert Wollny
Hi, I've prepared a GDCM-2.6 upload that uses the compressed scripts, but since depending on files from /usr/share/doc is a policy violation, I'd suggest the following 2-step procedure to get rid of the problem: 1. Apply the attached patch to the vtk6 debian scripts to install the perl

Bug#799322: pocl: With 0.11 some test are failing

2015-10-14 Thread Gert Wollny
Hi, I had a look into the package, but I for me with 0.11 an llvm-3.6 two tests are failing - this has also already been reported upstream: https://github.com/pocl/pocl/issues/181

Bug#759794: [Debian-med-packaging] Bug#759794: insighttoolkit4: FTBFS on amd64 with ENOSPC

2015-10-06 Thread Gert Wollny
Disk space used for building of ITK 4.8 with only 2 and 3 dimensions to wrap: chroot base system with all deps installed: 3.0GB Source code unpacked: ~1.0GB Build dir 36GB Debian dir 5.1GB Sum: 42GB Total:

Bug#800481: [Debian-med-packaging] Bug#800481: dcmtk: versioned -dev package makes transitions too painful

2015-10-03 Thread Gert Wollny
On Fri, 2015-10-02 at 15:57 +0200, Mathieu Malaterre wrote: > Forgot to quote section §8.4 Development files > > https://www.debian.org/doc/debian-policy/ch-sharedlibs.html#s > -sharedlibs-dev > > [...] > If there are development files associated with a shared library, the > source package

Bug#799471: Updated r-cran-beeswarm and plink1.9

2015-09-19 Thread Gert Wollny
Hello again, > I'm just looking into plink1.9 to fix #799471. I currently test the > build on a 32 bit arch, and would also try to compile the changes on > amd64. I'll ping you when it's done. I've created a patch that should fix the build failures reported in #799471, but since it only

Bug#799471: [Debian-med-packaging] Bug#799471: FTBFS on some architectures

2015-09-19 Thread Gert Wollny
The package seems to fail on all 64-bit architectures that are not x86_64 because the define __LP64__ is used to decide whether the SSE2 specific header emmintrin.h is available. However, __LP64__ is defined on all 64 pit archs and not only on x86_64. On Debian replacing all instances of

Bug#800964: Annual ping for Gert Wollny

2015-10-05 Thread Gert Wollny
Package: debian-maintainers Severity: normal Hi, Here is my (slightly late) annual ping. Thanks, Gert signature.asc Description: This is a digitally signed message part

Bug#759794: [Debian-med-packaging] Bug#759794: insighttoolkit4: FTBFS on amd64 with ENOSPC

2015-10-05 Thread Gert Wollny
Hello Steven, On Sun, 2015-10-04 at 11:09 -0500, Steve M. Robbins wrote: > There are two things that could probably help: > > > > - change the python-binding dimensions to use only 2 an 3. > > I can definitely make this change for the next upload. > Did you ever quantify whether this saves

Bug#804575: insighttoolkit4: build-depends on libdcmtk2-dev which is no longer built

2015-11-29 Thread Gert Wollny
> So let's say this is not urgent or RC, but it'd be good to change it > in the next upload. It is trivial to change anyway ;) Well, since itk-4.8.2 is out and gdcm was rejected by ftp master, I will do another upload shortly, and when the new gdcm version has passed NEW, we can request a new

Bug#733629: This should be solved upstream

2015-12-04 Thread Gert Wollny
Just letting double-conversion provide a *.cmake file is probably not sufficient, since the current version of ITK exposes the interface of double-conversion through itkNumberToString.h by including it without the leading subdirectory "double-conversion". The issue has now been reported upstream

Bug#756480: fix no longer needed

2015-12-04 Thread Gert Wollny
The reason I filed this bug is no longer relevant, because I added a patch to fix #733629 that doesn't require a cmake file. Hence it would probably be okay to tag this patch as wontfix. Best, Gert

Bug#724711: some notes

2015-12-08 Thread Gert Wollny
The last few days I did test the builds of ITK 4.8.2 on powerpc and armhf - both without python bindings). Even so compiling took more than 24 hours, which means this was an experiment I'm not going to repeat soon. On armhf I have only a Ubuntu 15.10 installation (g++ 4.8), it builds out of the

Bug#656321: mummy will be phased out.

2015-12-01 Thread Gert Wollny
Since mummy depends on libgccxml. gccxml is incompatible with g++-5 and no longer maintained by upstream, this package will be phased out. Best, Gert

Bug#798165: activiz.net will be phased out

2015-12-01 Thread Gert Wollny
activiz.net depends on mummy, which in turn depends on gccxml which is no longer maintained by upstream and doesn't produce usable code with g++-5. Hence this package will be phased out. Best, Gert

Bug#804578: [Debian-med-packaging] Bug#804578: Does not build using dcmtk 3.6.1

2015-12-02 Thread Gert Wollny
I've uploaded a patch to svn that (hopefully) catches all the cases of the CONDITION->OFCOndition transition. This new patch [1] replaces the initial one done by Andreas. Please see svn changelog for more details. Also note that this is untested, because "d/rules get-orig-source" failed on

Bug#804578: [Debian-med-packaging] Bug#804578: Does not build using dcmtk 3.6.1

2015-12-02 Thread Gert Wollny
Hi Andreas, On Wed, 2015-12-02 at 13:56 +0100, Andreas Tille wrote: > I checked this out and I'm afraid you did not really commited the > latest version of your patch set: That was a last minute change of the filename that I forgot to move to the d/p/series file. (sorry). > Wende Patch

Bug#807675: More failures apparently unrelated to "SCU Failed: 0006:0213 Data dictionary missing"

2015-12-11 Thread Gert Wollny
After fixing dcmtk (uploading right now) there are still failures: On one hand, during the build I get: cd build && ../tests/run.sh F: cannot initialize network: 0006:031c TCP Initialization Error: Address already in use E: Store Failed, file: dcmtkpp.iZA/data.dcm: E: 0006:0317 Peer aborted

Bug#807691: dcmtk: DCM_DICT_DEFAULT_PATH is not set propperly

2015-12-11 Thread Gert Wollny
Package: dcmtk Version: 3.6.1~20150924-1 Severity: important The dicom dict is installed in a versioned directory, but that information is not propagated to the osconfig.h file. workaround: set DCMDICTPATH=/usr/share/libdcmtk5/dicom.dic -- System Information: Debian Release: stretch/sid

Bug#746268: gdcm: hundreds of "sh: 1: dot: not found" messages

2015-12-14 Thread Gert Wollny
There are actually two alternatives to fix this bug on the upstream side: * Either convert the .dox files actual man pages and then use these directly (i.e, no longer invoking doxygen to create them). Since man pages are actually text files this would be also a proper source format to apply

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