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Re: Sight needs to be ported to insighttoolkit5 [Fwd: sight is marked for autoremoval from testing]

Well this is weird, I also built with pbuilder with sid (chroot updated last friday). Is it maybe testing on your side?


Dr. Flavien BRIDAULT
Director of Software Development
IRCAD France & IRCAD Africa

flavien.bridault@ircad.fr
Tél. : +33 (0)3 88 119 201
   IRCAD France
http://www.ircad.fr/
http://www.ircad.africa/

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IRCAD France
Hôpitaux Universitaires - 1, place de l'Hôpital - 67091 Strasbourg Cedex - FRANCE
Le 24/01/2022 à 17:39, Andreas Tille a écrit :
Hi,

I have no idea why salsa-ci fails unpacking sight.  Thus I can't verify
my issue to build the package on Salsa.  In any case I get something like


...
/build/sight-21.0.0/libs/core/core/tools/Dispatcher.hpp:180:30:   recursively required from 'static void sight::core::tools::Dispatcher<TSEQ, FUNCTOR>::invoke(const KeyType&,            Parameter&) [with KeyType = sight::core::tools::Type; Parameter = sight::io::itk::ITKSaverFunctor::Parameter; TSEQ = boost::mpl::v_mask<boost::mpl::vector10<signed char, unsigned char,  short int, short unsigned int, int, unsigned int, long int, long unsigned int, float, double>, 1>; FUNCTOR = sight::io::itk::ITKSaverFunctor]'
/build/sight-21.0.0/libs/core/core/tools/Dispatcher.hpp:180:30:   required from 'static void sight::core::tools::Dispatcher<TSEQ, FUNCTOR>::invoke(const KeyType&, Parameter&) [with      KeyType = sight::core::tools::Type; Parameter = sight::io::itk::ITKSaverFunctor::Parameter; TSEQ = boost::mpl::vector10<signed char, unsigned char, short int, short unsigned int, int,   unsigned int, long int, long unsigned int, float, double>; FUNCTOR = sight::io::itk::ITKSaverFunctor]'
/build/sight-21.0.0/libs/io/itk/ImageWriter.cpp:119:92:   required from here
/build/sight-21.0.0/libs/io/itk/itk.hxx:150:32: warning: 'sight::data::Array::sptr sight::data::Image::getDataArray() const' is deprecated: it will be removed in sight 22.0 [-           Wdeprecated-declarations]
  150 |         imageData->getDataArray()->setIsBufferOwner( false );
      |         ~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from /build/sight-21.0.0/libs/core/pch/pchData/pch.hpp:35:
/build/sight-21.0.0/libs/core/data/Image.hpp:670:32: note: declared here
  670 |     DATA_API data::Array::sptr getDataArray() const;
      |                                ^~~~~~~~~~~~
In file included from /build/sight-21.0.0/libs/io/itk/itk.hpp:74,
                 from /build/sight-21.0.0/libs/io/itk/ImageWriter.cpp:26:
/build/sight-21.0.0/libs/io/itk/itk.hxx:150:32: warning: 'sight::data::Array::sptr sight::data::Image::getDataArray() const' is deprecated: it will be removed in sight 22.0 [-           Wdeprecated-declarations]
  150 |         imageData->getDataArray()->setIsBufferOwner( false );
      |         ~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from /build/sight-21.0.0/libs/core/pch/pchData/pch.hpp:35:
/build/sight-21.0.0/libs/core/data/Image.hpp:670:32: note: declared here
  670 |     DATA_API data::Array::sptr getDataArray() const;
      |                                ^~~~~~~~~~~~
/build/sight-21.0.0/libs/io/vtk/vtk.cpp:138:6: error: 'VTK___INT64' was not declared in this scope; did you mean 'VTK_INT'?
  138 |     {VTK___INT64, core::tools::Type::create("int64")},
      |      ^~~~~~~~~~~
      |      VTK_INT
/build/sight-21.0.0/libs/io/vtk/vtk.cpp:139:6: error: 'VTK_UNSIGNED___INT64' was not declared in this scope; did you mean 'VTK_UNSIGNED_INT'?
  139 |     {VTK_UNSIGNED___INT64, core::tools::Type::create("uint64")},
      |      ^~~~~~~~~~~~~~~~~~~~
      |      VTK_UNSIGNED_INT


when trying to build the package using pbuilder (= in a minimum chroot).

Kind regards

     Andreas.

Am Mon, Jan 24, 2022 at 02:23:48PM +0100 schrieb Flavien Bridault:

Hi Andreas,

Well, there was no answer from ITK Uploaders here, but I filled a bug as you
recommended.

I also added a patch to temporarily disable the guilty filter and fix the
link stage, this builds fine on my side.

Please confirm this is ok for you.

Thanks as always for your time. :)


*Dr. Flavien BRIDAULT*
Director of Software Development
IRCAD France & IRCAD Africa

flavien.bridault@ircad.fr <mailto:flavien.bridault-louchez@ircad.fr>
Tél. : +33 (0)3 88 119 201
		IRCAD France
http://www.ircad.fr/
http://www.ircad.africa/ <http://www.ircad.fr/>

Suivez l'IRCAD sur Facebook
<http://www.facebook.com/pages/IRCAD/193785273990141>

*IRCAD France*
Hôpitaux Universitaires - 1, place de l'Hôpital - 67091 Strasbourg Cedex -
FRANCE

Le 21/01/2022 à 10:59, Andreas Tille a écrit :

Hi Flavien,

Am Fri, Jan 21, 2022 at 10:16:19AM +0100 schrieb Flavien Bridault:

Well, sorry I assumed this module was not built for a reason... It is
actually an experimental module for algorithms, that may be promoted in a
real category if they are judged good enough.

Seehttps://itk.org/Doxygen/html/group__ITKReview.html.

I intentionally have set ITK Uploaders in CC. ;-)

So I have no idea if Debian wants to enable this module considering this.

There is no "declared will of Debian".  May be the best idea is you
file a wishlist bug report so it is documented and adapt sight as
long as this feature is missing.


Otherwise, I can give a try to try to build it and propose a patch, but I
admit I was a bit afraid by the importance of the package. :)

If you add that patch to the wishlist bug report its chances are
way higher to get fixed.


I would prefer to hear the advice of someone maintaining this package before
proposing any modification, is there anyone on this list that could help?

I'm personally lacking the knowledge to give more sensible comments.

Kind regards

      Andreas.

*Dr. Flavien BRIDAULT*
Director of Software Development
IRCAD France & IRCAD Africa

flavien.bridault@ircad.fr  <mailto:flavien.bridault-louchez@ircad.fr>
Tél. : +33 (0)3 88 119 201
		IRCAD France
http://www.ircad.fr/
http://www.ircad.africa/  <http://www.ircad.fr/>

Suivez l'IRCAD sur Facebook
<http://www.facebook.com/pages/IRCAD/193785273990141>

*IRCAD France*
Hôpitaux Universitaires - 1, place de l'Hôpital - 67091 Strasbourg Cedex -
FRANCE

Le 20/01/2022 à 21:00, Andreas Tille a écrit :

Hi Flavien,

Am Thu, Jan 20, 2022 at 04:33:28PM +0100 schrieb Flavien Bridault:

I have understood the problem. The missing image filter has moved in an
optional module, ITKReview.

Two possible solutions:

1. modify the ITK package in order to enable the build of the ITKReview
module

I'm not sure whether I understand this correctly.  We probably want a
feature complete package.  If not our users might be surprised about
missing features in other applications as well.

2. remove the filter from sight build - this is what we did on Windows and
why it builds with ITK5.... ^^

Finally its your decision.


This image filter is really non-essential, so I guess it is easier to take
solution 2, can you confirm please ?

Its perfectly fine whatever you decide.

Kind regards

        Andreas.



Hi Andreas,

I am a bit disappointed it doesn't build because we do use ITK5 on
Windows.

Anyway, I'll take care of this of course, thanks for trying. :)

Cheers,


*Dr. Flavien BRIDAULT*
Director of Software Development
IRCAD France & IRCAD Africa

flavien.bridault@ircad.fr   <mailto:flavien.bridault-louchez@ircad.fr>
Tél. : +33 (0)3 88 119 201
		IRCAD France
http://www.ircad.fr/
http://www.ircad.africa/   <http://www.ircad.fr/>

Suivez l'IRCAD sur Facebook
<http://www.facebook.com/pages/IRCAD/193785273990141>

*IRCAD France*
Hôpitaux Universitaires - 1, place de l'Hôpital - 67091 Strasbourg Cedex
- FRANCE

Le 12/01/2022 à 15:17, Andreas Tille a écrit :

Hi Flavien,

as you can see below ITK4 is buggy and we switched to ITK5 anyway so
ITK4 will be removed.  To verify whether sight might build with ITK5
smoothly I simply replaced libinsighttoolkit4-dev by
libinsighttoolkit5-dev in (Build-)Depends[1], but obviously:

...
[ 81%] Building CXX object libs/io/dicom/test/CMakeFiles/io_dicomTest.dir/tu/DicomAnonymizerTest.cpp.o
cd /build/sight-21.0.0/obj-x86_64-linux-gnu/libs/io/dicom/test && /usr/bin/c++ -DBOOST_ALL_DYN_LINK -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_LOG_DYN_LINK -DBOOST_LOG_SETUP_DYN_LINK -DBOOST_REGEX_DYN_LINK -DBOOST_SPIRIT_USE_PHOENIX_V3 -DBOOST_THREAD_DONT_PROVIDE_DEPRECATED_FEATURES_SINCE_V3_0_0 -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_PROVIDES_FUTURE -DBOOST_THREAD_VERSION=2 -DIO_DICOMTEST_EXPORTS -I/build/sight-21.0.0/obj-x86_64-linux-gnu/libs/core/pch/pchCore/include/pchCore -I/build/sight-21.0.0/obj-x86_64-linux-gnu/libs/io/dicom/include -I/build/sight-21.0.0/libs -I/build/sight-21.0.0/libs/core -I/build/sight-21.0.0/obj-x86_64-linux-gnu/libs/io/base/include -I/build/sight-21.0.0/obj-x86_64-linux-gnu/libs/core/core/include -I/usr/include/libxml2 -I/build/sight-21.0.0/obj-x86_64-linux-gnu/libs/core/data/include -I/build/sight-21.0.0/obj-x86_64-linux-gnu/libs/core/service/include -I/build/sight-21.0.0/obj-x86_64-linux-gnu/libs/core/activity/include -I/build/sight-21.0.0/obj-x86_64-linux-gnu/libs/filter/dicom/include -I/build/sight-21.0.0/obj-x86_64-linux-gnu/libs/geometry/data/include -I/build/sight-21.0.0/obj-x86_64-linux-gnu/libs/io/zip/include -I/build/sight-21.0.0/obj-x86_64-linux-gnu/libs/core/utestData/include -I/build/sight-21.0.0/obj-x86_64-linux-gnu/libs/core/utest/include -isystem /usr/include/gdcm-3.0 -isystem /usr/lib -isystem /usr/include/cppunit -g -O2 -ffile-prefix-map=/build/sight-21.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIE -fvisibility=hidden -fvisibility-inlines-hidden -march=sandybridge -mtune=generic -mfpmath=sse -fvisibility=hidden -fvisibility-inlines-hidden -Wall -Wextra -Wconversion -Wno-unused-parameter -Wno-ignored-qualifiers -fPIC -std=gnu++17 -include "pch.hpp"  -Winvalid-pch -MD -MT libs/io/dicom/test/CMakeFiles/io_dicomTest.dir/tu/DicomAnonymizerTest.cpp.o -MF CMakeFiles/io_dicomTest.dir/tu/DicomAnonymizerTest.cpp.o.d -o CMakeFiles/io_dicomTest.dir/tu/DicomAnonymizerTest.cpp.o -c /build/sight-21.0.0/libs/io/dicom/test/tu/DicomAnonymizerTest.cpp
/build/sight-21.0.0/libs/filter/image/SpheroidExtraction.cpp:34:10: fatal error: itkLabelGeometryImageFilter.h: No such file or directory
      34 | #include <itkLabelGeometryImageFilter.h>
         |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.


... the situation is more complex.  Would you mind switching the
upstream code to ITK5?

Kind regards

        Andreas.


[1]https://salsa.debian.org/med-team/sight/-/commit/4dfa098d04116ef8c0320e6786e50337d0059ce7

----- Weitergeleitete Nachricht von Debian testing autoremoval watch<noreply@release.debian.org>    -----

Date: Wed, 12 Jan 2022 04:39:32 +0000
From: Debian testing autoremoval watch<noreply@release.debian.org>
To:sight@packages.debian.org
Subject: sight is marked for autoremoval from testing

sight 21.0.0-3 is marked for autoremoval from testing on 2022-02-09

It (build-)depends on packages with these RC bugs:
984284: insighttoolkit4: otb: ftbfs with GCC-11
    https://bugs.debian.org/984284



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https://salsa.debian.org/release-team/release-tools/-/blob/master/mailer/mail_autoremovals.pl

Autoremoval data is generated by:
https://salsa.debian.org/qa/udd/-/blob/master/udd/testing_autoremovals_gatherer.pl

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