Re: Sight needs to be ported to insighttoolkit5 [Fwd: sight is marked for autoremoval from testing]
Am Mon, Jan 24, 2022 at 05:53:13PM +0100 schrieb Flavien Bridault:
> Well this is weird, I also built with pbuilder with sid (chroot updated last
> friday). Is it maybe testing on your side?
Its definitely not testing since I never use a testing chroot for my
pbuilder. May be somebody else can check?
Kind regards
Andreas.
> 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_APIdata::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_APIdata::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
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > This mail is generated by:
> > > > > > > > > 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
> > > > > > > > >
> > > > > > > > > _______________________________________________
> > > > > > > > > Debian-med-packaging mailing list
> > > > > > > > > Debian-med-packaging@alioth-lists.debian.net
> > > > > > > > > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > ----- Ende weitergeleitete Nachricht -----
> > > > > > > > >
> > > > > >
> > > >
> > > >
> >
> >
> >
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