mirror of
https://codeberg.org/guix/guix.git
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gnu: itk-snap: Update to 4.2.2-0.6525125.
* gnu/packages/image-processing: Import (gnu packages ssh).
(itk-snap): Update to 4.2.2-0.6525125.
[source]: Fetch from the new official home on GitHub. Remove
itk-snap-alt-glibc-compat.patch.
[arguments]: Use gexps.
<#:configure-flags>: Remove "-DSNAP_VERSION_GIT_SHA1=release",
"-DSNAP_VERSION_GIT_TIMESTAMP=0", "-DCMAKE_POSITION_INDEPENDENT_CODE=ON",
"-DCMAKE_CXX_STANDARD=14".
<#:phases>{disable-gui-tests}: Disable more GUI tests.
{prepare-submodules}: Remove substitution in c3d checkout. Add digestible
submodule.
{fix-includes}: Delete phase.
{remove-bundled-jsoncpp}: New phase.
{wrap-executable}: Use gexp.
[inputs]: Replace insight-toolkit-4.12 with insight-toolkit-legacy. Replace
vtk-7 with vtk. Replace qtbase-5 with qtbase. Replace qtdeclarative-5 with
qtdeclarative. Add freetype, glew, jsoncpp and libssh. Remove bash-minimal,
fftw, fftwf, hdf5, vxl-1 and zlib.
[native-inputs]: Use new style. Update c3d and greedy checkouts. Add
digestible checkout. Remove googletest, qttools-5 and pkg-config.
* gnu/local.mk: Deregister itk-snap-alt-glibc-compat.patch.
* gnu/packages/patches/itk-snap-alt-glibc-compat.patch: Remove file.
Change-Id: I6a90a590fa773e838946d773e9b0a743129ee1f3
This commit is contained in:
Jake Forster
Andreas Enge
parent
82ab2e82f3
commit
6a6e8673a9
3 changed files with 105 additions and 133 deletions
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@ -1634,7 +1634,6 @@ dist_patch_DATA = \
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%D%/packages/patches/irrlicht-use-system-libs.patch \
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%D%/packages/patches/irrlicht-link-against-needed-libs.patch \
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%D%/packages/patches/isl-0.11.1-aarch64-support.patch \
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%D%/packages/patches/itk-snap-alt-glibc-compat.patch \
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%D%/packages/patches/jamesdsp-fix-bulid-on-pipewire-1.4.0.patch\
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%D%/packages/patches/jami-disable-webengine.patch \
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%D%/packages/patches/jami-enable-testing.patch \
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@ -106,6 +106,7 @@
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#:use-module (gnu packages serialization)
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#:use-module (gnu packages sphinx)
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#:use-module (gnu packages sqlite)
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#:use-module (gnu packages ssh)
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#:use-module (gnu packages swig)
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#:use-module (gnu packages tbb)
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#:use-module (gnu packages textutils)
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@ -1477,137 +1478,131 @@ combine the information contained in both.")
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#~(cons* "-DCMAKE_CXX_FLAGS=-std=c++14" #$cf))))))
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(define-public itk-snap
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;; The latest release, 4.2.2, segmentation faults on startup.
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;; The commit is version 4.4.0-alpha3.
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(let ((commit "65251254d44d68a6c0530984169784e35de020dd")
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(revision "0"))
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(package
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(name "itk-snap")
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(version "3.8.0")
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(version (git-version "4.2.2" revision commit))
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://git.code.sf.net/p/itk-snap/src")
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(commit (string-append "v" version))))
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(url "https://github.com/pyushkevich/itksnap")
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(commit commit)))
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(file-name (git-file-name name version))
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(sha256
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(base32 "15i5ixpryfrbf3vrrb5rici8fb585f25k0v1ljds16bp1f1msr4q"))
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(patches (search-patches "itk-snap-alt-glibc-compat.patch"))))
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(base32 "07dgcfklc55yj3ldcq6fc5fil8qfrv7z6c3xhbd293kz7kpjr4yc"))))
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(build-system cmake-build-system)
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(arguments
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`(#:configure-flags
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(list "-DSNAP_VERSION_GIT_SHA1=release"
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"-DSNAP_VERSION_GIT_BRANCH=release"
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"-DSNAP_VERSION_GIT_TIMESTAMP=0"
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"-DSNAP_PACKAGE_QT_PLUGINS=OFF"
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"-DCMAKE_POSITION_INDEPENDENT_CODE=ON"
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;; ISO C++17 does not allow dynamic exception specifications.
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"-DCMAKE_CXX_STANDARD=14")
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#:phases
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(modify-phases %standard-phases
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;; During the installation phase all libraries provided by all
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;; dependencies will be copied to the lib directory. That's insane,
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;; so we disable this.
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(add-after 'unpack 'do-not-copy-dependencies
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(lambda _
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(substitute* "CMakeLists.txt"
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(("install_qt5_executable\
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(list
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#:configure-flags
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#~(list "-DSNAP_VERSION_GIT_BRANCH=release"
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"-DSNAP_PACKAGE_QT_PLUGINS=OFF")
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#:phases
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#~(modify-phases %standard-phases
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;; During the installation phase all libraries provided by all
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;; dependencies will be copied to the lib directory. That's insane,
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;; so we disable this.
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(add-after 'unpack 'do-not-copy-dependencies
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(lambda _
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(substitute* "CMakeLists.txt"
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(("install_qt5_executable\
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\\(\\$\\{SNAP_MAIN_INSTALL_DIR\\}/\\$\\{SNAP_EXE\\}\\)")
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""))))
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(add-after 'unpack 'disable-gui-tests
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(lambda _
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;; The GUI tests just time out.
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(substitute* "CMakeLists.txt"
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((" (Workspace|DiffSpace|ProbeIntensity|RegionCompetition\
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|RandomForest|RandomForestBailOut)")
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""))))
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(add-after 'unpack 'make-reproducible
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(lambda _
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(substitute* "CMakeLists.txt"
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(("TODAY\\(SNAP_VERSION_COMPILE_DATE\\)")
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"SET(SNAP_VERSION_COMPILE_DATE \"(removed for reproducibility)\")"))))
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(add-after 'unpack 'prepare-submodules
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(lambda* (#:key inputs #:allow-other-keys)
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(rmdir "Submodules/c3d")
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(copy-recursively (assoc-ref inputs "c3d-src")
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"Submodules/c3d")
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(substitute* '("Submodules/c3d/adapters/BiasFieldCorrectionN4.cxx"
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"Submodules/c3d/adapters/ApplyMetric.cxx")
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(("vcl_") "std::"))
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(rmdir "Submodules/greedy")
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(symlink (assoc-ref inputs "greedy-src")
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"Submodules/greedy")))
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(add-after 'unpack 'fix-includes
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(lambda _
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(substitute* "GUI/Model/RegistrationModel.cxx"
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(("<vnl_symmetric_eigensystem.h>")
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"<vnl/algo/vnl_symmetric_eigensystem.h>"))))
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(add-before 'check 'prepare-tests
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(lambda _
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;; Needed by at least one test.
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(setenv "HOME" "/tmp")))
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(add-after 'install 'wrap-executable
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(let ((out (assoc-ref outputs "out")))
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(wrap-program (string-append out "/bin/itksnap")
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`("QT_PLUGIN_PATH" ":" prefix
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,(map (lambda (label)
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(string-append (assoc-ref inputs label)
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"/lib/qt5/plugins"))
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'("qtbase" "qtdeclarative"))))))))))
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""))))
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(add-after 'unpack 'disable-gui-tests
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(lambda _
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;; The GUI tests just segmentation fault.
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(substitute* "CMakeLists.txt"
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((" (Workspace|DiffSpace|ProbeIntensity|RegionCompetition\
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|RandomForest|RandomForestBailOut|NaNs|4DContinuousRenderingD|EdgeAttraction\
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|EchoCartesianDicomLoading|LabelSmoothing|PreferencesDialog|MeshImport\
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|MeshWorkspace|SegmentationMesh|VolumeRendering|Reloading|4DToMC|MCTo4D\
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|DeformationGrid)")
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""))))
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(add-after 'unpack 'make-reproducible
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(lambda _
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(substitute* "CMakeLists.txt"
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(("TODAY\\(SNAP_VERSION_COMPILE_DATE\\)")
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"SET(SNAP_VERSION_COMPILE_DATE \"(removed for reproducibility)\")"))))
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(add-after 'unpack 'prepare-submodules
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(lambda _
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(rmdir "Submodules/c3d")
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(symlink #$(this-package-native-input "c3d-checkout")
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"Submodules/c3d")
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(rmdir "Submodules/digestible")
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(symlink #$(this-package-native-input "digestible-checkout")
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"Submodules/digestible")
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(rmdir "Submodules/greedy")
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(symlink #$(this-package-native-input "greedy-checkout")
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"Submodules/greedy")))
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(add-after 'unpack 'remove-bundled-jsoncpp
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(lambda _
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(substitute* "CMakeLists.txt"
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((" Common/JSon/jsoncpp\\.cpp") ""))))
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(add-before 'check 'prepare-tests
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(lambda _
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;; Needed by at least one test.
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(setenv "HOME" "/tmp")))
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(add-after 'install 'wrap-executable
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(lambda _
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(wrap-program (string-append #$output "/bin/itksnap")
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(list
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"QT_PLUGIN_PATH"
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'suffix
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(list (string-append #$(this-package-input "qtbase")
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"/lib/qt6/plugins")
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(string-append #$(this-package-input "qtdeclarative")
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"/lib/qt6/plugins")))))))))
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(inputs
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(list bash-minimal
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curl
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fftw
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fftwf
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(list curl
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freetype
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glew
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glu
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hdf5
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insight-toolkit-legacy
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jsoncpp
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libssh
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mesa-opencl
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;; This package does not build with either insight-toolkit 5.0.0
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;; and not with 4.13. It really needs to be 4.12.
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insight-toolkit-4.12
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vtk-7
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qtbase-5
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qtdeclarative-5
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vxl-1
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zlib))
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qtbase
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qtdeclarative
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vtk))
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(native-inputs
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`(("googletest" ,googletest)
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("qttools-5" ,qttools-5)
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("pkg-config" ,pkg-config)
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("c3d-src"
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,(let* ((commit "f521358db26e00002c911cc47bf463b043942ad3")
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(revision "1")
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(version (git-version "0" revision commit)))
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/pyushkevich/c3d")
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(commit commit)))
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(file-name (git-file-name "c3d" version))
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(sha256
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(base32
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"0kyv3rxrxwr8c3sa9zv01lsnhk95b27gx1s870k3yi8qp52h7bx3")))))
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;; We are using an arbitrary commit from 2017 because the latest
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;; version breaks the build...
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("greedy-src"
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,(let* ((commit "97e340f7e8e66597599144947775e6039e79a0d3")
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(revision "1")
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(version (git-version "0" revision commit)))
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/pyushkevich/greedy")
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(commit commit)))
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(file-name (git-file-name "greedy" version))
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(sha256
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(base32
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"0k5bc9za4jrc8z9dj08z1rkcp5xf0gnd1d2jmi1w9ny4vxh2q2ab")))))))
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(list
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doxygen
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;; Use the submodule commits in this version of ITK-SNAP.
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/pyushkevich/c3d")
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(commit "a86a2a32db8635c1535522332fee68bc56eacaa2")))
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(file-name "c3d-checkout")
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(sha256
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(base32 "0da3ikx7pqlrmvhkmzil269j6kyd84pphy1mls8v69gmzl89piis")))
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/pyushkevich/digestible")
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(commit "1b66709e99c43d280bb472e1a0e36185ef2ea412")))
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(file-name "digestible-checkout")
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(sha256
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(base32 "1m1b954prq6l3byfdgxw2y17xsg81agd516g5n6ps60dqnxw8hqs")))
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/pyushkevich/greedy")
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(commit "f10152c5374da08ee024c4c60ef8882876bd0808")))
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(file-name "greedy-checkout")
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(sha256
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(base32 "0xk1l0h4wis4nkfwjnvh624bdlhy7l26djibk4l00wzv0vvq21qv")))))
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(home-page "https://sourceforge.net/p/itk-snap/")
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(synopsis "Medical image segmentation")
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(description "ITK-SNAP is a tool for segmenting anatomical structures in
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medical images. It provides an automatic active contour segmentation
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pipeline, along with supporting a manual segmentation toolbox. ITK-SNAP has a
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full-featured UI aimed at clinical researchers.")
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;; This includes the submodules greedy and c3d.
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(license license:gpl3+)))
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;; This includes the submodules greedy, c3d and digestible.
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(license license:gpl3+))))
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(define-public metapixel
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;; Follow stable branch.
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@ -1,22 +0,0 @@
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Retrieved from ALT Linux.
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https://git.altlinux.org/tasks/273587/build/300/x86_64/srpm/itk-snap-3.8.0-alt6.src.rpm
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diff --git a/GUI/Qt/main.cxx b/GUI/Qt/main.cxx
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index 576f7160..ceab92e6 100644
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--- a/GUI/Qt/main.cxx
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+++ b/GUI/Qt/main.cxx
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@@ -51,12 +51,13 @@ using namespace std;
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#if defined (__unix__) || (defined (__APPLE__) && defined (__MACH__))
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#include <signal.h>
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+#include <string.h>
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#include <execinfo.h>
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void SegmentationFaultHandler(int sig)
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{
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cerr << "*************************************" << endl;
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- cerr << "ITK-SNAP: " << sys_siglist[sig] << endl;
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+ cerr << "ITK-SNAP: " << strsignal(sig) << " (" << sigabbrev_np(sig) << ")" << endl;
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cerr << "BACKTRACE: " << endl;
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void *array[50];
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int nsize = backtrace(array, 50);
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