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gnu: itk-snap: Fix build.
* gnu/packages/patches/itk-snap-alt-glibc-compat.patch: New patch. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/image-processing.scm (itk-snap): Apply it. [phases]: Delete trailing #t. [inputs]: Use new style. Replace vtk-6 with vtk-7.
This commit is contained in:
Maxim Cournoyer
parent
607e48ba3c
commit
887dec8a51
3 changed files with 46 additions and 29 deletions
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@ -1302,6 +1302,7 @@ dist_patch_DATA = \
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%D%/packages/patches/ipxe-reproducible-geniso.patch \
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%D%/packages/patches/irrlicht-use-system-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/json-c-0.13-CVE-2020-12762.patch \
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%D%/packages/patches/json-c-0.12-CVE-2020-12762.patch \
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%D%/packages/patches/jsoncpp-pkg-config-version.patch \
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@ -1032,7 +1032,8 @@ (define-public itk-snap
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(commit (string-append "v" version))))
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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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(base32 "15i5ixpryfrbf3vrrb5rici8fb585f25k0v1ljds16bp1f1msr4q"))
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(patches (search-patches "itk-snap-alt-glibc-compat.patch"))))
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(build-system cmake-build-system)
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(arguments
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`(#:configure-flags
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@ -1051,22 +1052,19 @@ (define-public itk-snap
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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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#t))
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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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#t))
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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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#t))
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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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@ -1077,19 +1075,16 @@ (define-public itk-snap
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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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#t))
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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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#t))
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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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#t))
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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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@ -1098,23 +1093,22 @@ (define-public itk-snap
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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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#t))))))
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'("qtbase" "qtdeclarative"))))))))))
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(inputs
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`(("curl" ,curl)
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("fftw" ,fftw)
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("fftwf" ,fftwf)
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("glu" ,glu)
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("hdf5" ,hdf5)
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("mesa" ,mesa-opencl)
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;; This package does not build with either insight-toolkit 5.0.0 and
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;; not with 4.13. It really needs to be 4.12.
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("itk" ,insight-toolkit-4.12)
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("vtk" ,vtk-6)
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("qtbase" ,qtbase-5)
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("qtdeclarative" ,qtdeclarative)
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("vxl" ,vxl-1)
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("zlib" ,zlib)))
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(list curl
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fftw
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fftwf
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glu
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hdf5
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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
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vxl-1
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zlib))
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(native-inputs
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`(("googletest" ,googletest)
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("qttools" ,qttools)
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22
gnu/packages/patches/itk-snap-alt-glibc-compat.patch
Normal file
22
gnu/packages/patches/itk-snap-alt-glibc-compat.patch
Normal file
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@ -0,0 +1,22 @@
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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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