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.

3 files changed, 46 insertions, 29 deletions

diff --git a/gnu/local.mk b/gnu/local.mk
index 0cd874dae7..c4d774052b 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1302,6 +1302,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/ipxe-reproducible-geniso.patch	        \
   %D%/packages/patches/irrlicht-use-system-libs.patch		\
   %D%/packages/patches/isl-0.11.1-aarch64-support.patch	\
+  %D%/packages/patches/itk-snap-alt-glibc-compat.patch		\
   %D%/packages/patches/json-c-0.13-CVE-2020-12762.patch	\
   %D%/packages/patches/json-c-0.12-CVE-2020-12762.patch	\
   %D%/packages/patches/jsoncpp-pkg-config-version.patch		\
diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm
index 08aeaed202..d0d80c08cf 100644
--- a/gnu/packages/image-processing.scm
+++ b/gnu/packages/image-processing.scm
@@ -1032,7 +1032,8 @@ combine the information contained in both.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "15i5ixpryfrbf3vrrb5rici8fb585f25k0v1ljds16bp1f1msr4q"))))
+        (base32 "15i5ixpryfrbf3vrrb5rici8fb585f25k0v1ljds16bp1f1msr4q"))
+       (patches (search-patches "itk-snap-alt-glibc-compat.patch"))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags
@@ -1051,22 +1052,19 @@ combine the information contained in both.")
              (substitute* "CMakeLists.txt"
                (("install_qt5_executable\
 \\(\\$\\{SNAP_MAIN_INSTALL_DIR\\}/\\$\\{SNAP_EXE\\}\\)")
-                ""))
-             #t))
+                ""))))
          (add-after 'unpack 'disable-gui-tests
            (lambda _
              ;; The GUI tests just time out.
              (substitute* "CMakeLists.txt"
                (("  (Workspace|DiffSpace|ProbeIntensity|RegionCompetition\
 |RandomForest|RandomForestBailOut)")
-                ""))
-             #t))
+                ""))))
          (add-after 'unpack 'make-reproducible
            (lambda _
              (substitute* "CMakeLists.txt"
                (("TODAY\\(SNAP_VERSION_COMPILE_DATE\\)")
-                "SET(SNAP_VERSION_COMPILE_DATE \"(removed for reproducibility)\")"))
-             #t))
+                "SET(SNAP_VERSION_COMPILE_DATE \"(removed for reproducibility)\")"))))
          (add-after 'unpack 'prepare-submodules
            (lambda* (#:key inputs #:allow-other-keys)
              (rmdir "Submodules/c3d")
@@ -1077,19 +1075,16 @@ combine the information contained in both.")
                (("vcl_") "std::"))
              (rmdir "Submodules/greedy")
              (symlink (assoc-ref inputs "greedy-src")
-                      "Submodules/greedy")
-             #t))
+                      "Submodules/greedy")))
          (add-after 'unpack 'fix-includes
            (lambda _
              (substitute* "GUI/Model/RegistrationModel.cxx"
                (("<vnl_symmetric_eigensystem.h>")
-                "<vnl/algo/vnl_symmetric_eigensystem.h>"))
-             #t))
+                "<vnl/algo/vnl_symmetric_eigensystem.h>"))))
          (add-before 'check 'prepare-tests
            (lambda _
              ;; Needed by at least one test.
-             (setenv "HOME" "/tmp")
-             #t))
+             (setenv "HOME" "/tmp")))
          (add-after 'install 'wrap-executable
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let ((out (assoc-ref outputs "out")))
@@ -1098,23 +1093,22 @@ combine the information contained in both.")
                    ,(map (lambda (label)
                            (string-append (assoc-ref inputs label)
                                           "/lib/qt5/plugins"))
-                         '("qtbase" "qtdeclarative"))))
-               #t))))))
+                         '("qtbase" "qtdeclarative"))))))))))
     (inputs
-     `(("curl" ,curl)
-       ("fftw" ,fftw)
-       ("fftwf" ,fftwf)
-       ("glu" ,glu)
-       ("hdf5" ,hdf5)
-       ("mesa" ,mesa-opencl)
-       ;; This package does not build with either insight-toolkit 5.0.0 and
-       ;; not with 4.13.  It really needs to be 4.12.
-       ("itk" ,insight-toolkit-4.12)
-       ("vtk" ,vtk-6)
-       ("qtbase" ,qtbase-5)
-       ("qtdeclarative" ,qtdeclarative)
-       ("vxl" ,vxl-1)
-       ("zlib" ,zlib)))
+     (list curl
+           fftw
+           fftwf
+           glu
+           hdf5
+           mesa-opencl
+           ;; This package does not build with either insight-toolkit 5.0.0
+           ;; and not with 4.13.  It really needs to be 4.12.
+           insight-toolkit-4.12
+           vtk-7
+           qtbase-5
+           qtdeclarative
+           vxl-1
+           zlib))
     (native-inputs
      `(("googletest" ,googletest)
        ("qttools" ,qttools)
diff --git a/gnu/packages/patches/itk-snap-alt-glibc-compat.patch b/gnu/packages/patches/itk-snap-alt-glibc-compat.patch
new file mode 100644
index 0000000000..764c5da2c2
--- /dev/null
+++ b/gnu/packages/patches/itk-snap-alt-glibc-compat.patch
@@ -0,0 +1,22 @@
+Retrieved from ALT Linux.
+https://git.altlinux.org/tasks/273587/build/300/x86_64/srpm/itk-snap-3.8.0-alt6.src.rpm
+
+diff --git a/GUI/Qt/main.cxx b/GUI/Qt/main.cxx
+index 576f7160..ceab92e6 100644
+--- a/GUI/Qt/main.cxx
++++ b/GUI/Qt/main.cxx
+@@ -51,12 +51,13 @@ using namespace std;
+ #if defined (__unix__) || (defined (__APPLE__) && defined (__MACH__))
+ 
+ #include <signal.h>
++#include <string.h>
+ #include <execinfo.h>
+ 
+ void SegmentationFaultHandler(int sig)
+ {
+   cerr << "*************************************" << endl;
+-  cerr << "ITK-SNAP: " << sys_siglist[sig] << endl;
++  cerr << "ITK-SNAP: " << strsignal(sig) << " (" << sigabbrev_np(sig) << ")" << endl;
+   cerr << "BACKTRACE: " << endl;
+   void *array[50];
+   int nsize = backtrace(array, 50);