Build Fixes for Ubuntu 26

.github/workflows/build.yaml

@@ -1,108 +1,91 @@
 # GitHub action to build software.
-# Linux builds include pre-built dependencies via containers.
+# The Linux build uses a pre-built dependency container image.
 # The Windows and MacOS builds build dependencies each run.
 
 name: Build
 on:
   pull_request:
 
 jobs:
-  ubuntu_20_04_build:
+  ubuntu_26_04_build:
     runs-on: ubuntu-latest
-    container: ghcr.io/rg2/xreg-deps-ubuntu-20.04:latest
+    container: ghcr.io/rg2/xreg-deps-ubuntu-26.04:latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - run: ./.github/workflows/linux_cmake_build
         shell: bash
       - run: ./dist/ubuntu_dist_pkgs
         shell: bash
-      - run: ./.github/workflows/linux_make_dist ubuntu-20.04
+      - run: ./.github/workflows/linux_make_dist ubuntu-26.04
         shell: bash
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         with:
-          name: ubuntu-20.04-build
-          path: xreg-ubuntu-20.04.tar.gz
+          name: ubuntu-26.04-build
+          path: xreg-ubuntu-26.04.tar.gz
 
-  ubuntu_18_04_build:
+  ubuntu_24_04_build:
     runs-on: ubuntu-latest
-    container: ghcr.io/rg2/xreg-deps-ubuntu-18.04:latest
+    container: ghcr.io/rg2/xreg-deps-ubuntu-24.04:latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - run: ./.github/workflows/linux_cmake_build
         shell: bash
       - run: ./dist/ubuntu_dist_pkgs
         shell: bash
-      - run: ./.github/workflows/linux_make_dist ubuntu-18.04
+      - run: ./.github/workflows/linux_make_dist ubuntu-24.04
         shell: bash
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         with:
-          name: ubuntu-18.04-build
-          path: xreg-ubuntu-18.04.tar.gz
+          name: ubuntu-24.04-build
+          path: xreg-ubuntu-24.04.tar.gz
 
-  ubuntu_16_04_build:
+  ubuntu_22_04_build:
     runs-on: ubuntu-latest
-    container: ghcr.io/rg2/xreg-deps-ubuntu-16.04:latest
+    container: ghcr.io/rg2/xreg-deps-ubuntu-22.04:latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - run: ./.github/workflows/linux_cmake_build
         shell: bash
       - run: ./dist/ubuntu_dist_pkgs
         shell: bash
-      - run: ./.github/workflows/linux_make_dist ubuntu-16.04
+      - run: ./.github/workflows/linux_make_dist ubuntu-22.04
         shell: bash
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         with:
-          name: ubuntu-16.04-build
-          path: xreg-ubuntu-16.04.tar.gz
-
-  centos_7_build:
-    runs-on: ubuntu-latest
-    container: ghcr.io/rg2/xreg-deps-centos-7:latest
-
-    steps:
-      - uses: actions/checkout@v2
-      - run: ./.github/workflows/linux_cmake_build
-        shell: bash
-      - run: ./dist/centos_dist_pkgs
-        shell: bash
-      - run: ./.github/workflows/linux_make_dist centos-7
-        shell: bash
-      - uses: actions/upload-artifact@v2
-        with:
-          name: centos-7-build
-          path: xreg-centos-7.tar.gz
-
-  windows_build:
-    runs-on: windows-2019
-
-    steps:
-      - uses: actions/checkout@v2
-      - uses: ilammy/msvc-dev-cmd@v1
-      - run: example_build_script_win.cmd
-        shell: cmd
-      - run: .github\workflows\win_make_dist.cmd
-        shell: cmd
-      - uses: actions/upload-artifact@v2
-        with:
-          name: win-64-build
-          path: xreg-win64.zip
+          name: ubuntu-22.04-build
+          path: xreg-ubuntu-22.04.tar.gz
 
-  macos_build:
-    runs-on: macos-10.15
+#  windows_build:
+#    runs-on: windows-2022
+#
+#    steps:
+#      - uses: actions/checkout@v4
+#      - uses: ilammy/msvc-dev-cmd@v1
+#      - run: example_build_script_win.cmd
+#        shell: cmd
+#      - run: .github\workflows\win_make_dist.cmd
+#        shell: cmd
+#      - uses: actions/upload-artifact@v4
+#        with:
+#          name: win-64-build
+#          path: xreg-win64.zip
 
-    steps:
-      - uses: actions/checkout@v2
-      - run: brew install ninja
-      - run: XREG_INSTALL_DIR="$HOME/xreg_install" ./example_build_script_2
-        shell: bash
-      - run: mkdir xreg-macos-10.15
-      - run: python3 ./dist/make_macos_dist.py $HOME/xreg_install xreg-macos-10.15 ../xreg_deps_install
-      - run: cp LICENSE xreg-macos-10.15 && cp ./dist/dist_readme/README.txt xreg-macos-10.15
-      - run: tar czf xreg-macos-10.15.tar.gz xreg-macos-10.15
-      - uses: actions/upload-artifact@v2
-        with:
-          name: macos-10.15-build
-          path: xreg-macos-10.15.tar.gz
+#  macos_build:
+#    runs-on: macos-15-intel
+#
+#    steps:
+#      - uses: actions/checkout@v4
+#      - run: brew install ninja
+#      - run: XREG_INSTALL_DIR="$HOME/xreg_install" ./example_build_script_2
+#        shell: bash
+#      - run: mkdir xreg-macos-15
+#      - run: python3 ./dist/make_macos_dist.py $HOME/xreg_install xreg-macos-15 ../xreg_deps_install
+#      - run: cp LICENSE xreg-macos-15 && cp ./dist/dist_readme/README.txt xreg-macos-15
+#      - run: tar czf xreg-macos-15.tar.gz xreg-macos-15
+#      - uses: actions/upload-artifact@v4
+#        with:
+#          name: macos-15-build
+#          path: xreg-macos-15.tar.gz

.github/workflows/linux_make_dist

@@ -3,7 +3,7 @@ XREG_NAME="xreg-${1}"
 
 mkdir $XREG_NAME
 
-LD_LIBRARY_PATH="/usr/local/lib:/usr/local/lib64:/opt/tbb/lib/intel64/gcc4.7:$LD_LIBRARY_PATH" \
+LD_LIBRARY_PATH="/usr/local/lib:/usr/local/lib64:$LD_LIBRARY_PATH" \
     python3 ./dist/make_linux_dist.py /usr/local $XREG_NAME
 
 cp ./dist/dist_readme/README.txt $XREG_NAME

CMakeLists.txt

@@ -99,7 +99,6 @@ find_package(ITK REQUIRED)
 include(${ITK_USE_FILE})
 
 find_package(VTK REQUIRED)
-include(${VTK_USE_FILE})
 
 find_package(OpenCV REQUIRED)
 

docker/Dockerfile.ubuntu_dev_base

@@ -1,29 +1,23 @@
 # This Docker file is used to build an ubuntu image with the necessary
 # packages installed to complete an xReg build (along with its dependencies)
 
-ARG os_version=16.04
+ARG os_version=26.04
 
 FROM ubuntu:${os_version}
 
 # DEBIAN_FRONTEND=noninteractive is needed to avoid an interactive prompt
-# to set the timezone with 20.04 images.
+# to set the timezone with images of 20.04 or more recent.
 
 RUN export DEBIAN_FRONTEND=noninteractive && \
     apt-get update && apt-get install -y --no-install-recommends \
       build-essential \
       ca-certificates \
       cmake \
+      ninja-build \
+      libtbb-dev \
       wget \
       libssl-dev \
       git \
       libglew-dev \
       libxt-dev && \
     rm -rf /var/lib/apt/lists/*
-
-# Build a recent version of cmake
-RUN mkdir cmake_build && cd cmake_build && \
-    wget https://github.com/Kitware/CMake/releases/download/v3.18.2/cmake-3.18.2.tar.gz && \
-    tar xf cmake-3.18.2.tar.gz && cd cmake-3.18.2 && mkdir build && cd build && \
-    cmake -DCMAKE_BUILD_TYPE=Release .. && cmake --build . && cmake --build . --target install && \
-    cd / && rm -rf cmake_build
-

docker/Dockerfile.xreg

@@ -6,7 +6,7 @@ ARG os_name=ubuntu
 
 # for ubuntu choose 16.04, 18.04, or 20.04
 # for centos choose 7 or 8
-ARG os_version=16.04
+ARG os_version=26.04
 
 FROM xreg-deps-${os_name}-${os_version}
 
@@ -17,9 +17,8 @@ COPY . .
 RUN mkdir build && cd build && \
     cmake -G Ninja -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS:BOOL=ON \
                    -DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON \
-                   -DTBB_DIR:PATH="/opt/tbb/cmake" \
                    -DXREG_USE_LEGACY_FIND_TBB:BOOL=OFF \
           .. && \
-    cmake --build . && cmake --build . --target install && \
+    cmake --build . --parallel 2 && cmake --build . --target install && \
     cd / && rm -rf xreg_build
 

docker/Dockerfile.xreg-deps

@@ -7,7 +7,7 @@ ARG os_name=ubuntu
 
 # for ubuntu choose 16.04, 18.04, or 20.04
 # for centos choose 7 or 8
-ARG os_version=16.04
+ARG os_version=26.04
 
 # e.g. by running Dockerfile.ubuntu_dev_base or Dockerfile.centos_dev_base
 FROM xreg-dev-base-${os_name}-${os_version} as xreg-dev-base-cust-deps
@@ -21,46 +21,34 @@ RUN mkdir ffmpeg_dl && cd ffmpeg_dl && \
     mv ffmpeg-*-amd64-static/ffmpeg /usr/local/bin && \
     cd / && rm -rf ffmpeg_dl
 
-# Get a more recent version of TBB than what is probably in the package manager
-# At least one that works better w/ CMake
-RUN mkdir tbb_dl && cd tbb_dl && \
-    wget https://github.com/intel/tbb/releases/download/2018_U1/tbb2018_20170919oss_lin.tgz && \
-    tar xf tbb2018_20170919oss_lin.tgz && \
-    mv tbb2018_20170919oss /opt && cd /opt && ln -s tbb2018_20170919oss tbb && \
-    cd / && rm -rf tbb_dl
-
-# building ninja as it is able to build quicker than make
-RUN mkdir ninja_build && cd ninja_build && \
-    wget https://github.com/ninja-build/ninja/archive/v1.10.1.tar.gz && \
-    tar xf v1.10.1.tar.gz && cd ninja-1.10.1 && mkdir build && cd build && \
-    cmake -DCMAKE_BUILD_TYPE=Release .. && cmake --build . && cmake --build . --target install && \
-    cd / && rm -rf ninja_build
-
 FROM xreg-dev-base-cust-deps as xreg-deps
 
 WORKDIR /
 
-# bring in boost 1.74 header only
+# bring in boost header only
 RUN mkdir boost_dl && cd boost_dl && \
-    wget https://boostorg.jfrog.io/artifactory/main/release/1.74.0/source/boost_1_74_0.tar.gz && \
-    tar xf boost_1_74_0.tar.gz && cd boost_1_74_0 && mv boost /usr/local/include && \
+    wget https://archives.boost.io/release/1.87.0/source/boost_1_87_0.tar.bz2 && \
+    tar xf boost_1_87_0.tar.bz2 && cd boost_1_87_0 && mv boost /usr/local/include && \
     cd / && rm -rf boost_dl
 
-# bring in eigen 3.3.4 header only
+# bring in eigen header only, but needs to install cmake files
 RUN mkdir eigen_dl && cd eigen_dl && \
-    wget https://gitlab.com/libeigen/eigen/-/archive/3.3.4/eigen-3.3.4.tar.gz && \
-    tar xf eigen-3.3.4.tar.gz && cd eigen-3.3.4 && \
-    mv Eigen /usr/local/include && mv unsupported /usr/local/include && \
-    mv signature_of_eigen3_matrix_library /usr/local/include && \
+    wget https://gitlab.com/libeigen/eigen/-/archive/3.4.1/eigen-3.4.1.tar.bz2 && \
+    tar xf eigen-3.4.1.tar.bz2 && cd eigen-3.4.1 && \
+    mkdir build && cd build && \
+    cmake -DCMAKE_INSTALL_PREFIX:PATH="/usr/local" \
+          -DINCLUDE_INSTALL_DIR:PATH="/usr/local/include" \
+          .. && \
+    cmake --build . && cmake --build . --target install && \
     cd / && rm -rf eigen_dl
 
-# bring in viennacl 1.7.1 header only
+# bring in viennacl header only
 RUN mkdir viennacl_dl && cd viennacl_dl && \
     wget https://github.com/viennacl/viennacl-dev/archive/release-1.7.1.tar.gz && \
     tar xf release-1.7.1.tar.gz && cd viennacl-dev-release-1.7.1 && mv viennacl /usr/local/include && \
     cd / && rm -rf viennacl_dl
 
-# build format 5.3.0
+# build format
 RUN mkdir fmt_build && cd fmt_build && \
     wget https://github.com/fmtlib/fmt/archive/5.3.0.tar.gz && \
     tar xf 5.3.0.tar.gz && cd fmt-5.3.0 && \
@@ -69,11 +57,12 @@ RUN mkdir fmt_build && cd fmt_build && \
                    -DCMAKE_CXX_STANDARD:STRING="11" -DFMT_USE_CPP11:BOOL=ON \
                    -DFMT_TEST:BOOL=OFF -DFMT_INSTALL:BOOL=ON \
                    -DFMT_DOC:BOOL=OFF \
+                   -DCMAKE_POLICY_VERSION_MINIMUM=3.5 \
           .. && \
     cmake --build . && cmake --build . --target install && \
     cd / && rm -rf fmt_build
 
-# build nlopt 2.5.0
+# build nlopt
 RUN mkdir nlopt_build && cd nlopt_build && \
     wget https://github.com/stevengj/nlopt/archive/v2.5.0.tar.gz && \
     tar xf v2.5.0.tar.gz && cd nlopt-2.5.0 && \
@@ -84,55 +73,60 @@ RUN mkdir nlopt_build && cd nlopt_build && \
                    -DNLOPT_OCTAVE:BOOL=OFF -DNLOPT_MATLAB:BOOL=OFF \
                    -DNLOPT_GUILE:BOOL=OFF -DNLOPT_SWIG:BOOL=OFF \
                    -DNLOPT_LINK_PYTHON:BOOL=OFF \
+                   -DCMAKE_POLICY_VERSION_MINIMUM=3.5 \
          .. && \
     cmake --build . && cmake --build . --target install && \
     cd / && rm -rf nlopt_build
 
-# build ITK 5.2.1
+# build ITK
 RUN mkdir itk_build && cd itk_build && \
-    wget https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.2.1/InsightToolkit-5.2.1.zip && \
+    wget https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.2.1/InsightToolkit-5.2.1.tar.gz && \
     tar xf InsightToolkit-5.2.1.tar.gz && cd InsightToolkit-5.2.1 && \
     mkdir build && cd build && \
     cmake -G Ninja -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS:BOOL=ON \
           -DCMAKE_CXX_STANDARD:STRING="11" \
+          -DCMAKE_CXX_FLAGS:STRING="-include cstdint" \
+          -DCMAKE_C_FLAGS:STRING="-std=gnu17" \
           -DBUILD_TESTING:BOOL=OFF -DBUILD_EXAMPLES:BOOL=OFF \
           -DITK_USE_GPU:BOOL=OFF -DModule_ITKReview:BOOL=ON \
           -DModule_LabelErodeDilate:BOOL=ON \
+          -DITK_USE_SYSTEM_EIGEN=ON \
+          -DCMAKE_POLICY_VERSION_MINIMUM=3.5 \
          .. && \
     cmake --build . && cmake --build . --target install && \
     cd / && rm -rf itk_build
 
-# build OpenCV 3.4.12
+# build OpenCV
 RUN mkdir opencv_build && cd opencv_build && \
-    wget https://github.com/opencv/opencv/archive/3.4.12.tar.gz && \
-    tar xf 3.4.12.tar.gz && cd opencv-3.4.12 && \
+    wget https://github.com/opencv/opencv/archive/refs/tags/4.12.0.tar.gz && \
+    tar xf 4.12.0.tar.gz && cd opencv-4.12.0 && \
     mkdir build && cd build && \
     cmake -G Ninja -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS:BOOL=ON \
                    -DCMAKE_CXX_STANDARD:STRING="11" \
                    -DBUILD_TESTS:BOOL=OFF -DBUILD_EXAMPLES:BOOL=OFF \
                    -DBUILD_DOCS:BOOL=OFF -DBUILD_WITH_DEBUG_INFO:BOOL=OFF \
-                   -DWITH_TBB:BOOL=ON -DBUILD_TBB:BOOL=OFF -DTBB_INCLUDE_DIRS:PATH="/opt/tbb/include" \
+                   -DWITH_TBB:BOOL=ON -DBUILD_TBB:BOOL=OFF \
                    -DWITH_IPP:BOOL=OFF -DWITH_VTK:BOOL=OFF \
                    -DWITH_CUBLAS:BOOL=OFF -DWITH_CUDA:BOOL=OFF \
-                   -DWITH_CUFFT:BOOL=OFF -DWITH_OPENCL:BOOL=OFF \
-                   -DBUILD_opencv_python2:BOOL=OFF -DBUILD_opencv_python3:BOOL=OFF \
+                   -DWITH_OPENCL:BOOL=OFF \
+                   -DBUILD_opencv_java_bindings_generator:BOOL=OFF \
+                   -DBUILD_opencv_python_tests:BOOL=OFF \
+                   -DBUILD_opencv_python_bindings_generator:BOOL=OFF \
                    -DBUILD_opencv_highgui:BOOL=OFF -DWITH_GSTREAMER:BOOL=OFF \
          .. && \
     cmake --build . && cmake --build . --target install && \
     cd / && rm -rf opencv_build
-
-# build VTK 8.2.0
+    
+# build VTK, note --parallel 2 is used in order to avoid OOM errors
 RUN mkdir vtk_build && cd vtk_build && \
-    wget https://www.vtk.org/files/release/8.2/VTK-8.2.0.tar.gz && \
-    tar xf VTK-8.2.0.tar.gz && cd VTK-8.2.0 && \
+    wget https://vtk.org/files/release/9.6/VTK-9.6.2.tar.gz && \
+    tar xf VTK-9.6.2.tar.gz && cd VTK-9.6.2 && \
     mkdir build && cd build && \
-    TBB_ROOT="/opt/tbb" \
     cmake -G Ninja -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS:BOOL=ON \
           -DCMAKE_CXX_STANDARD:STRING="11" \
-          -DVTK_Group_Imaging:BOOL=ON -DVTK_Group_Views:BOOL=ON \
+          -DVTK_GROUP_ENABLE_Imaging=YES -DVTK_GROUP_ENABLE_Views=YES \
           -DBUILD_TESTING:BOOL=OFF \
           -DVTK_SMP_IMPLEMENTATION_TYPE:STRING="TBB" \
          .. && \
-    cmake --build . && cmake --build . --target install && \
+    cmake --build . --parallel 2 && cmake --build . --target install && \
     cd / && rm -rf vtk_build
-