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ENH: Update ANTs #173

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ENH: Update ANTs #173

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7e30b9f
ENH: Update ANTs
cookpa Feb 26, 2025
e9b237b
COMP: Set CMAKE_OSX_ROOT
cookpa Feb 27, 2025
085bc97
COMP: Try to set SDK path that works on different systems
cookpa Feb 27, 2025
7ba0ae0
COMP: Remove redundant flags
cookpa Feb 28, 2025
ee0f1b3
COMP: Resolve linking errors
cookpa Feb 28, 2025
5184496
COMP: Give up trying to fix linking order issues
cookpa Feb 28, 2025
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2 changes: 1 addition & 1 deletion .github/workflows/package-build.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ jobs:
name: ${{ matrix.config.os }} (${{ matrix.config.r }})

strategy:
fail-fast: true
fail-fast: false
matrix:
config:
- { os: ubuntu-latest, r: "release" }
Expand Down
11 changes: 7 additions & 4 deletions configure
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Expand Up @@ -5,8 +5,9 @@ CXX_STD=CXX17
ITKRCMAKE=`${R_HOME}/bin/Rscript -e 'a<-ITKR:::itkIncludes(); cat(a)'`
ITKRLIB=`${R_HOME}/bin/Rscript -e 'a<-ITKR:::itkLibs(); cat(a)'`
compflags=`${R_HOME}/bin/Rscript -e 'a<-ITKR:::itkCompileFlags(); cat(a)'`
osx_sysroot=""
if [[ `uname` == 'Darwin' ]] ; then
compflags=" ${compflags} -isystem /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1 -stdlib=libc++ "
osx_sysroot=$(xcrun --show-sdk-path)
fi
ITKDIR=`${R_HOME}/bin/Rscript -e 'a<-ITKR:::itkDir(); cat(a)'`
ITKTAG=`${R_HOME}/bin/Rscript -e 'env = asNamespace("ITKR"); if ("itkTag" %in% names(env)) cat(ITKR::itkTag()) else cat("")'`
Expand Down Expand Up @@ -50,7 +51,7 @@ fi
echo $OSTYPE $needVCL_CAN_STATIC_CONST_INIT_FLOAT

if [[ `uname` == 'Darwin' ]] ; then
PKG_CPPFLAGS="${PKG_CPPFLAGS} -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1""
PKG_CPPFLAGS="${PKG_CPPFLAGS} -isysroot${osx_sysroot}"
fi

echo "PKG_CPPFLAGS=${PKG_CPPFLAGS} -I\${ITK} -I\${PWD} -I\${myantssource}/Examples/include/ \
Expand All @@ -68,6 +69,8 @@ echo "libants=\`find \${myantslib} -name \"lib*.a\"\`" >> Makevars
# echo "libitk=\`find \\\`\$(R_HOME)/bin/Rscript -e 'ITKR:::itkLibs()'\\\` -name \"lib*.a\"\` " >> Makevars
echo "libitk=\`find ${ITKRLIB} -name \"lib*.a\"\`" >> Makevars

# Duplicate libants and libitk to avoid issues with the order of the libraries. This isn't a good solution but
# cmake's suggested ordering didn't work either
echo "PKG_LIBS=${PKG_LIBS} \${libants} \${libitk} \${libants} \${libitk} \
\${libants} \${libitk} \${libants} \${libitk} \${libants} \${libitk}" >> Makevars

Expand All @@ -89,8 +92,7 @@ ThresholdImage LabelClustersUniquely SurfaceBasedSmoothing" >> Makevars

# get / set up ANTs code
antsgit=https://github.com/ANTsX/ANTs.git
antstag=d87f266dffdbcef00407d260eab20f4738a98825 # with itk v5.3rc04 2023 nov 25
antstag=1892feff83b792b563500f379fff7733da5465a6
antstag=fc0589fd23826e53d51e67eb8a3f9a3d63e63a14 # 2025-02-26, label geometry measures
antsrtag=`git log --pretty=format:'%H' -n 1`
if [[ ! -s ants/CMakeLists.txt ]] ; then
git clone $antsbranch $antsgit ants
Expand Down Expand Up @@ -121,6 +123,7 @@ cd ./antb
cmake -DITK_DIR:PATH=${ITKDIR} \
-DCMAKE_C_FLAGS="${CMAKE_C_FLAGS} ${compflags} -DNDEBUG "\
-DCMAKE_CXX_FLAGS="${CMAKE_CXX_FLAGS} ${compflags} -DNDEBUG "\
-DCMAKE_OSX_SYSROOT="${osx_sysroot}" \
-DBUILD_SHARED_LIBS=OFF \
-DANTS_INSTALL_LIBS_ONLY=ON \
-DBUILD_ALL_ANTS_APPS=OFF \
Expand Down
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