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Add support for Windows
Add support for building and testing on Windows OS in a consistent manner to Linux and macOS. On Windows, this uses RTools to provide the necessary build tools. Testing is performed in CircleCI as it offers a more powerful build machine under the free plan. Co-authored-by: Artur-man <artur-man@hotmail.com>
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Lines changed: 149 additions & 27 deletions

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‎.circleci/config.yml‎

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@@ -18,6 +18,12 @@ executors:
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environment:
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RUNNER_OS: macos
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resource_class: m4pro.medium
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windows:
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machine:
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image: windows-server-2022-gui:current
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environment:
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RUNNER_OS: windows
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resource_class: windows.large
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jobs:
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r-build:
@@ -32,8 +38,12 @@ jobs:
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steps:
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- checkout
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- run:
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name: Set environment
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name: Set library for default R package installation
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command: |
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# All packages will be installed into the directory
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# referenced by the R_LIBS environment variable.
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mkdir -p $HOME/Rlibs
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ls -la ${R_LIBS}
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echo "export R_LIBS=$HOME/Rlibs" >> $BASH_ENV
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- run:
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name: Install R << parameters.r-version >>
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brew tap r-lib/rig
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brew install --cask rig
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rig add $R_VERSION
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# on macOS the R package is installed into a MAJOR.MINOR directory
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# the PATCH is ignored (only one patch version supported) the
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# architecture is added as a suffix (arm64, x86_64) to allow for
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# installations to coexist
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rig default "${R_VERSION%.*}-arm64"
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elif [ "$RUNNER_OS" == "linux" ]; then
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`which sudo` curl -L https://rig.r-pkg.org/deb/rig.gpg -o /etc/apt/trusted.gpg.d/rig.gpg
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`which sudo` sh -c 'echo "deb http://rig.r-pkg.org/deb rig main" > /etc/apt/sources.list.d/rig.list'
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`which sudo` apt update
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`which sudo` apt install r-rig
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sudo rig add $R_VERSION
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sudo rig default $R_VERSION
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elif [ "$RUNNER_OS" == "windows" ]; then
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choco install rig -y
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export PATH="$PATH:/c/Program Files/rig"
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rig add $R_VERSION
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echo "export PATH=\"/c/Program Files/R/R-$R_VERSION/bin:\${PATH}\"" >> $BASH_ENV
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echo "export R_HOME=\"/c/Program Files/R/R-$R_VERSION/\"" >> $BASH_ENV
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fi
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- run:
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name: System Dependencies
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sudo rm -rf /var/lib/apt/lists/*
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elif [ "$RUNNER_OS" == "macos" ]; then
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brew install cmake
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elif [ "$RUNNER_OS" == "windows" ]; then
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choco install rtools -y
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echo "RTOOLS_HOME=$(ls -d /c/rtools* | head -n 1)" >> $BASH_ENV
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fi
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- run:
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name: Configuration Information
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command: |
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mkdir -p ${R_LIBS}
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c++ --version
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if [ "$RUNNER_OS" == "windows" ]; then
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export PATH="${RTOOLS_HOME}/usr/bin:${RTOOLS_HOME}/x86_64-w64-mingw32.static.posix/bin:${R_HOME}/bin:${PATH}"
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fi
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echo "R_LIBS is: ${R_LIBS}"
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c++ --version || gcc --version || echo "no c++ compiler found"
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cmake --version || echo "cmake not found"
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which R
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R --version
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make --version || echo "make not found"
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R --version || echo "R not found"
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- run:
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name: Install R packages
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command: |
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R -e "install.packages(c('remotes'), lib=c('${R_LIBS}'), repo='https://cloud.r-project.org/')"
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R -e "install.packages(c('remotes'), repo='https://cloud.r-project.org/')"
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- run:
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name: Build and test
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no_output_timeout: 30m
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command: |
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set -x
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R -e "remotes::install_git(c('.'), lib=c('${R_LIBS}'), configure.vars=c('MAKEJ=3'))"
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R -e "remotes::install_git(c('.'), configure.vars=c('MAKEJ=3'))"
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workflows:
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r-build-test:
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matrix:
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parameters:
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r-version: ['4.3.1', '4.4.1']
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os: ["macos-arm"]
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os: ["macos-arm", "windows"]
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filters:
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branches:
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only:

‎DESCRIPTION‎

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@@ -1,20 +1,23 @@
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Package: SimpleITK
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Version: 2.0.0
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Date: 2020-09-17
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Title: Bindings to SimpleITK Image segmentation and registration toolkit
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Version: 2.5.3
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Date: 2025-11-20
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Title: SimpleITK: A Simplified Interface to the Insight Toolkit
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Authors@R: c(person("Richard", "Beare", role = c("aut", "cre"),
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email = "Richard.Beare@ieee.org"),
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person("Bradley", "Lowekamp", role = "aut",
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email = "blowekamp@mail.nih.gov"),
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person("Ziv", "Yaniv", role="aut",
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email = "zivrafael.yaniv@nih.gov"))
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Author: Richard Beare, Bradley Lowekamp, plus loads of others
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email = "zivyaniv@nih.gov"))
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Author: Richard Beare, Bradley Lowekamp, Ziv Yaniv plus loads of others
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Depends: R (>= 3.4)
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Imports: methods
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Imports: methods,
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desc
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Description: This package is an interface to SimpleITK, which is a simplified
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interface to the Insight Toolkit (ITK) for medical image segmentation
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and registration.
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License: Apache License 2.0
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URL: http://www.simpleitk.org, http://www.itk.org
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BugReports: http://issues.itk.org
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Note: The first url in the URL field below is the SimpleITK repository, and is used
20+
by the config script under the assumption that it is the first in the list.
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URL: https://github.com/SimpleITK/SimpleITK, https://www.simpleitk.org, https://www.itk.org
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BugReports: https://github.com/SimpleITK/SimpleITK/issues
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Maintainer: Richard Beare <Richard.Beare@ieee.org>

‎README.md‎

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@@ -26,10 +26,13 @@ Use multicore compilation and build additional modules not included in the defau
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remotes::install_github("SimpleITK/SimpleITKRInstaller", configure.vars=c("MAKEJ=6", "ADDITIONAL_SITK_MODULES=-DSimpleITK_USE_ELASTIX=ON\\ -DModule_ITKIODCMTK:BOOL=ON"))
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```
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Note:
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On Linux and Mac requires [CMake](https://cmake.org/) and [git](https://git-scm.com/) in the path.
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30-
Requires _cmake_ and _git_ in the path.
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32-
Tested on Linux and Mac.
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On Windows requires [rtools](https://cran.r-project.org/bin/windows/Rtools/) installation and setting the `RTOOLS_HOME` environment variable. For example:
33+
```R
34+
Sys.setenv(RTOOLS_HOME = "C:/rtools45")
35+
```
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# How to Cite
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‎configure‎

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#
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# Requires git and cmake
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#
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export SimpleITKGit=https://github.com/SimpleITK/SimpleITK
10-
export SITKTAG=v2.5.3
9+
export SimpleITKGit=$(Rscript -e "d <- desc::desc(file='DESCRIPTION'); urls <- strsplit(d\$get_field('URL'), ',')[[1]]; cat(trimws(urls[1]))")
10+
export SITKTAG=v$(Rscript -e "cat(desc::desc_get_field('Version', file='DESCRIPTION'))")
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1212
export PKGBASED=$(pwd)
1313
echo ${PKGBASED}

‎configure.win‎

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#!/usr/bin/env sh
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set -e
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# configure script that will fetch and build SimpleITK, then move the results
5+
# to somewhere that R can install. It takes a long time and uses
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# a substantial amount of disk space
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#
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# Requires rtools (https://cran.r-project.org/bin/windows/Rtools/)
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#
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# --- Settings ---
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# Load shared configuration for all OS (SimpleITK repository URL and tag)
13+
export SimpleITKGit=$(Rscript -e "d <- desc::desc(file='DESCRIPTION'); urls <- strsplit(d\$get_field('URL'), ',')[[1]]; cat(trimws(urls[1]))")
14+
export SITKTAG=v$(Rscript -e "cat(desc::desc_get_field('Version', file='DESCRIPTION'))")
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16+
PKGBASED=$(pwd)
17+
echo "$PKGBASED"
18+
19+
# --- Check R_HOME and RTOOLS_HOME---
20+
if [ -z "$R_HOME" ]; then
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echo "Environment variable \"R_HOME\" is not set!" 1>&2
22+
exit 1
23+
fi
24+
25+
if [ -z "$RTOOLS_HOME" ]; then
26+
echo "Environment variable \"RTOOLS_HOME\" is not set!" 1>&2
27+
exit 1
28+
fi
29+
30+
export PATH="${RTOOLS_HOME}/usr/bin:${RTOOLS_HOME}/x86_64-w64-mingw32.static.posix/bin:${PATH}"
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# Use Rscript on Windows
33+
RCALL="${R_HOME}/bin/Rscript.exe"
34+
export RCALL
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36+
# --- Build location: short path to avoid ITK limit ---
37+
BUILDDIR="C:/bld"
38+
echo "Using short build directory: $BUILDDIR"
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mkdir -p "$BUILDDIR"
40+
41+
# Pull compiler flags from R (optional but kept for parity)
42+
CC="$("${R_HOME}/bin/R.exe" CMD config CC)"
43+
CXX="$("${R_HOME}/bin/R.exe" CMD config CXX)"
44+
CFLAGS="$("${R_HOME}/bin/R.exe" CMD config CFLAGS)"
45+
CXXFLAGS="$("${R_HOME}/bin/R.exe" CMD config CXX11FLAGS)"
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CPPFLAGS="$("${R_HOME}/bin/R.exe" CMD config CPPFLAGS)"
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export CC CXX CFLAGS CXXFLAGS CPPFLAGS
48+
49+
# Parallelism (default 1 if not provided)
50+
: "${MAKEJ:=1}"
51+
export MAKEJ
52+
53+
# --- Build in SITK directory ---
54+
(
55+
cd "$BUILDDIR"
56+
57+
if [ ! -d SimpleITK ]; then
58+
git clone "$SimpleITKGit"
59+
cd SimpleITK
60+
git checkout "$SITKTAG"
61+
else
62+
cd SimpleITK
63+
git fetch --tags
64+
git checkout "$SITKTAG"
65+
fi
66+
67+
SITK_SRC="$(pwd)"
68+
69+
mkdir -p ../Build
70+
cd ../Build
71+
72+
echo "Path:"
73+
echo $PWD
74+
75+
# Configure with Unix Makefiles (Rtools toolchain)
76+
cmake -G "Unix Makefiles" \
77+
-DWRAP_DEFAULT=OFF \
78+
-DWRAP_R=ON \
79+
-DSimpleITK_BUILD_DISTRIBUTE=ON \
80+
-DBUILD_EXAMPLES=OFF \
81+
-DBUILD_TESTING=OFF \
82+
-DITK_SKIP_PATH_LENGTH_CHECK=ON \
83+
-DCMAKE_BUILD_TYPE=MinSizeRel \
84+
-DITK_USE_BUILD_DIR:BOOL=ON \
85+
${ADDITIONAL_SITK_MODULES} \
86+
"${BUILDDIR}/SimpleITK/SuperBuild/"
87+
88+
echo "Parallel build using -j${MAKEJ}"
89+
echo $PWD
90+
# Build the specific target with parallel jobs
91+
cmake --build . --target SimpleITK-build -- -j"${MAKEJ}"
92+
93+
# Remove ITK-build to save space (if present)
94+
[ -d ITK-build ] && rm -rf ITK-build
95+
96+
# Move wrapped R package into the package root using R
97+
"${RCALL}" -f "${PKGBASED}/sitkmove.R" --args \
98+
"SimpleITK-build/Wrapping/R/Packaging/SimpleITK" \
99+
"${PKGBASED}"
100+
)

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