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Merged
vfonov merged 2 commits into from
Aug 11, 2026
Merged

Resolve run paths relative to the loader, not the install prefix #232

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70d91b8
Resolve run paths relative to the loader, not the install prefix
gdevenyi Aug 6, 2026
92e78b4
Pass the install RPATH as STRING rather than PATH
gdevenyi Aug 6, 2026
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13 changes: 12 additions & 1 deletion CMakeLists.txt
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Expand Up @@ -157,7 +157,18 @@ SET(CPACK_STRIP_FILES ON)

# MAC OS X magick
SET(MACOSX_RPATH ON)
SET(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX})

# Resolve run paths relative to the loaded object instead of baking in
# CMAKE_INSTALL_PREFIX, so a moved install still finds its libraries. Every
# component uses this: binaries land in <prefix>/bin and libraries in
# <prefix>/lib, and "<origin>/../lib" is correct from both -- from a library in
# lib/ it normalises back to the same directory.
IF(APPLE)
SET(MT_RPATH_ORIGIN "@loader_path")
ELSE()
SET(MT_RPATH_ORIGIN "$ORIGIN")
ENDIF()
SET(CMAKE_INSTALL_RPATH ${MT_RPATH_ORIGIN}/../lib${LIB_SUFFIX})
SET(CMAKE_SKIP_RPATH OFF)
SET(CMAKE_SKIP_INSTALL_RPATH OFF)
SET(CMAKE_INSTALL_RPATH_USE_LINK_PATH FALSE)
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2 changes: 1 addition & 1 deletion cmake-modules/BuildABC.cmake
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Expand Up @@ -102,7 +102,7 @@ macro(build_ABC install_prefix staging_prefix)
-DCOMPILE_STANDALONEGUI:BOOL=OFF
-DCMAKE_SKIP_RPATH:BOOL=OFF
-DCMAKE_SKIP_INSTALL_RPATH:BOOL=OFF
-DCMAKE_INSTALL_RPATH:PATH=${install_prefix}/lib${LIB_SUFFIX}
-DCMAKE_INSTALL_RPATH:PATH=${MT_RPATH_ORIGIN}/../lib${LIB_SUFFIX}
${CMAKE_EXTERNAL_PROJECT_ARGS}
INSTALL_COMMAND $(MAKE) install DESTDIR=${staging_prefix}
INSTALL_DIR ${staging_prefix}/${install_prefix}
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2 changes: 1 addition & 1 deletion cmake-modules/BuildANTS.cmake
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Expand Up @@ -98,7 +98,7 @@ macro(build_ANTS install_prefix staging_prefix itk_dir ) #boost_dir
-DITK_USE_FFTWD:BOOL=ON
-DITK_USE_FFTWF:BOOL=ON
-DITK_USE_SYSTEM_FFTW:BOOL=ON
-DCMAKE_INSTALL_RPATH:PATH=${install_prefix}/lib${LIB_SUFFIX}
-DCMAKE_INSTALL_RPATH:PATH=${MT_RPATH_ORIGIN}/../lib${LIB_SUFFIX}
${CMAKE_EXTERNAL_PROJECT_ARGS}
INSTALL_COMMAND $(MAKE) install DESTDIR=${staging_prefix}
INSTALL_DIR ${staging_prefix}/${install_prefix}
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2 changes: 1 addition & 1 deletion cmake-modules/BuildBEAST.cmake
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Expand Up @@ -43,7 +43,7 @@ macro(build_BEAST install_prefix staging_prefix )
-DCMAKE_SKIP_RPATH:BOOL=OFF
-DCMAKE_SKIP_INSTALL_RPATH:BOOL=OFF
-DMACOSX_RPATH:BOOL=ON
-DCMAKE_INSTALL_RPATH:PATH=${install_prefix}/lib${LIB_SUFFIX}
-DCMAKE_INSTALL_RPATH:PATH=${MT_RPATH_ORIGIN}/../lib${LIB_SUFFIX}
-DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}
-DCMAKE_INSTALL_PREFIX:PATH=${install_prefix}
-DZLIB_LIBRARY:PATH=${ZLIB_LIBRARY}
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2 changes: 1 addition & 1 deletion cmake-modules/BuildBICGL.cmake
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Expand Up @@ -31,7 +31,7 @@ macro(build_bicgl bicgl_location install_prefix staging_prefix)
-DCMAKE_SKIP_RPATH:BOOL=OFF
-DCMAKE_SKIP_INSTALL_RPATH:BOOL=OFF
-DMACOSX_RPATH:BOOL=ON
-DCMAKE_INSTALL_RPATH:PATH=${install_prefix}/lib${LIB_SUFFIX}
-DCMAKE_INSTALL_RPATH:PATH=${MT_RPATH_ORIGIN}/../lib${LIB_SUFFIX}
${CMAKE_OSX_EXTERNAL_PROJECT_ARGS}
INSTALL_COMMAND $(MAKE) install DESTDIR=${staging_prefix}
INSTALL_DIR ${staging_prefix}/${install_prefix}
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2 changes: 1 addition & 1 deletion cmake-modules/BuildC3D.cmake
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Expand Up @@ -103,7 +103,7 @@ macro(build_C3D install_prefix staging_prefix)
-DCMAKE_SKIP_RPATH:BOOL=OFF
-DCMAKE_SKIP_INSTALL_RPATH:BOOL=OFF
-DMACOSX_RPATH:BOOL=ON
-DCMAKE_INSTALL_RPATH:PATH=${install_prefix}/lib${LIB_SUFFIX}
-DCMAKE_INSTALL_RPATH:PATH=${MT_RPATH_ORIGIN}/../lib${LIB_SUFFIX}
${CMAKE_EXTERNAL_PROJECT_ARGS}
INSTALL_COMMAND $(MAKE) install DESTDIR=${staging_prefix}
INSTALL_DIR ${staging_prefix}/${install_prefix}
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2 changes: 1 addition & 1 deletion cmake-modules/BuildEZMINC.cmake
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Expand Up @@ -104,7 +104,7 @@ macro(build_EZMINC install_prefix staging_prefix libminc_dir bicpl_dir itk_dir)
-DCMAKE_SKIP_RPATH:BOOL=OFF
-DCMAKE_SKIP_INSTALL_RPATH:BOOL=OFF
-DMACOSX_RPATH:BOOL=ON
-DCMAKE_INSTALL_RPATH:PATH=${install_prefix}/lib${LIB_SUFFIX}
-DCMAKE_INSTALL_RPATH:PATH=${MT_RPATH_ORIGIN}/../lib${LIB_SUFFIX}
${CMAKE_EXTERNAL_PROJECT_ARGS}
INSTALL_COMMAND $(MAKE) install DESTDIR=${staging_prefix}
INSTALL_DIR ${staging_prefix}/${install_prefix}
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2 changes: 1 addition & 1 deletion cmake-modules/BuildElastix.cmake
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Expand Up @@ -146,7 +146,7 @@ macro(build_Elastix install_prefix staging_prefix)
-DCMAKE_SKIP_RPATH:BOOL=OFF
-DCMAKE_SKIP_INSTALL_RPATH:BOOL=OFF
-DMACOSX_RPATH:BOOL=ON
-DCMAKE_INSTALL_RPATH:PATH=${install_prefix}/lib${LIB_SUFFIX}
-DCMAKE_INSTALL_RPATH:PATH=${MT_RPATH_ORIGIN}/../lib${LIB_SUFFIX}
${CMAKE_EXTERNAL_PROJECT_ARGS}
INSTALL_COMMAND $(MAKE) install DESTDIR=${staging_prefix}
INSTALL_DIR ${staging_prefix}/${install_prefix}
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2 changes: 1 addition & 1 deletion cmake-modules/BuildFFTW3D.cmake
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Expand Up @@ -90,7 +90,7 @@ macro(build_fftw3d install_prefix staging_prefix)
-DCMAKE_SKIP_RPATH:BOOL=OFF
-DCMAKE_SKIP_INSTALL_RPATH:BOOL=OFF
-DMACOSX_RPATH:BOOL=ON
-DCMAKE_INSTALL_RPATH:PATH=${install_prefix}/lib${LIB_SUFFIX}
-DCMAKE_INSTALL_RPATH:PATH=${MT_RPATH_ORIGIN}/../lib${LIB_SUFFIX}
-DINSTALL_LIB_DIR:PATH=${install_prefix}/lib${LIB_SUFFIX}
-DINSTALL_INC_DIR:PATH=${install_prefix}/include
${CMAKE_EXTERNAL_PROJECT_ARGS}
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2 changes: 1 addition & 1 deletion cmake-modules/BuildFFTW3F.cmake
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Expand Up @@ -88,7 +88,7 @@ macro(build_fftw3f install_prefix staging_prefix)
-DCMAKE_SKIP_RPATH:BOOL=OFF
-DCMAKE_SKIP_INSTALL_RPATH:BOOL=OFF
-DMACOSX_RPATH:BOOL=ON
-DCMAKE_INSTALL_RPATH:PATH=${install_prefix}/lib${LIB_SUFFIX}
-DCMAKE_INSTALL_RPATH:PATH=${MT_RPATH_ORIGIN}/../lib${LIB_SUFFIX}
-DINSTALL_LIB_DIR:PATH=${install_prefix}/lib${LIB_SUFFIX}
-DINSTALL_INC_DIR:PATH=${install_prefix}/include
${CMAKE_EXTERNAL_PROJECT_ARGS}
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2 changes: 1 addition & 1 deletion cmake-modules/BuildFREEGLUT.cmake
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Expand Up @@ -77,7 +77,7 @@ ExternalProject_Add(FREEGLUT
-DFREEGLUT_WAYLAND:BOOL=OFF
-DCMAKE_SKIP_INSTALL_RPATH:BOOL=OFF
-DMACOSX_RPATH:BOOL=ON
-DCMAKE_INSTALL_RPATH:PATH=${install_prefix}/lib${LIB_SUFFIX}
-DCMAKE_INSTALL_RPATH:PATH=${MT_RPATH_ORIGIN}/../lib${LIB_SUFFIX}
-DCMAKE_INSTALL_PREFIX:PATH=${install_prefix}
${CMAKE_EXTERNAL_PROJECT_ARGS}
"-DCMAKE_CXX_FLAGS:STRING=-fPIC ${CMAKE_CXX_FLAGS}"
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2 changes: 1 addition & 1 deletion cmake-modules/BuildGIFTI.cmake
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Expand Up @@ -27,7 +27,7 @@ ExternalProject_Add(GIFTI
-DCMAKE_SKIP_RPATH:BOOL=OFF
-DCMAKE_SKIP_INSTALL_RPATH:BOOL=OFF
-DMACOSX_RPATH:BOOL=ON
-DCMAKE_INSTALL_RPATH:PATH=${install_prefix}/lib${LIB_SUFFIX}
-DCMAKE_INSTALL_RPATH:PATH=${MT_RPATH_ORIGIN}/../lib${LIB_SUFFIX}
-DCMAKE_INSTALL_PREFIX:PATH=${install_prefix}
"-DCMAKE_CXX_FLAGS_RELEASE:STRING=${GIFTI_CMAKE_CXX_FLAGS_RELEASE}"
"-DCMAKE_C_FLAGS_RELEASE:STRING=${GIFTI_CMAKE_C_FLAGS_RELEASE}"
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2 changes: 1 addition & 1 deletion cmake-modules/BuildHDF5.cmake
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Expand Up @@ -77,7 +77,7 @@ ExternalProject_Add(HDF5
-DCMAKE_SKIP_RPATH:BOOL=OFF
-DCMAKE_SKIP_INSTALL_RPATH:BOOL=OFF
-DMACOSX_RPATH:BOOL=ON
-DCMAKE_INSTALL_RPATH:PATH=${install_prefix}/lib${LIB_SUFFIX}
-DCMAKE_INSTALL_RPATH:PATH=${MT_RPATH_ORIGIN}/../lib${LIB_SUFFIX}
-DCMAKE_INSTALL_PREFIX:PATH=${install_prefix}
# Must be RELATIVE to the install prefix. Passing the absolute ${install_prefix}
# made HDF5 emit a broken package config: `include(${PACKAGE_PREFIX_DIR}//app/install/-targets.cmake)`,
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2 changes: 1 addition & 1 deletion cmake-modules/BuildITKv4.cmake
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Expand Up @@ -190,7 +190,7 @@ macro(build_itkv4 install_prefix staging_prefix minc_dir)
-DCMAKE_SKIP_RPATH:BOOL=OFF
-DCMAKE_SKIP_INSTALL_RPATH:BOOL=OFF
-DMACOSX_RPATH:BOOL=ON
-DCMAKE_INSTALL_RPATH:PATH=${install_prefix}/lib${LIB_SUFFIX}
-DCMAKE_INSTALL_RPATH:PATH=${MT_RPATH_ORIGIN}/../lib${LIB_SUFFIX}
${CMAKE_EXTERNAL_PROJECT_ARGS}
${CMAKE_ITK_HDF5_SETTINGS}
-DBUILD_EXAMPLES:BOOL=OFF
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2 changes: 1 addition & 1 deletion cmake-modules/BuildJPEG.cmake
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Expand Up @@ -70,7 +70,7 @@ macro(build_jpeg install_prefix staging_prefix)
-DMACOSX_RPATH:BOOL=ON
-DWITH_SIMD:BOOL=OFF
-DWITH_TURBOJPEG:BOOL=OFF
-DCMAKE_INSTALL_RPATH:PATH=${install_prefix}/lib${LIB_SUFFIX}
-DCMAKE_INSTALL_RPATH:PATH=${MT_RPATH_ORIGIN}/../lib${LIB_SUFFIX}
-DCMAKE_INSTALL_PREFIX:PATH=${install_prefix}
${CMAKE_EXTERNAL_PROJECT_ARGS}
"-DCMAKE_CXX_FLAGS:STRING=-fPIC ${CMAKE_CXX_FLAGS}"
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2 changes: 1 addition & 1 deletion cmake-modules/BuildLibarchive.cmake
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Expand Up @@ -66,7 +66,7 @@ macro(build_libarchive install_prefix staging_prefix)
-DCMAKE_SKIP_RPATH:BOOL=OFF
-DCMAKE_SKIP_INSTALL_RPATH:BOOL=OFF
-DMACOSX_RPATH:BOOL=ON
-DCMAKE_INSTALL_RPATH:PATH=${install_prefix}/lib${LIB_SUFFIX}
-DCMAKE_INSTALL_RPATH:PATH=${MT_RPATH_ORIGIN}/../lib${LIB_SUFFIX}
-DINSTALL_LIB_DIR:PATH=${install_prefix}/lib${LIB_SUFFIX}
-DINSTALL_INC_DIR:PATH=${install_prefix}/include
-DENABLE_EXPAT:BOOL=OFF
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2 changes: 1 addition & 1 deletion cmake-modules/BuildNETCDF.cmake
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Expand Up @@ -76,7 +76,7 @@ macro(build_netcdf install_prefix staging_prefix)
-DENABLE_LARGE_FILE_SUPPORT:BOOL=ON
-DCMAKE_SKIP_INSTALL_RPATH:BOOL=OFF
-DMACOSX_RPATH:BOOL=ON
-DCMAKE_INSTALL_RPATH:PATH=${install_prefix}/lib${LIB_SUFFIX}
-DCMAKE_INSTALL_RPATH:PATH=${MT_RPATH_ORIGIN}/../lib${LIB_SUFFIX}
-DENABLE_NETCDF4:BOOL=OFF
-DENABLE_NETCDF_4:BOOL=OFF
-DCMAKE_INSTALL_PREFIX:PATH=${install_prefix}
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2 changes: 1 addition & 1 deletion cmake-modules/BuildNIFTI.cmake
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Expand Up @@ -86,7 +86,7 @@ macro(build_nifti install_prefix staging_prefix)
-DCMAKE_SKIP_RPATH:BOOL=OFF
-DCMAKE_SKIP_INSTALL_RPATH:BOOL=OFF
-DMACOSX_RPATH:BOOL=ON
-DCMAKE_INSTALL_RPATH:PATH=${install_prefix}/${CMAKE_INSTALL_LIBDIR}
-DCMAKE_INSTALL_RPATH:PATH=${MT_RPATH_ORIGIN}/../${CMAKE_INSTALL_LIBDIR}
-DCMAKE_INSTALL_PREFIX:PATH=${install_prefix}
-DCMAKE_INSTALL_LIBDIR:PATH=${CMAKE_INSTALL_LIBDIR}
# NIFTI's CMakeLists uses its own NIFTI_INSTALL_LIBRARY_DIR variable
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2 changes: 1 addition & 1 deletion cmake-modules/BuildOpenBLAS.cmake
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Expand Up @@ -86,7 +86,7 @@ macro(build_open_blas install_prefix staging_prefix build_parallel)
-DNO_WARMAP:BOOL=ON
-DUSE_THREAD:BOOL=OFF
-DUSE_OPENMP:BOOL=OFF
-DCMAKE_INSTALL_RPATH:PATH=${install_prefix}/lib${LIB_SUFFIX}
-DCMAKE_INSTALL_RPATH:PATH=${MT_RPATH_ORIGIN}/../lib${LIB_SUFFIX}
-DCMAKE_INSTALL_PREFIX:PATH=${install_prefix}
${CMAKE_EXTERNAL_PROJECT_ARGS}
"-DCMAKE_CXX_FLAGS:STRING=-fPIC ${CMAKE_CXX_FLAGS}"
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2 changes: 1 addition & 1 deletion cmake-modules/BuildOpenJPEG.cmake
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Expand Up @@ -66,7 +66,7 @@ macro(build_openjpeg install_prefix staging_prefix)
-DCMAKE_SKIP_INSTALL_RPATH:BOOL=OFF
-DMACOSX_RPATH:BOOL=ON
-DBUILD_CODEC:BOOL=OFF
-DCMAKE_INSTALL_RPATH:PATH=${install_prefix}/${CMAKE_INSTALL_LIBDIR}
-DCMAKE_INSTALL_RPATH:PATH=${MT_RPATH_ORIGIN}/../${CMAKE_INSTALL_LIBDIR}
-DCMAKE_INSTALL_PREFIX:PATH=${install_prefix}
${CMAKE_EXTERNAL_PROJECT_ARGS}
"-DCMAKE_CXX_FLAGS:STRING=-fPIC ${CMAKE_CXX_FLAGS}"
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2 changes: 1 addition & 1 deletion cmake-modules/BuildPatchMorphology.cmake
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Expand Up @@ -46,7 +46,7 @@ macro(build_PatchMorphology install_prefix staging_prefix itk_dir)
-DCMAKE_SKIP_RPATH:BOOL=OFF
-DCMAKE_SKIP_INSTALL_RPATH:BOOL=OFF
-DMACOSX_RPATH:BOOL=ON
-DCMAKE_INSTALL_RPATH:PATH=${install_prefix}/lib${LIB_SUFFIX}
-DCMAKE_INSTALL_RPATH:PATH=${MT_RPATH_ORIGIN}/../lib${LIB_SUFFIX}
-DNETCDF_INCLUDE_DIR:PATH=${NETCDF_INCLUDE_DIR}
-DHDF5_C_INCLUDE_DIR:PATH=${HDF5_INCLUDE_DIR}
-DHDF5_CPP_INCLUDE_DIR:PATH=${HDF5_INCLUDE_DIR}
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2 changes: 1 addition & 1 deletion cmake-modules/BuildZLIB.cmake
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Expand Up @@ -78,7 +78,7 @@ ExternalProject_Add(ZLIB
-DCMAKE_SKIP_RPATH:BOOL=OFF
-DCMAKE_SKIP_INSTALL_RPATH:BOOL=OFF
-DMACOSX_RPATH:BOOL=ON
-DCMAKE_INSTALL_RPATH:PATH=${install_prefix}/lib${LIB_SUFFIX}
-DCMAKE_INSTALL_RPATH:PATH=${MT_RPATH_ORIGIN}/../lib${LIB_SUFFIX}

@gdevenyi gdevenyi Aug 6, 2026

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Agreed, changed in the follow-up commit — all 21 sites now use -DCMAKE_INSTALL_RPATH:STRING=.

Worth noting the :PATH spelling predates this branch (I only changed the value, not the type) and it does work: the full build linked below produced correct run paths with it, and the generated ZLIB-cfgcmd.txt carried $ORIGIN/../lib through untouched. But STRING is what a list of run paths actually is, and it removes any question about a PATH-typed entry normalising $ORIGIN / @loader_path.

-DINSTALL_LIB_DIR:PATH=${install_prefix}/lib${LIB_SUFFIX}
-DINSTALL_INC_DIR:PATH=${install_prefix}/include
${CMAKE_EXTERNAL_PROJECT_ARGS}
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11 changes: 10 additions & 1 deletion minc-toolkit-config.apple.sh.cmake
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@@ -1,5 +1,14 @@
# minc-toolkit configuration parameters for @MINC_TOOLKIT_VERSION_FULL@
export MINC_TOOLKIT=@CMAKE_INSTALL_PREFIX@
# Locate the toolkit from this script's own path so a relocated install needs
# no editing. This file installs at the top of the prefix, so its directory is
# the prefix. BASH_SOURCE is bash-only; every other shell falls back to the
# path baked in at configure time, which is the previous behaviour.
if [ -n "${BASH_SOURCE:-}" ] && [ -f "${BASH_SOURCE}" ]; then
MINC_TOOLKIT=$(cd -- "$(dirname -- "${BASH_SOURCE}")" && pwd -P)
else
MINC_TOOLKIT=@CMAKE_INSTALL_PREFIX@
fi
export MINC_TOOLKIT
export MINC_TOOLKIT_VERSION="@MINC_TOOLKIT_VERSION_FULL@"
export PATH=${MINC_TOOLKIT}/bin:${MINC_TOOLKIT}/pipeline:${PATH}
export PERL5LIB=${MINC_TOOLKIT}/perl:${MINC_TOOLKIT}/pipeline${PERL5LIB:+:$PERL5LIB}
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11 changes: 10 additions & 1 deletion minc-toolkit-config.unix.sh.cmake
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@@ -1,5 +1,14 @@
# minc-toolkit configuration parameters for @MINC_TOOLKIT_VERSION_FULL@
export MINC_TOOLKIT=@CMAKE_INSTALL_PREFIX@
# Locate the toolkit from this script's own path so a relocated install needs
# no editing. This file installs at the top of the prefix, so its directory is
# the prefix. BASH_SOURCE is bash-only; every other shell falls back to the
# path baked in at configure time, which is the previous behaviour.
if [ -n "${BASH_SOURCE:-}" ] && [ -f "${BASH_SOURCE}" ]; then
MINC_TOOLKIT=$(cd -- "$(dirname -- "${BASH_SOURCE}")" && pwd -P)
Comment on lines +6 to +7

@gdevenyi gdevenyi Aug 6, 2026

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Checked this against bash 5.3.15, and the failure mode does not occur — cd+pwd -P already normalises both cases.

The concern needs BASH_SOURCE to be a bare basename while the script is not in the current directory. Bash only produces a bare name when it found the file in the cwd, in which case the cwd is the right answer:

how it is sourced BASH_SOURCE holds resolved MINC_TOOLKIT
explicit relative path ../onpath/x.sh .../onpath ✅
bare name, found via PATH .../elsewhere/../onpath/x.sh (full) .../onpath ✅
bare name, found in cwd x.sh (bare) cwd, which is where the script lives ✅

So the PATH case keeps the full path rather than the basename, and the bare-name case only happens when dirname . is already correct. Both come out right after cd -- "$(dirname -- ...)" && pwd -P.

Happy to add a command -v / realpath normalisation as belt-and-braces if you would rather not depend on that behaviour, but on the evidence it is not currently reachable.

else
MINC_TOOLKIT=@CMAKE_INSTALL_PREFIX@
fi
export MINC_TOOLKIT
export MINC_TOOLKIT_VERSION="@MINC_TOOLKIT_VERSION_FULL@"
export PATH=${MINC_TOOLKIT}/bin:${MINC_TOOLKIT}/pipeline:${PATH}
export PERL5LIB=${MINC_TOOLKIT}/perl:${MINC_TOOLKIT}/pipeline${PERL5LIB:+:$PERL5LIB}
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