BUG: Restore eigen_internal export to ITK's main targets set (#6239) by hjmjohnson · Pull Request #6247 · InsightSoftwareConsortium/ITK

hjmjohnson · 2026-05-09T16:20:29Z

Restores eigen_internal to ITK's main ${ITK3P_INSTALL_EXPORT_NAME} export set so find_package(ITK) resolves it for downstream consumers (closes #6239 — SimpleITK CI red since 2026-05-01).

Scope note: this addresses only the most immediate regression. The broader Eigen3 design questions (header-path policy #5952 vs #6225, symbol mangling, VNL→Eigen migration, the _SYSTEM_INCLUDE_DIRS asymmetry #6224) remain in the master tracking issue #6230 and are deliberately not touched here.

Root cause (issue #6239)

Commit 64ddc666 (Eigen 5.0.1 vendored update, 2026-05-01) silently moved eigen_internal out of ITK's main ${ITK3P_INSTALL_EXPORT_NAME} export set into a standalone ITKInternalEigen3Targets. Because ITKConfig.cmake only loads ITKTargets.cmake, downstream find_package(ITK) could no longer resolve eigen_internal and any consumer using FetchContent with FIND_PACKAGE_ARGS (SimpleITK's pattern) hit a target-collision cascade as CMake fell back to add_subdirectory.

The fix re-adds the install rule that registers eigen_internal in the main export set while keeping the standalone ITKInternalEigen3Targets install for find_package(ITKInternalEigen3) consumers. Both export sets now reference the same target — same pattern as every other ITK-vendored third party (NrrdIO, NIFTI, Expat, OpenJPEG, DICOMParser).

Local verification — SimpleITK before/after differential

Reproduced against latest SimpleITK upstream (853c78a9, 2026-05-09) using two parallel ITK installs at the same configuration (ITK_BUILD_DEFAULT_MODULES=ON + Module_ITKIOTransformMINC=ON + Module_ITKReview=ON, matching SuperBuild/External_ITK.cmake):

	source	install prefix
baseline	upstream/main `7820bbcfb8` (no fix)	`~/src/ITK-eigen-baseline-install`
fix-applied	this PR's tip	`~/src/ITK-build-test-tree-eigen/install-fix`

Pre-flight: eigen_internal in installed ITKTargets.cmake

$ grep -c 'add_library(ITK::eigen_internal' install-fix/lib/cmake/ITK-6.0/ITKTargets.cmake
1
$ grep -c 'add_library(ITK::eigen_internal' ITK-eigen-baseline-install/lib/cmake/ITK-6.0/ITKTargets.cmake
0
$ find ITK-eigen-baseline-install -name 'ITKInternalEigen3Targets*.cmake'
ITK-eigen-baseline-install/share/ITKInternalEigen3Targets.cmake     # orphan; not loaded by ITKConfig

SimpleITK configure against each install:

cmake -G Ninja -S ~/src/SimpleITK -B sitk-bld \
  -DBUILD_TESTING=OFF -DBUILD_EXAMPLES=OFF -DWRAP_DEFAULT=OFF \
  -DITK_DIR=<install>/lib/cmake/ITK-6.0

	`find_package(ITK)`	FetchContent fallback (`_deps/itk-src/`)	Error cascade
baseline	FAILED	YES — materialized	`add_library cannot create target "itksys" because an imported target with the same name already exists` (exact #6239 cascade)
this PR	`-- ITK found via find_package()`	NO	unrelated SimpleITK codegen issues that reproduce on either ITK

The fix resolves the export-set regression cleanly. Verification comment with full reproduction steps posted to this PR.

What remains for #6230

This PR does not address (deferred per #6230 design discussion 2026-05-07/09):

Q1 header-path policy — keep ITK_EIGEN(X) for ITK internals; PRs ENH: Use standard header approach for eigen e.g. itk_Eigenvalues #5952 (per-module wrappers) and ENH: Migrate Eigen3 includes to canonical <Eigen/x> via Eigen3::Eigen (supersedes #5952) #6225 (canonical <Eigen/X> migration) both pending design resolution.
Q2 symbol mangling — current state (no mangling) preserved; @phcerdan and @blowekamp comments 2026-05-07 lean against, @thewtex pro.
Q3 Eigen3::Eigen consumer exposure — emerging consensus is "no, use ITK::ITKEigen3Module" but no code change here.
Q4 SYSTEM include treatment — ITKModuleMacros: _SYSTEM_INCLUDE_DIRS does not support in-source paths (blocks SYSTEM treatment of vendored Eigen) #6224 unchanged; the architecturally-correct fix per blowekamp's 2026-05-07 comment is target-property propagation through eigen_internal, not _SYSTEM_INCLUDE_DIRS glue. Larger refactor.
System-Eigen CI matrix — still manual per ENH: Update vendored Eigen3 to 5.0.1+master; verify USE_SYSTEM 3.3/3.4/5.x #6176.
CTest find_package smoke test — would be the highest-leverage automated guard but requires new test infrastructure (no third-party module currently has its own test/); deferred to avoid precedent-setting in a regression-fix PR.
UpdateFromUpstream.sh overlay-patch checklist — was prototyped in an earlier revision of this PR but removed per maintainer preference; documenting the no-mangling decision and the dual-export requirement belongs elsewhere.

hjmjohnson · 2026-05-09T16:26:38Z

@greptile review

hjmjohnson · 2026-05-09T16:29:35Z

SimpleITK build verification — before/after differential

Reproduced the SimpleITK failure against latest SimpleITK upstream (853c78a9, 2026-05-09) using two parallel ITK installs:

	source	install prefix
baseline	upstream/main `7820bbcfb8` (no fix)	`~/src/ITK-eigen-baseline-install`
fix-applied	this PR's tip `5dfd84ac7b`	`~/src/ITK-build-test-tree-eigen/install-fix`

Both ITK builds: ITK_BUILD_DEFAULT_MODULES=ON + Module_ITKIOTransformMINC=ON + Module_ITKReview=ON (the SimpleITK Superbuild's required set per SuperBuild/External_ITK.cmake).

Pre-flight: `eigen_internal` in installed `ITKTargets.cmake`

$ grep -c 'add_library(ITK::eigen_internal' \
    install-fix/lib/cmake/ITK-6.0/ITKTargets.cmake
1
$ grep -c 'add_library(ITK::eigen_internal' \
    ITK-eigen-baseline-install/lib/cmake/ITK-6.0/ITKTargets.cmake
0
$ find ITK-eigen-baseline-install -name 'ITKInternalEigen3Targets*.cmake'
ITK-eigen-baseline-install/share/ITKInternalEigen3Targets.cmake

Baseline confirms eigen_internal is absent from the main ITKTargets.cmake and lives in an orphan ITKInternalEigen3Targets.cmake that ITKConfig.cmake never loads.

SimpleITK configure against each install

cmake -G Ninja -S ~/src/SimpleITK -B sitk-bld \
  -DBUILD_TESTING=OFF -DBUILD_EXAMPLES=OFF -DWRAP_DEFAULT=OFF \
  -DITK_DIR=<install>/lib/cmake/ITK-6.0

Baseline (no fix): find_package(ITK) partially fails → SimpleITK's FetchContent ... FIND_PACKAGE_ARGS fallback materializes _deps/itk-src/ and tries add_subdirectory, producing the exact cascade from #6239:

CMake Error at .../Modules/ThirdParty/KWSys/src/KWSys/CMakeLists.txt:749 (add_library):
  add_library cannot create target "itksys" because an imported target with
  the same name already exists.
CMake Error at .../Modules/ThirdParty/KWSys/src/KWSys/CMakeLists.txt:764 (target_link_libraries):
  Cannot specify link libraries for target "itksys" which is not built by
  this project.

_deps/itk-src/ directory present → FetchContent fallback was triggered.

PR #6247: find_package(ITK) resolves cleanly:

-- ITK found via find_package()

_deps/itk-src/ NOT present → no FetchContent fallback. Configure proceeds past the eigen-related code path. (The configure ultimately stops on unrelated SimpleITK-specific issues — Python SimpleITKBasicFiltersGeneratedHeaders.i codegen — which are independent of the eigen export-set fix and reproduce on either ITK regardless.)

Differential summary

	`find_package(ITK)`	FetchContent fallback	Error cascade
baseline (no fix)	FAILED	yes — `_deps/itk-src/` present	`itksys` imported-target collision (exact #6239)
PR #6247	`-- ITK found via find_package()`	no	unrelated SimpleITK codegen issues

The fix resolves the export-set regression cleanly. Whatever else SimpleITK CI surfaces is independent of this PR.

…SoftwareConsortium#6239) Commit 64ddc66 (Eigen 5.0.1 vendored update, 2026-05-01) silently moved eigen_internal out of ITK's main `${ITK3P_INSTALL_EXPORT_NAME}` export set into a standalone `ITKInternalEigen3Targets`. Because `ITKConfig.cmake` only loads `ITKTargets.cmake`, downstream `find_package(ITK)` could no longer resolve `eigen_internal` and any consumer using FetchContent with `FIND_PACKAGE_ARGS` (SimpleITK's pattern) hit a target-collision cascade as CMake fell back to `add_subdirectory`. Re-add the install rule that registers `eigen_internal` in `${ITK3P_INSTALL_EXPORT_NAME}` while keeping the existing standalone `ITKInternalEigen3Targets` install for `find_package(ITKInternalEigen3)` consumers. Both export sets now reference the same target. Issue: InsightSoftwareConsortium#6239

blowekamp · 2026-05-09T16:39:16Z

How was the ITK eigen for updated? ITK commit 7aa8ae2 indicates set of changes in the eigen fork:

# By Eigen Upstream
* upstream-Eigen3:
  Eigen3 2026-03-12 (b581628e)

Were these changes from the prior eigen commit included in the update to the fork?

hjmjohnson · 2026-05-09T23:12:26Z

Downstream-consumer end-to-end verification (BRAINSTools + SimpleITK)

Built two real-world ITK consumers against the install-fix ITK install (this PR's tip, ITK 6.0 with ITK_BUILD_DEFAULT_MODULES=ON + Module_ITKIOTransformMINC=ON + Module_ITKReview=ON). All against latest upstream tips of each consumer.

SimpleITK — full build ✅

Source: SimpleITK/main at 853c78a9 (2026-05-09)
cmake -DITK_DIR=…/install-fix/lib/cmake/ITK-6.0 -DBUILD_TESTING=OFF -DBUILD_EXAMPLES=OFF -DWRAP_DEFAULT=OFF
cmake --build -j6 → 984/984 targets, 0 errors, 4 warnings (warnings are SimpleITK-internal, not Eigen-related)
find_package(ITK) resolution: -- ITK found via find_package() clean
No _deps/itk-src/ materialized (no FetchContent fallback was triggered)
Zero Eigen mentions in the build log
All libSimpleITK*.a artifacts produced

BRAINSTools — configure clean, build blocked by unrelated module-config issue ⚠️

Source: BRAINSTools/main at 67acae44 (2026-04-12)
cmake -DUSE_SYSTEM_ITK=ON -DITK_DIR=…/install-fix/lib/cmake/ITK-6.0 -DBRAINSTools_REQUIRES_VTK=OFF -DBRAINSTools_BUILD_DICOM_SUPPORT=OFF
Outer Superbuild configure: ✅ clean
Inner ANTs configure: ✅ find_package(ITK 5.4 ...) succeeded (ITK 6.0 satisfies the ≥ 5.4 floor; no version-pin enforcement); ITK_VERSION_MAJOR=6 recorded in ANTs CMakeCache
Inner ANTs build: ❌ fatal error: 'itkLabelImageGenericInterpolateImageFunction.h' file not found in antsRegistrationTemplateHeader.h:21 — unrelated to Eigen; needs Module_GenericLabelInterpolator=ON enabled in the ITK install. This is a pre-existing ANTs+ITK6 module-set integration issue independent of PR BUG: Restore eigen_internal export to ITK's main targets set (#6239) #6247.
Eigen path through ANTs configure resolved cleanly; the eigen_internal import target is correctly available.

Bottom line for this PR

The Eigen export-set regression #6239 is fixed for both downstream consumers tested. Where builds proceed past configure, no Eigen-related compile or link errors appear. The one BRAINSTools subbuild that failed died on a missing remote-module header — a separate ITK-build-time configuration concern unrelated to the eigen_internal install rule.

Reproducer state preserved: ~/src/ITK-build-test-tree-eigen/install-fix/, /tmp/sitk-fix-fullbld/, /tmp/brains-bld/.

github-actions Bot added type:Bug Inconsistencies or issues which will cause an incorrect result under some or all circumstances type:Infrastructure Infrastructure/ecosystem related changes, such as CMake or buildbots area:ThirdParty Issues affecting the ThirdParty module labels May 9, 2026

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hjmjohnson force-pushed the eigen-robustness-2026-05-09 branch from 5dfd84a to c1715d9 Compare May 9, 2026 16:29

hjmjohnson marked this pull request as ready for review May 9, 2026 16:32

hjmjohnson mentioned this pull request May 9, 2026

ENH: Master tracking — Eigen3 third-party design for ITK 6.x #6230

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BUG: Restore eigen_internal export to ITK's main targets set (#6239)#6247

BUG: Restore eigen_internal export to ITK's main targets set (#6239)#6247
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hjmjohnson commented May 9, 2026

SimpleITK build verification — before/after differential

Pre-flight: eigen_internal in installed ITKTargets.cmake

SimpleITK configure against each install

Differential summary

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blowekamp commented May 9, 2026

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hjmjohnson commented May 9, 2026

Downstream-consumer end-to-end verification (BRAINSTools + SimpleITK)

SimpleITK — full build ✅

BRAINSTools — configure clean, build blocked by unrelated module-config issue ⚠️

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hjmjohnson commented May 9, 2026 •

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Pre-flight: `eigen_internal` in installed `ITKTargets.cmake`