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/.

Four minor ITK-side overlays that previously lived only in ITK proper as post-import patches (commits f6eb95b9f8 and 85577ae354 on the InsightSoftwareConsortium/ITK side): 1. cmake_minimum_required(VERSION 3.16.3) — bump from 3.10.2 to match ITK's minimum CMake requirement. 2. if(FALSE) ... endif() wrapper -> #[[ ... #]] block-comment wrapper around the upstream-Eigen CMakeLists.txt body. The block-comment form is cleaner; both achieve 'skip the upstream Eigen config' when this file is included into ITK's third-party glue. 3. Remove duplicate ITK_USE_EIGEN_MPL2_ONLY option(...) declaration (the option is also declared once earlier in the file). 4. Trim a stray BUILD_INTERFACE comment line. Carrying these in the fork makes the next ITK subtree-update truly no-op rather than re-introducing the pre-fixup forms. Issue: InsightSoftwareConsortium/ITK#6239 PR: InsightSoftwareConsortium/ITK#6247

hjmjohnson · 2026-05-10T12:25:54Z

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?

This was done incorrectly with the previous eigen update. I am preparing a new PR to properly include the set of ITK vendored patches in the ITK/eigen branch. Tests are running now. A new PR that supercedes this PR is expected later this morning. I'm currently running a matrix of builds using both vendored and system installed eigen for SimpleITK, BRAINSTools.

hjmjohnson · 2026-05-10T14:33:59Z

Superceeded by #6249.

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

This comment was marked as resolved.

Sign in to view

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

Open

hjmjohnson mentioned this pull request May 10, 2026

ENH: Pin vendored Eigen3 fork to tagged release 5.0.1 (closes #6239, supersedes #6247) #6249

Draft

hjmjohnson closed this May 10, 2026

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Uh oh!

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
hjmjohnson wants to merge 1 commit into
InsightSoftwareConsortium:mainfrom
hjmjohnson:eigen-robustness-2026-05-09

hjmjohnson commented May 9, 2026 •

edited

Loading

Uh oh!

hjmjohnson commented May 9, 2026

Uh oh!

hjmjohnson commented May 9, 2026

Uh oh!

This comment was marked as resolved.

blowekamp commented May 9, 2026

Uh oh!

hjmjohnson commented May 9, 2026

Uh oh!

hjmjohnson commented May 10, 2026

Uh oh!

hjmjohnson commented May 10, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

Uh oh!

Conversation

hjmjohnson commented May 9, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

hjmjohnson commented May 9, 2026

Uh oh!

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

Uh oh!

This comment was marked as resolved.

blowekamp commented May 9, 2026

Uh oh!

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 ⚠️

Bottom line for this PR

Uh oh!

hjmjohnson commented May 10, 2026

Uh oh!

hjmjohnson commented May 10, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

hjmjohnson commented May 9, 2026 •

edited

Loading

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