[ENH][packages/slicer] Introduce external packages

[asiangoldfish]

To minimise Slicer's footprint, packages should be installed separately. This is currently not implemented, and as a temporary solution packages are instead symlinked to Slicer's source tree. This patch uses Plots as an example.

[RafaelPalomar]

@asiangoldfish, modularity is one of the key selling points of SystoleOS, and also one of the most difficult to implement. This PR delivers on the most simple approach we discussed last week (modularity can be achieved by developers tweaking the package. e.g., commenting out, adding modules to the slicer pacakge).

@asiangoldfish, please add to this PR an external module. The one that will be immediately useful to us is the OpenIGTLinkIF. This could also help for testing of your external modules approach.

[RafaelPalomar]

Since this won't lead to a binary installation, I would call this slicer-plots-src

[asiangoldfish]

@RafaelPalomar After symlinking OpenIGTLinkIF to Slicer's source tree, I noticed that OpenIGTLinkIO is required as build input. This project uses vtkMutexLock from VTK, which is deprecated from version 9.2. Seems like it also was removed from the project.

Error log:

/tmp/guix-build-openigtlinkio-a262c1f.drv-0/OpenIGTLinkIO-32feaaa5fcff433dec4f071cf7aaa9106e5e5124/Logic/igtlioCircularSectionBuffer.cxx:14:10: fatal error: vtkMutexLock.h: No such file or directory
   14 | #include <vtkMutexLock.h>
      |          ^~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [Logic/CMakeFiles/igtlioLogic.dir/build.make:135: Logic/CMakeFiles/igtlioLogic.dir/igtlioCircularSectionBuffer.cxx.o] Error 1
make[2]: *** Waiting for unfinished jobs....
/tmp/guix-build-openigtlinkio-a262c1f.drv-0/OpenIGTLinkIO-32feaaa5fcff433dec4f071cf7aaa9106e5e5124/Logic/igtlioCircularBuffer.cxx:14:10: fatal error: vtkMutexLock.h: No such file or directory
   14 | #include <vtkMutexLock.h>
      |          ^~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [Logic/CMakeFiles/igtlioLogic.dir/build.make:121: Logic/CMakeFiles/igtlioLogic.dir/igtlioCircularBuffer.cxx.o] Error 1
/tmp/guix-build-openigtlinkio-a262c1f.drv-0/OpenIGTLinkIO-32feaaa5fcff433dec4f071cf7aaa9106e5e5124/Logic/igtlioConnector.cxx:36:10: fatal error: vtkMutexLock.h: No such file or directory
   36 | #include <vtkMutexLock.h>
      |          ^~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [Logic/CMakeFiles/igtlioLogic.dir/build.make:149: Logic/CMakeFiles/igtlioLogic.dir/igtlioConnector.cxx.o] Error 1
make[2]: Leaving directory '/tmp/guix-build-openigtlinkio-a262c1f.drv-0/build'
make[1]: *** [CMakeFiles/Makefile2:226: Logic/CMakeFiles/igtlioLogic.dir/all] Error 2
make[1]: Leaving directory '/tmp/guix-build-openigtlinkio-a262c1f.drv-0/build'
make: *** [Makefile:139: all] Error 2
error: in phase 'build': uncaught exception:

A snippet from igtlioCircularSectionBuffer.cxx:

// VTK includes
#include "igtlioCircularSectionBuffer.h"

#include <vtkObjectFactory.h>
#include <vtkMutexLock.h>
#include <vtksys/SystemTools.hxx>

[oeramo]

@asiangoldfish Similar errors regarding vtkMutexLock were a recurring thing in the IGSIO package. You may want to look at how I patched it in https://github.com/SystoleOS/guix-systole/blob/SCRUM-112-Build-PlusToolkit/guix-systole/packages/patches/0024-BUG-packages-igsio-replace-mutex-lock.patch.

[asiangoldfish]

@RafaelPalomar Hi. In commit facba45 I get the following error:

/tmp/guix-build-slicer-5.8-5.8.1.drv-0/Slicer-11eaf62e5a70b828021ff8beebbdd14d10d4f51c/Modules/External/OpenIGTLinkIF/OpenIGTLinkIF/MRML/vtkMRMLIGTLConnectorNode.cxx:40:10: fatal error: vtkMRMLMarkupsFiducialNode.h: No such file or directory
   40 | #include "vtkMRMLMarkupsFiducialNode.h"
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [Modules/External/OpenIGTLinkIF/OpenIGTLinkIF/MRML/CMakeFiles/vtkSlicerOpenIGTLinkIFModuleMRML.dir/build.make:79: Modules/External/OpenIGTLinkIF/OpenIGTLinkIF/MRML/CMakeFiles/vtkSlicerOpenIGTLinkIFModuleMRML.dir/vtkMRMLIGTLConnectorNode.cxx.o] Error 1

I would think that linking against Slicer's vtkSlicerMarkupsModuleMRML would solve this problem, but that seems to not be the case.

[RafaelPalomar]

I would think that linking against Slicer's vtkSlicerMarkupsModuleMRML would solve this problem, but that seems to not be the case.

@asiangoldfish, have a look a some of the patches for some of the "heavily" modified extensions in the gentoo-overlay. I remember having to add include and link dirs, etc. in some. I can think of: https://github.com/SystoleOS/gentoo-overlay/blob/master/Slicer-Extension/SlicerIGSIO/files/0001-ENH-Port-SlicerIGSIO-to-Systole-Slicer.patch

[asiangoldfish]

@RafaelPalomar Do you remember if you encountered errors related to DCMTK? Example:

CMake Warning (dev) at CMake/SlicerMacroBuildLoadableModule.cmake:191 (add_library):
  Policy CMP0028 is not set: Double colon in target name means ALIAS or
  IMPORTED target.  Run "cmake --help-policy CMP0028" for policy details.
  Use the cmake_policy command to set the policy and suppress this warning.

  Target "qSlicerOpenIGTLinkIFModule" links to target "DCMTK::ofstd" but the
  target was not found.  Perhaps a find_package() call is missing for an
  IMPORTED target, or an ALIAS target is missing?
Call Stack (most recent call first):
  Modules/External/OpenIGTLinkIF/OpenIGTLinkIF/CMakeLists.txt:84 (slicerMacroBuildLoadableModule)
This warning is for project developers.  Use -Wno-dev to suppress it.

[..]

CMake Error at CMake/SlicerMacroBuildLoadableModule.cmake:191 (add_library):
  Target "qSlicerOpenIGTLinkRemoteModule" links to target "DCMTK::ofstd" but
  the target was not found.  Perhaps a find_package() call is missing for an
  IMPORTED target, or an ALIAS target is missing?
Call Stack (most recent call first):
  CMake/SlicerMacroBuildLoadableModule.cmake:347 (slicerMacroBuildLoadableModule)
  Modules/External/OpenIGTLinkIF/OpenIGTLinkRemote/CMakeLists.txt:48 (slicerMacroBuildQtModule)

In commit 3143a36 I used find_package(DCMTK REQUIRED COMPONENTS ofstd [..]) in the top level CMakeLists.txt and added DCMTK as libraries to link against. I tested this with the module of OpenIGTLinkIF, which was unsuccessful.

[RafaelPalomar]

This is superseded by #57 and #58