Building Slicer from /opt directory reports "permission denied" error

Development
1

I am getting an error when compiling Slicer on Ubu22.04 (from git master, cloned on Jan24) but it is a bit cryptic. Could you let me know what could be happening?

After 3 hours of building, it ends with:

-- Setting CPACK_PACKAGE_NAME to 'Slicer'
-- Setting CPACK_PACKAGE_VENDOR to 'slicer.org'
-- Setting CPACK_PACKAGE_VERSION_MAJOR to '5'
-- Setting CPACK_PACKAGE_VERSION_MINOR to '9'
-- Setting CPACK_PACKAGE_VERSION_PATCH to '0'
-- Setting CPACK_PACKAGE_VERSION to '5.9.0-2025-01-28'
-- Setting CPACK_PACKAGE_INSTALL_DIRECTORY to 'Slicer 5.9.0-2025-01-28'
-- Setting CPACK_PACKAGE_DESCRIPTION_FILE to '/opt/Slicer_src/README.md'
-- Setting CPACK_RESOURCE_FILE_LICENSE to '/opt/Slicer_src/License.txt'
-- Setting CPACK_PACKAGE_DESCRIPTION_SUMMARY to 'Medical Visualization and Processing Environment for Research'
-- Configuring incomplete, errors occurred!
make[2]: *** [CMakeFiles/Slicer.dir/build.make:127: Slicer-prefix/src/Slicer-stamp/Slicer-configure] Error 1
make[1]: *** [CMakeFiles/Makefile2:1826: CMakeFiles/Slicer.dir/all] Error 2
make: *** [Makefile:91: all] Error 2
2

Thanks for the report :pray:

The actual error is likely reported earlier in the log, it would be great if you could scroll up to identify it :ok_hand:

Once we understand the issue, we will consider adding additional checks earlier so that “root” problem is reported earlier.

3

Thanks for the hint, I see this mid-wise in the build:


CMake Error: Could not open file for write in copy operation /opt/Slicer_src/Utilities/Scripts/SlicerWizard/__version__.py.tmp
CMake Error: : System Error: Permission denied
CMake Error at Utilities/Scripts/SlicerWizard/CMakeLists.txt:12 (configure_file):
  configure_file Problem configuring file
4

Thanks for looking this up! That’s helpful.

It looks like you’re building the project in the /opt/ directory, which is likely owned by the root user. This is probably causing the error we’re seeing.

In this case, __version__.py needs to be configured within the source tree[1], but it’s likely not writable in your setup.

To resolve this, you can:

  1. Build and develop from your home directory, or
  2. Update the permissions for /opt/Slicer_src.

Unless you have a specific reason to build in /opt/, I recommend option (1).

  1. Slicer/Utilities/Scripts/SlicerWizard/CMakeLists.txt at 50c891821df013133a4de0c4e7e9ed514c17ae5e · Slicer/Slicer · GitHub ↩︎

1 Like
5

Thanks a lot for the swift clarification!

As a suggestion, since it’s not overly common that the build dir interacts with the source dir, may I suggest the following (pseudocode) improvement in the main CMakeLists, to inform the user about the error more easily/quickly? So that error happens right away, not after x hours and in the middle of the log.

if(CMAKE_VERSION VERSION_GREATER "3.21.0") 
   file(COPY_FILE  ${CMAKE_SOURCE_DIR}/README.md ${CMAKE_SOURCE_DIR}/Utilities/Scripts/SlicerWizard/.tmp_txt RESULT result)
   if(NOT result)
      message(ERROR "You need write permissions in the source dir")
   endif()
endif()

Thanks again!

PS: This would also help with: Variable Slicer_WC_LAST_CHANGED_DATE is expected to be defined - #9 by miniminic

6

I typically use /opt/s as a build directory on mac (need to create it first and change permissions with sudo). Keeping the build directory short avoids path length errors.