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QT error with singularity container #94

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willgpaik opened this issue Jan 13, 2025 · 3 comments
Open

QT error with singularity container #94

willgpaik opened this issue Jan 13, 2025 · 3 comments

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@willgpaik
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Hello,

I am trying to install DSI Studio using Singularity on Rocky 9 Linux, but I keep encountering the following error message::

Apptainer> dsi_studio 
DSI Studio version: Hou "侯" Dec 26 2024
Detected locale "C" with character encoding "ANSI_X3.4-1968", which is not UTF-8.
Qt depends on a UTF-8 locale, and has switched to "C.UTF-8" instead.
If this causes problems, reconfigure your locale. See the locale(1) manual
for more information.
qt.qpa.plugin: Could not find the Qt platform plugin "xcb" in ""
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

I attempted to resolve the issue by setting QT_QPA_PLATFORM=xcb, but this did not fix the problem. I tried launching the container with the following command:

singularity shell --bind /tmp/.X11-unix:/tmp/.X11-unix --env DISPLAY=$DISPLAY --env QT_QPA_PLATFORM=xcb dsistudio_latest.sif

I also tried running it using Docker on Fedora, but encountered the same error message.
@frankyeh
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frankyeh commented Jan 16, 2025 via email

@willgpaik
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Hello Frank,

Thank you for the reply. I'm trying to install from source instead since container cannot be used for GUI. I installed TIPL (2022 version) and now installing DSI-Studio. However, I'm getting following errors:

n file included from /tmp/DSI-Studio-2024.06.12/libs/tracking/fib_data.hpp:6,
                 from /tmp/DSI-Studio-2024.06.12/build/dsi_studio_autogen/EWIEGA46WW/../../../auto_track.h:7,
                 from /tmp/DSI-Studio-2024.06.12/build/dsi_studio_autogen/EWIEGA46WW/moc_auto_track.cpp:9,
                 from /tmp/DSI-Studio-2024.06.12/build/dsi_studio_autogen/mocs_compilation.cpp:2:
/tmp/DSI-Studio-2024.06.12/libs/mapping/connectometry_db.hpp:49:28: error: ‘tipl::io::gz_mat_read’ has not been declared
   49 |     bool is_odf_consistent(tipl::io::gz_mat_read& m);
      |                            ^~~~
/tmp/DSI-Studio-2024.06.12/libs/tracking/fib_data.hpp:14:15: error: ‘tipl::io::gz_mat_read’ has not been declared
   14 |     bool read(tipl::io::gz_mat_read& mat_reader);
      |               ^~~~
/tmp/DSI-Studio-2024.06.12/libs/tracking/fib_data.hpp:46:19: error: ‘tipl::io::gz_mat_read’ has not been declared
   46 |     bool add_data(tipl::io::gz_mat_read& mat_reader);
      |                   ^~~~
/tmp/DSI-Studio-2024.06.12/libs/tracking/fib_data.hpp:160:15: error: ‘gz_mat_read’ in namespace ‘tipl::io’ does not name a type; did you mean ‘mat_read’?
  160 |     tipl::io::gz_mat_read* mat_reader = nullptr;
      |               ^~~~~~~~~~~
      |               mat_read
/tmp/DSI-Studio-2024.06.12/libs/tracking/fib_data.hpp:174:62: error: ‘tipl::io::gz_mat_read’ has not been declared
  174 |     item(const std::string& name_,const tipl::shape<3>& dim_,tipl::io::gz_mat_read* mat_reader_,unsigned int index_):
      |                                                              ^~~~
/tmp/DSI-Studio-2024.06.12/libs/tracking/fib_data.hpp: In constructor ‘item::item(const std::string&, const tipl::shape<3>&, int*, unsigned int)’:
/tmp/DSI-Studio-2024.06.12/libs/tracking/fib_data.hpp:175:66: error: class ‘item’ does not have any field named ‘mat_reader’
  175 |         image_data(tipl::make_image((const float*)nullptr,dim_)),mat_reader(mat_reader_),image_index(index_),name(name_)
      |                                                                  ^~~~~~~~~~
/tmp/DSI-Studio-2024.06.12/libs/tracking/fib_data.hpp: In member function ‘void item::get_minmax()’:
/tmp/DSI-Studio-2024.06.12/libs/tracking/fib_data.hpp:211:41: error: no matching function for call to ‘minmax_value(const float*, const float*)’
  211 |         auto result = tipl::minmax_value(I.begin(),I.end());
      |                       ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
In file included from /tmp/build/include/morphology/../numerical/basic_op.hpp:6,
                 from /tmp/build/include/morphology/morphology.hpp:7,
                 from /tmp/build/include/TIPL/tipl.hpp:17,
                 from /tmp/DSI-Studio-2024.06.12/libs/mapping/connectometry_db.hpp:6:
/tmp/build/include/morphology/../numerical/../numerical/numerical.hpp:831:17: note: candidate: ‘template<class iterator_type, class value_type> void tipl::minmax_value(iterator_type, iterator_type, value_type&, value_type&)’
  831 | __INLINE__ void minmax_value(iterator_type iter,iterator_type end,value_type& minv,value_type& maxv)
      |                 ^~~~~~~~~~~~
/tmp/build/include/morphology/../numerical/../numerical/numerical.hpp:831:17: note:   candidate expects 4 arguments, 2 provided
/tmp/build/include/morphology/../numerical/../numerical/numerical.hpp:851:6: note: candidate: ‘template<class T, class value_type> void tipl::minmax_value(const T&, value_type&, value_type&)’
  851 | void minmax_value(const T& data,value_type& minv,value_type& maxv)
      |      ^~~~~~~~~~~~
/tmp/build/include/morphology/../numerical/../numerical/numerical.hpp:851:6: note:   candidate expects 3 arguments, 2 provided
/tmp/DSI-Studio-2024.06.12/libs/tracking/fib_data.hpp: At global scope:
/tmp/DSI-Studio-2024.06.12/libs/tracking/fib_data.hpp:229:15: error: ‘gz_mat_read’ in namespace ‘tipl::io’ does not name a type; did you mean ‘mat_read’?
  229 |     tipl::io::gz_mat_read mat_reader;
      |               ^~~~~~~~~~~
      |               mat_read
/tmp/DSI-Studio-2024.06.12/libs/tracking/fib_data.hpp: In member function ‘bool fib_data::has_odfs() const’:
/tmp/DSI-Studio-2024.06.12/libs/tracking/fib_data.hpp:374:38: error: ‘mat_reader’ was not declared in this scope
  374 |     bool has_odfs(void) const{return mat_reader.has("odf0");}
      |                                      ^~~~~~~~~~
In file included from /tmp/DSI-Studio-2024.06.12/build/dsi_studio_autogen/EWIEGA46WW/../../../view_image.h:7,
                 from /tmp/DSI-Studio-2024.06.12/build/dsi_studio_autogen/EWIEGA46WW/moc_view_image.cpp:9,
                 from /tmp/DSI-Studio-2024.06.12/build/dsi_studio_autogen/mocs_compilation.cpp:27:
/tmp/DSI-Studio-2024.06.12/build/dsi_studio_autogen/EWIEGA46WW/../../../cmd/img.hpp: At global scope:
/tmp/DSI-Studio-2024.06.12/build/dsi_studio_autogen/EWIEGA46WW/../../../cmd/img.hpp:49:56: error: ‘tipl::io::gz_mat_read’ has not been declared
   49 |     bool read_mat_image(const std::string& metric_name,tipl::io::gz_mat_read& mat);
      |                                                        ^~~~
/tmp/DSI-Studio-2024.06.12/build/dsi_studio_autogen/EWIEGA46WW/../../../cmd/img.hpp: In member function ‘variant_image& variant_image::operator=(const variant_image&)’:
/tmp/DSI-Studio-2024.06.12/build/dsi_studio_autogen/EWIEGA46WW/../../../cmd/img.hpp:23:71: warning: no return statement in function returning non-void [-Wreturn-type]
   23 |     variant_image& operator=(const variant_image& rhs){copy_from(rhs);}
      |                                                                       ^
      |                                                                       return *this;
/tmp/DSI-Studio-2024.06.12/build/dsi_studio_autogen/EWIEGA46WW/../../../view_image.h: At global scope:
/tmp/DSI-Studio-2024.06.12/build/dsi_studio_autogen/EWIEGA46WW/../../../view_image.h:32:15: error: ‘gz_nifti’ in namespace ‘tipl::io’ does not name a type; did you mean ‘nifti’?
   32 |     tipl::io::gz_nifti nifti;
      |               ^~~~~~~~
      |               nifti
/tmp/DSI-Studio-2024.06.12/build/dsi_studio_autogen/EWIEGA46WW/../../../view_image.h:105:15: error: ‘gz_mat_read’ in namespace ‘tipl::io’ does not name a type; did you mean ‘mat_read’?
  105 |     tipl::io::gz_mat_read mat;
      |               ^~~~~~~~~~~
      |               mat_read

It appears that compiler cannot properly link header files. Can you provide a solution to fix the errors? Since I'm trying to install it on RHEL, I cannot simply use pre-compiled versions due to GLIBC version issue.

@frankyeh
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frankyeh commented Jan 22, 2025 via email

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@frankyeh @willgpaik