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Build error: undefined references to libgio-2.0 symbols #243

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godot11 opened this issue Sep 6, 2021 · 1 comment
Open

Build error: undefined references to libgio-2.0 symbols #243

godot11 opened this issue Sep 6, 2021 · 1 comment

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@godot11
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godot11 commented Sep 6, 2021 •
edited

I'm compiling SimEx from the develop branch, but I'm hitting a wall. System is Ubuntu 18.04 LTS. I'm using Intel compliers (OpenAPI 4.4.20(1), ifort and icc version 2021.3.0).

After I set up the environment with ./install.sh conda-env and activating it, the build fails with a dozen of undefined refs in libgio-2.0. Specifically:

[ 42%] Building C object CMakeFiles/geoptimiser.dir/src/hdfsee-render.c.o
[ 43%] Linking C executable geoptimiser
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_spawn_async_with_fds'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_utf8_validate_len'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_source_set_dispose_function'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_ref_count_dec'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_unix_get_passwd_entry'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_uri_join'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_uri_split_with_user'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_canonicalize_filename'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_spawn_async_with_pipes_and_fds'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_uri_split_network'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_uri_is_valid'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_file_set_contents_full'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_ptr_array_steal'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_atomic_ref_count_init'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_atomic_ref_count_dec'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_ref_count_init'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_atomic_ref_count_inc'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_memdup2'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_ref_count_inc'
collect2: error: ld returned 1 exit status
CMakeFiles/geoptimiser.dir/build.make:117: recipe for target 'geoptimiser' failed
make[5]: *** [geoptimiser] Error 1
CMakeFiles/Makefile2:257: recipe for target 'CMakeFiles/geoptimiser.dir/all' failed
make[4]: *** [CMakeFiles/geoptimiser.dir/all] Error 2
Makefile:145: recipe for target 'all' failed
make[3]: *** [all] Error 2
Modules/Diffractors/CrystFELPhotonDiffractor/CMakeFiles/crystfel.dir/build.make:85: recipe for target 'Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel-stamp/crystfel-build' failed
make[2]: *** [Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel-stamp/crystfel-build] Error 2
CMakeFiles/Makefile2:333: recipe for target 'Modules/Diffractors/CrystFELPhotonDiffractor/CMakeFiles/crystfel.dir/all' failed
make[1]: *** [Modules/Diffractors/CrystFELPhotonDiffractor/CMakeFiles/crystfel.dir/all] Error 2
Makefile:135: recipe for target 'all' failed
make: *** [all] Error 2

I attempted to both sudo apt-get install libglib2.0-dev (it was already installed), and conda install -c anaconda glib, but it didn't change anything. I do have a suspicious warning from ./install.sh conda:

CMake Warning at libcrystfel/CMakeLists.txt:132 (add_library):
  Cannot generate a safe runtime search path for target libcrystfel because
  files in some directories may conflict with libraries in implicit
  directories:

    runtime library [libz.so.1] in /usr/lib/x86_64-linux-gnu may be hidden by files in:
      /home/nagyg/anaconda3/envs/simex/lib

  Some of these libraries may not be found correctly.

But I'm not convinced it's relevant: I complied everything successfully on another system with Ubuntu 20.04 and GNU compliers following the same steps, and the same warning came up there as well.

I changed exactly two things in the install.sh:

  • line 113: uncomment export FC=ifort
  • line 144: use -j1 with cmake (for organized log)

Do you have any insight about what may be the cause?

Full outputs of ./install.sh conda-env, ./install.sh conda, conda list and dpkg -l | grep libglib are below. Please tell me if you need anything else.

--> [spoiler, click] <--

Output of ./install.sh conda-env - seems OK:

conda-env
Create conda environment simex
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

Downloading and Extracting Packages

pillow-8.3.2         | 692 KB    |            |   0% 
pillow-8.3.2         | 692 KB    | 2          |   2% 
pillow-8.3.2         | 692 KB    | ########## | 100% 
pillow-8.3.2         | 692 KB    | ########## | 100% 

qtpy-1.11.0          | 37 KB     |            |   0% 
qtpy-1.11.0          | 37 KB     | ########## | 100% 
qtpy-1.11.0          | 37 KB     | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Installing pip dependencies: ...working... Ran pip subprocess with arguments:
['/home/nagyg/anaconda3/envs/simex/bin/python', '-m', 'pip', 'install', '-U', '-r', '/home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt']
Pip subprocess output:
Collecting xraydb
  Using cached xraydb-4.4.7-py3-none-any.whl
Collecting cfelpyutils
  Using cached cfelpyutils-1.0.1-py3-none-any.whl (23 kB)
Collecting openpmd-api
  Using cached openPMD_api-0.14.2-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (6.9 MB)
Collecting extra_geom
  Using cached EXtra_geom-1.5.0-py3-none-any.whl
Requirement already satisfied: scipy in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from xraydb->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 1)) (1.7.1)
Requirement already satisfied: numpy in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from xraydb->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 1)) (1.21.2)
Requirement already satisfied: sqlalchemy in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from xraydb->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 1)) (1.4.23)
Collecting future
  Using cached future-0.18.2-py3-none-any.whl
Requirement already satisfied: matplotlib in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from extra_geom->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 4)) (3.4.3)
Requirement already satisfied: h5py>=2.7.1 in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from extra_geom->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 4)) (2.8.0)
Requirement already satisfied: six in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from h5py>=2.7.1->extra_geom->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 4)) (1.16.0)
Requirement already satisfied: pyparsing>=2.2.1 in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from matplotlib->extra_geom->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 4)) (2.4.7)
Requirement already satisfied: kiwisolver>=1.0.1 in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from matplotlib->extra_geom->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 4)) (1.3.2)
Requirement already satisfied: python-dateutil>=2.7 in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from matplotlib->extra_geom->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 4)) (2.8.2)
Requirement already satisfied: pillow>=6.2.0 in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from matplotlib->extra_geom->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 4)) (8.3.2)
Requirement already satisfied: cycler>=0.10 in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from matplotlib->extra_geom->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 4)) (0.10.0)
Requirement already satisfied: greenlet!=0.4.17 in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from sqlalchemy->xraydb->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 1)) (1.1.1)
Requirement already satisfied: importlib-metadata in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from sqlalchemy->xraydb->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 1)) (4.8.1)
Requirement already satisfied: typing-extensions>=3.6.4 in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from importlib-metadata->sqlalchemy->xraydb->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 1)) (3.10.0.0)
Requirement already satisfied: zipp>=0.5 in /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages (from importlib-metadata->sqlalchemy->xraydb->-r /home/nagyg/Software/SimEx/condaenv.64xh7u_t.requirements.txt (line 1)) (3.5.0)
Installing collected packages: future, cfelpyutils, xraydb, openpmd-api, extra-geom
Successfully installed cfelpyutils-1.0.1 extra-geom-1.5.0 future-0.18.2 openpmd-api-0.14.2 xraydb-4.4.7

done
#
# To activate this environment, use
#
#     $ conda activate simex
#
# To deactivate an active environment, use
#
#     $ conda deactivate

conda environment was deployed. Please run the following to install SIMEX Platform:

 conda activate simex
 ./install.sh conda

Output of ./install conda after changing into the new env:

conda
mkdir: created directory 'build'
Changed dir to /home/nagyg/Software/SimEx/build.
-- The C compiler identification is GNU 7.5.0
-- The CXX compiler identification is GNU 7.5.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found PythonInterp: /home/nagyg/anaconda3/envs/simex/bin/python3 (found suitable version "3.7.10", minimum required is "3.5") 
PYPATH=lib/python3.7/site-packages
-- ************************ checking python dependencies *****************************
-- Python module Bio is found
-- Python module Cython is found
-- Python module dill is found
-- Python module h5py is found
-- Python module matplotlib is found
-- Python module mpi4py is found
-- Python module openpmd_api is found
-- Python module numpy is found
-- Python module periodictable is found
-- Python module pint is found
-- Python module pyFAI is found
-- Python module scipy is found
-- Python module setuptools is found
-- Python module xraydb is found
-- **************** Including modules (default OFF) ****************
CHECKING Analyzers/S2EReconstruction_DM
CHECKING Analyzers/S2EReconstruction_EMC
CHECKING Detectors/XCSITPhotonDetector
CHECKING Diffractors/CrystFELPhotonDiffractor
CHECKING Diffractors/GAPDPhotonDiffractor
CHECKING Diffractors/SingFELPhotonDiffractor
CHECKING Others/s2e
CHECKING Others/sdf
CHECKING PhotonInteractors/FEFFPhotonInteractor
CHECKING Propagators/WavePropagator/wpg
CHECKING Sources/GenesisPhotonSource
-- ***** Including module S2EReconstruction_DM from: Analyzers/S2EReconstruction_DM ****
-- Found MKL: /opt/intel/oneapi/mkl/2021.3.0  
-- *********************************************************
-- ***** Including module S2EReconstruction_EMC from: Analyzers/S2EReconstruction_EMC ****
-- Python module Cython.Distutils is found
-- Python module numpy is found
-- Python module h5py is found
-- *********************************************************
-- ***** Including module CrystFELPhotonDiffractor from: Diffractors/CrystFELPhotonDiffractor ****
CMake Warning (dev) at Modules/Diffractors/CrystFELPhotonDiffractor/CMakeLists.txt:6 (FIND_PACKAGE):
  Policy CMP0074 is not set: find_package uses <PackageName>_ROOT variables.
  Run "cmake --help-policy CMP0074" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  Environment variable HDF5_ROOT is set to:

    /home/nagyg/anaconda3/envs/simex

  For compatibility, CMake is ignoring the variable.
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found HDF5: /home/nagyg/anaconda3/envs/simex/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/home/nagyg/anaconda3/envs/simex/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so;/home/nagyg/anaconda3/envs/simex/lib/libhdf5_cpp.so;/home/nagyg/anaconda3/envs/simex/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/home/nagyg/anaconda3/envs/simex/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.3") found components: C CXX 
HDF5_INCLUDE_DIRS= /home/nagyg/anaconda3/envs/simex/include
HDF5_INCLUDE_DIR= /home/nagyg/anaconda3/envs/simex/include
HDF5_DEFINITIONS= -DBOOST_MATH_DISABLE_FLOAT128
HDF5_C_LIBRARIES= /home/nagyg/anaconda3/envs/simex/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/home/nagyg/anaconda3/envs/simex/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so
HDF5_CXX_LIBRARIES= /home/nagyg/anaconda3/envs/simex/lib/libhdf5_cpp.so;/home/nagyg/anaconda3/envs/simex/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/home/nagyg/anaconda3/envs/simex/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so
HDF5_Fortran_LIBRARIES= 
HDF5_HL_LIBRARIES= 
HDF5_Fortran_HL_LIBRARIES= 
HDF5_LIBRARIES= /home/nagyg/anaconda3/envs/simex/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/home/nagyg/anaconda3/envs/simex/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so;/home/nagyg/anaconda3/envs/simex/lib/libhdf5_cpp.so;/home/nagyg/anaconda3/envs/simex/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/home/nagyg/anaconda3/envs/simex/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so
HDF5_FOUND= TRUE
HDF5_VERSION= 1.10.3
HDF5_LIBRARY_DIRS= 
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1") 
-- Found GSL: /usr/include (found version "2.4") 
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") 
-- *********************************************************
-- ***** Including module SingFELPhotonDiffractor from: Diffractors/SingFELPhotonDiffractor ****
-- Python module numba is found
-- Python module numpy is found
-- Python module scipy is found
-- Python module mpi4py is found
-- Python module h5py is found
-- *********************************************************
-- ***** Including module s2e from: Others/s2e ****
-- *********************************************************
-- ***** Including module sdf from: Others/sdf ****
-- *********************************************************
-- ***** Including module wpg from: Propagators/WavePropagator/wpg ****
-- *********************************************************
-- ***** Including module GenesisPhotonSource from: Sources/GenesisPhotonSource ****
-- *********************************************************
-- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE) 
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    BOOST_ROOT
    GEANT4_ROOT
    XCSIT_ROOT
    XERCESC_ROOT


-- Build files have been written to: /home/nagyg/Software/SimEx/build
[  1%] Creating directories for 'recon_dm'
[  2%] Performing download step (download, verify and extract) for 'recon_dm'
-- Downloading...
   dst='/home/nagyg/Software/SimEx/build/Modules/Analyzers/S2EReconstruction_DM/recon_dm-prefix/src/master.zip'
   timeout='none'
   inactivity timeout='none'
-- Using src='https://github.com/eucall-software/emc_and_dm/archive/master.zip'
-- [download 100% complete]
-- Downloading... done
-- extracting...
     src='/home/nagyg/Software/SimEx/build/Modules/Analyzers/S2EReconstruction_DM/recon_dm-prefix/src/master.zip'
     dst='/home/nagyg/Software/SimEx/build/Modules/Analyzers/S2EReconstruction_DM/recon_dm-prefix/src/recon_dm'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[  4%] No update step for 'recon_dm'
[  5%] Performing patch step for 'recon_dm'
[  6%] No configure step for 'recon_dm'
[  8%] Performing build step for 'recon_dm'
object_recon.c: In function ‘setup’:
object_recon.c:266:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  fscanf(fp, "%d %d", &qmax, &num_supp) ;
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
object_recon.c:281:13: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
             fscanf(fp, "%d", &supp[s][i]) ;
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
object_recon.c:363:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fp, "%lf", &intens) ;
     ^~~~~~~~~~~~~~~~~~~~~~~~~~
object_recon.c:412:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
    fscanf(fp, "%lf", &x[i][j][k]) ;
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[  9%] No install step for 'recon_dm'
[ 11%] Completed 'recon_dm'
[ 11%] Built target recon_dm
[ 12%] Creating directories for 'recon_emc'
[ 13%] Performing download step (download, verify and extract) for 'recon_emc'
-- Downloading...
   dst='/home/nagyg/Software/SimEx/build/Modules/Analyzers/S2EReconstruction_EMC/recon_emc-prefix/src/master.zip'
   timeout='none'
   inactivity timeout='none'
-- Using src='https://github.com/eucall-software/emc_and_dm/archive/master.zip'
-- [download 100% complete]
-- Downloading... done
-- extracting...
     src='/home/nagyg/Software/SimEx/build/Modules/Analyzers/S2EReconstruction_EMC/recon_emc-prefix/src/master.zip'
     dst='/home/nagyg/Software/SimEx/build/Modules/Analyzers/S2EReconstruction_EMC/recon_emc-prefix/src/recon_emc'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[ 15%] No update step for 'recon_emc'
[ 16%] No patch step for 'recon_emc'
[ 18%] No configure step for 'recon_emc'
[ 19%] Performing build step for 'recon_emc'
running build_ext
cythoning rotateIntens.pyx to rotateIntens.c
building 'rotateIntens' extension
creating build
creating build/temp.linux-x86_64-3.7
gcc -pthread -B /home/nagyg/anaconda3/envs/simex/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages/numpy/core/include -I/home/nagyg/anaconda3/envs/simex/include/python3.7m -c rotateIntens.c -o build/temp.linux-x86_64-3.7/rotateIntens.o -O2
In file included from /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969:0,
                 from /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from rotateIntens.c:620:
/home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it with " \
  ^~~~~~~
gcc -pthread -shared -B /home/nagyg/anaconda3/envs/simex/compiler_compat -L/home/nagyg/anaconda3/envs/simex/lib -Wl,-rpath=/home/nagyg/anaconda3/envs/simex/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.7/rotateIntens.o -o /home/nagyg/Software/SimEx/build/Modules/Analyzers/S2EReconstruction_EMC/recon_emc-prefix/src/recon_emc/EMC_Src/supp_py_modules/rotateIntens.cpython-37m-x86_64-linux-gnu.so
/home/nagyg/anaconda3/envs/simex/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/nagyg/Software/SimEx/build/Modules/Analyzers/S2EReconstruction_EMC/recon_emc-prefix/src/recon_emc/EMC_Src/supp_py_modules/rotateIntens.pyx
  tree = Parsing.p_module(s, pxd, full_module_name)
[ 20%] No install step for 'recon_emc'
[ 22%] Completed 'recon_emc'
[ 22%] Built target recon_emc
[ 23%] Creating directories for 'crystfel'
[ 25%] Performing download step (download, verify and extract) for 'crystfel'
-- Downloading...
   dst='/home/nagyg/Software/SimEx/build/Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel-0.9.1.tar.gz'
   timeout='none'
   inactivity timeout='none'
-- Using src='http://www.desy.de/~twhite/crystfel/crystfel-0.9.1.tar.gz'
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-- Downloading... done
-- extracting...
     src='/home/nagyg/Software/SimEx/build/Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel-0.9.1.tar.gz'
     dst='/home/nagyg/Software/SimEx/build/Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[ 26%] No update step for 'crystfel'
[ 27%] No patch step for 'crystfel'
[ 29%] Performing configure step for 'crystfel'
-- The C compiler identification is GNU 7.5.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Found HDF5: /home/nagyg/anaconda3/envs/simex/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/home/nagyg/anaconda3/envs/simex/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.3") found components: C 
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1") 
-- Found GSL: /usr/include (found version "2.4") 
-- Found TIFF: /home/nagyg/anaconda3/envs/simex/lib/libtiff.so (found version "4.3.0")  
-- Looking for CL_VERSION_2_2
-- Looking for CL_VERSION_2_2 - found
-- Found OpenCL: /usr/lib/x86_64-linux-gnu/libOpenCL.so (found version "2.2") 
-- Checking for module 'glib-2.0'
--   Found glib-2.0, version 2.56.4
-- Checking for one of the modules 'msgpack'
-- MessagePack not found.
-- Checking for one of the modules 'libzmq'
-- ZMQ not found.
-- Checking for one of the modules 'gtk+-3.0'
-- Checking for one of the modules 'gtk+-2.0'
-- Using GTK 2
-- Checking for one of the modules 'gdk-2.0'
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-- Checking for one of the modules 'gdk-pixbuf-2.0'
-- Performing Test HAVE_DIAG_COLOR
-- Performing Test HAVE_DIAG_COLOR - Success
-- This is a packaged release version
-- Looking for fcntl.h
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-- Found Curses: /usr/lib/x86_64-linux-gnu/libcurses.so  
-- Could NOT find XGANDALF (missing: XGANDALF_LIBRARIES XGANDALF_INCLUDES) 
-- Could NOT find PINKINDEXER (missing: PINKINDEXER_LIBRARIES PINKINDEXER_INCLUDES) 
-- Could NOT find FDIP (missing: FDIP_LIBRARIES) 
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") 
-- Found FLEX: /usr/bin/flex (found version "2.6.4") 
-- Found BISON: /usr/bin/bison (found version "3.0.4") 
-- Found Doxygen: /usr/bin/doxygen (found version "1.8.13") found components: doxygen dot 
-- Checking for one of the modules 'fftw3'
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-- Looking for gzbuffer - found
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-- Looking for forkpty - found
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-- Looking for forkpty - not found
-- Found forkpty() in pty.h
-- Configuring done
CMake Warning at libcrystfel/CMakeLists.txt:132 (add_library):
  Cannot generate a safe runtime search path for target libcrystfel because
  files in some directories may conflict with libraries in implicit
  directories:

    runtime library [libz.so.1] in /usr/lib/x86_64-linux-gnu may be hidden by files in:
      /home/nagyg/anaconda3/envs/simex/lib

  Some of these libraries may not be found correctly.


-- Generating done
-- Build files have been written to: /home/nagyg/Software/SimEx/build/Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel-build
[ 30%] Performing build step for 'crystfel'
[  1%] [BISON][symopp] Building parser with bison 3.0.4
[  2%] [FLEX][symopl] Building scanner with flex 2.6.4
[  3%] Building C object libcrystfel/CMakeFiles/libcrystfel.dir/src/reflist.c.o
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[ 34%] Building C object CMakeFiles/pattern_sim.dir/src/diffraction.c.o
[ 35%] Building C object CMakeFiles/pattern_sim.dir/src/cl-utils.c.o
[ 36%] Building C object CMakeFiles/pattern_sim.dir/src/diffraction-gpu.c.o
/home/nagyg/Software/SimEx/build/Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel/src/diffraction-gpu.c: In function ‘check_sinc_lut’:
/home/nagyg/Software/SimEx/build/Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel/src/diffraction-gpu.c:124:2: warning: ‘clCreateImage2D’ is deprecated [-Wdeprecated-declarations]
  gctx->sinc_luts[n-1] = clCreateImage2D(gctx->ctx,
  ^~~~
In file included from /home/nagyg/Software/SimEx/build/Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel/src/diffraction-gpu.c:42:0:
/usr/include/CL/cl.h:1402:1: note: declared here
 clCreateImage2D(cl_context              /* context */,
 ^~~~~~~~~~~~~~~
/home/nagyg/Software/SimEx/build/Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel/src/diffraction-gpu.c: In function ‘setup_gpu’:
/home/nagyg/Software/SimEx/build/Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel/src/diffraction-gpu.c:445:2: warning: ‘clCreateCommandQueue’ is deprecated [-Wdeprecated-declarations]
  gctx->cq = clCreateCommandQueue(gctx->ctx, dev, 0, &err);
  ^~~~
In file included from /home/nagyg/Software/SimEx/build/Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel/src/diffraction-gpu.c:42:0:
/usr/include/CL/cl.h:1443:1: note: declared here
 clCreateCommandQueue(cl_context                     /* context */,
 ^~~~~~~~~~~~~~~~~~~~
[ 36%] Linking C executable pattern_sim
[ 36%] Built target pattern_sim
[ 37%] Building C object CMakeFiles/hdfsee.dir/src/hdfsee.c.o
[ 38%] Building C object CMakeFiles/hdfsee.dir/src/dw-hdfsee.c.o
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[ 40%] Linking C executable hdfsee
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[ 41%] Building C object CMakeFiles/geoptimiser.dir/src/geoptimiser.c.o
[ 42%] Building C object CMakeFiles/geoptimiser.dir/src/hdfsee-render.c.o
[ 43%] Linking C executable geoptimiser
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_spawn_async_with_fds'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_utf8_validate_len'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_source_set_dispose_function'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_ref_count_dec'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_unix_get_passwd_entry'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_uri_join'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_uri_split_with_user'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_canonicalize_filename'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_spawn_async_with_pipes_and_fds'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_uri_split_network'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_uri_is_valid'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_file_set_contents_full'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_ptr_array_steal'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_atomic_ref_count_init'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_atomic_ref_count_dec'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_ref_count_init'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_atomic_ref_count_inc'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_memdup2'
//home/nagyg/anaconda3/envs/simex/lib/libgio-2.0.so.0: undefined reference to `g_ref_count_inc'
collect2: error: ld returned 1 exit status
CMakeFiles/geoptimiser.dir/build.make:117: recipe for target 'geoptimiser' failed
make[5]: *** [geoptimiser] Error 1
CMakeFiles/Makefile2:257: recipe for target 'CMakeFiles/geoptimiser.dir/all' failed
make[4]: *** [CMakeFiles/geoptimiser.dir/all] Error 2
Makefile:145: recipe for target 'all' failed
make[3]: *** [all] Error 2
Modules/Diffractors/CrystFELPhotonDiffractor/CMakeFiles/crystfel.dir/build.make:85: recipe for target 'Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel-stamp/crystfel-build' failed
make[2]: *** [Modules/Diffractors/CrystFELPhotonDiffractor/crystfel-prefix/src/crystfel-stamp/crystfel-build] Error 2
CMakeFiles/Makefile2:333: recipe for target 'Modules/Diffractors/CrystFELPhotonDiffractor/CMakeFiles/crystfel.dir/all' failed
make[1]: *** [Modules/Diffractors/CrystFELPhotonDiffractor/CMakeFiles/crystfel.dir/all] Error 2
Makefile:135: recipe for target 'all' failed
make: *** [all] Error 2

Output of conda list in the fresh new environment:

WARNING conda.core.prefix_data:_load_site_packages(293): Problem reading non-conda package record at lib/python3.7/site-packages/pyFAI-0.15.0-py3.7-linux-x86_64.egg-info/PKG-INFO. Please verify that you still need this, and if so, that this is still installed correctly. Reinstalling this package may help.
# packages in environment at /home/nagyg/anaconda3/envs/simex:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
alsa-lib                  1.2.3                h516909a_0    conda-forge
argcomplete               1.12.3             pyhd8ed1ab_2    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
biopython                 1.79             py37h5e8e339_0    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.17.2               h7f98852_0    conda-forge
ca-certificates           2020.10.14                    0    anaconda
certifi                   2020.6.20                py37_0    anaconda
cfelpyutils               1.0.1                    pypi_0    pypi
cmake                     3.21.2               h8897547_0    conda-forge
cycler                    0.10.0                     py_2    conda-forge
cython                    0.29.24          py37hcd2ae1e_0    conda-forge
dbus                      1.13.6               h48d8840_2    conda-forge
debugpy                   1.4.1            py37hcd2ae1e_0    conda-forge
decorator                 5.0.9              pyhd8ed1ab_0    conda-forge
dill                      0.3.4              pyhd8ed1ab_0    conda-forge
entrypoints               0.3             pyhd8ed1ab_1003    conda-forge
expat                     2.4.1                h9c3ff4c_0    conda-forge
extra-geom                1.5.0                    pypi_0    pypi
fabio                     0.12.0           py37hb1e94ed_0    conda-forge
fftw                      3.3.9           nompi_h74d3f13_101    conda-forge
fontconfig                2.13.1            hba837de_1005    conda-forge
freetype                  2.10.4               h0708190_1    conda-forge
future                    0.18.2                   pypi_0    pypi
gettext                   0.19.8.1          h0b5b191_1005    conda-forge
glib                      2.68.4               h9c3ff4c_0    conda-forge
glib-tools                2.68.4               h9c3ff4c_0    conda-forge
glymur                    0.9.4              pyhd8ed1ab_0    conda-forge
greenlet                  1.1.1            py37hcd2ae1e_0    conda-forge
gst-plugins-base          1.18.4               hf529b03_2    conda-forge
gstreamer                 1.18.4               h76c114f_2    conda-forge
h5py                      2.8.0           py37hfb8609e_1004    conda-forge
hdf5                      1.10.3               hc401514_2    conda-forge
icu                       68.1                 h58526e2_0    conda-forge
importlib-metadata        4.8.1            py37h89c1867_0    conda-forge
importlib_metadata        4.8.1                hd8ed1ab_0    conda-forge
importlib_resources       5.2.2              pyhd8ed1ab_0    conda-forge
ipykernel                 6.3.1            py37h6531663_0    conda-forge
ipython                   7.27.0           py37h6531663_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
jbig                      2.1               h7f98852_2003    conda-forge
jedi                      0.18.0           py37h89c1867_2    conda-forge
jpeg                      9d                   h36c2ea0_0    conda-forge
jupyter_client            7.0.2              pyhd8ed1ab_0    conda-forge
jupyter_core              4.7.1            py37h89c1867_0    conda-forge
kiwisolver                1.3.2            py37h2527ec5_0    conda-forge
krb5                      1.19.2               hcc1bbae_0    conda-forge
lcms2                     2.12                 hddcbb42_0    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
lerc                      2.2.1                h9c3ff4c_0    conda-forge
libblas                   3.9.0           11_linux64_openblas    conda-forge
libcblas                  3.9.0           11_linux64_openblas    conda-forge
libclang                  11.1.0          default_ha53f305_1    conda-forge
libcurl                   7.78.0               h2574ce0_0    conda-forge
libdeflate                1.7                  h7f98852_5    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libevent                  2.1.10               hcdb4288_3    conda-forge
libffi                    3.3                  h58526e2_2    conda-forge
libgcc-ng                 11.1.0               hc902ee8_8    conda-forge
libgfortran               3.0.0                         1    conda-forge
libgfortran-ng            11.1.0               h69a702a_8    conda-forge
libgfortran5              11.1.0               h6c583b3_8    conda-forge
libglib                   2.68.4               h3e27bee_0    conda-forge
libgomp                   11.1.0               hc902ee8_8    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblapack                 3.9.0           11_linux64_openblas    conda-forge
libllvm10                 10.0.1               he513fc3_3    conda-forge
libllvm11                 11.1.0               hf817b99_2    conda-forge
libnghttp2                1.43.0               h812cca2_0    conda-forge
libogg                    1.3.4                h7f98852_1    conda-forge
libopenblas               0.3.17          pthreads_h8fe5266_1    conda-forge
libopus                   1.3.1                h7f98852_1    conda-forge
libpng                    1.6.37               h21135ba_2    conda-forge
libpq                     13.3                 hd57d9b9_0    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libssh2                   1.10.0               ha56f1ee_0    conda-forge
libstdcxx-ng              11.1.0               h56837e0_8    conda-forge
libtiff                   4.3.0                hf544144_1    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libuv                     1.42.0               h7f98852_0    conda-forge
libvorbis                 1.3.7                h9c3ff4c_0    conda-forge
libwebp-base              1.2.1                h7f98852_0    conda-forge
libxcb                    1.13              h7f98852_1003    conda-forge
libxkbcommon              1.0.3                he3ba5ed_0    conda-forge
libxml2                   2.9.12               h72842e0_0    conda-forge
libxslt                   1.1.33               h15afd5d_2    conda-forge
llvmlite                  0.36.0           py37h9d7f4d0_0    conda-forge
lxml                      4.6.3            py37h77fd288_0    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
mako                      1.1.5              pyhd8ed1ab_0    conda-forge
markupsafe                2.0.1            py37h5e8e339_0    conda-forge
matplotlib                3.4.3            py37h89c1867_0    conda-forge
matplotlib-base           3.4.3            py37h1058ff1_0    conda-forge
matplotlib-inline         0.1.2              pyhd8ed1ab_2    conda-forge
mpi                       1.0                       mpich    conda-forge
mpi4py                    3.1.1            py37h1e5cb63_0    conda-forge
mpich                     3.4.2              h846660c_100    conda-forge
mysql-common              8.0.25               ha770c72_2    conda-forge
mysql-libs                8.0.25               hfa10184_2    conda-forge
ncurses                   6.2                  h58526e2_4    conda-forge
nest-asyncio              1.5.1              pyhd8ed1ab_0    conda-forge
nomkl                     1.0                  h5ca1d4c_0    conda-forge
nspr                      4.30                 h9c3ff4c_0    conda-forge
nss                       3.69                 hb5efdd6_0    conda-forge
numba                     0.53.1           py37hb11d6e1_1    conda-forge
numexpr                   2.7.3            py37he8f5f7f_0    conda-forge
numpy                     1.21.2           py37h31617e3_0    conda-forge
olefile                   0.46               pyh9f0ad1d_1    conda-forge
openjpeg                  2.4.0                hb52868f_1    conda-forge
openpmd-api               0.14.2                   pypi_0    pypi
openssl                   1.1.1l               h7f98852_0    conda-forge
packaging                 21.0               pyhd8ed1ab_0    conda-forge
parso                     0.8.2              pyhd8ed1ab_0    conda-forge
pcre                      8.45                 h9c3ff4c_0    conda-forge
periodictable             1.5.2                      py_0    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    8.3.2            py37h0f21c89_0    conda-forge
pint                      0.17               pyhd8ed1ab_1    conda-forge
pip                       21.2.4             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.20             pyha770c72_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
py3nvml                   0.2.5            py37hc8dfbb8_2    conda-forge
pyfai                     0.15.0          py37h3010b51_1002    conda-forge
pyfftw                    0.12.0           py37h433d886_2    conda-forge
pygments                  2.10.0             pyhd8ed1ab_0    conda-forge
pyparsing                 2.4.7              pyh9f0ad1d_0    conda-forge
pyqt                      5.12.3           py37h89c1867_7    conda-forge
pyqt-impl                 5.12.3           py37he336c9b_7    conda-forge
pyqt5-sip                 4.19.18          py37hcd2ae1e_7    conda-forge
pyqtchart                 5.12             py37he336c9b_7    conda-forge
pyqtwebengine             5.12.1           py37he336c9b_7    conda-forge
python                    3.7.10          hffdb5ce_100_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.7                     2_cp37m    conda-forge
pyzmq                     22.2.1           py37h336d617_0    conda-forge
qt                        5.12.9               hda022c4_4    conda-forge
qtconsole                 5.1.1              pyhd8ed1ab_0    conda-forge
qtpy                      1.11.0             pyhd8ed1ab_0    conda-forge
readline                  8.1                  h46c0cb4_0    conda-forge
rhash                     1.4.1                h7f98852_0    conda-forge
scipy                     1.7.1            py37hf2a6cf1_0    conda-forge
setuptools                57.4.0           py37h89c1867_0    conda-forge
silx                      0.15.2               hd8ed1ab_0    conda-forge
silx-base                 0.15.2           py37h219a48f_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sqlalchemy                1.4.23           py37h5e8e339_0    conda-forge
sqlite                    3.36.0               h9cd32fc_0    conda-forge
tk                        8.6.11               h27826a3_1    conda-forge
tornado                   6.1              py37h5e8e339_1    conda-forge
traitlets                 5.1.0              pyhd8ed1ab_0    conda-forge
typing_extensions         3.10.0.0           pyha770c72_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
wheel                     0.37.0             pyhd8ed1ab_1    conda-forge
xmltodict                 0.12.0                     py_0    conda-forge
xorg-libxau               1.0.9                h7f98852_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xraydb                    4.4.7                    pypi_0    pypi
xz                        5.2.5                h516909a_1    conda-forge
zeromq                    4.3.4                h9c3ff4c_1    conda-forge
zipp                      3.5.0              pyhd8ed1ab_0    conda-forge
zlib                      1.2.11            h516909a_1010    conda-forge
zstd                      1.5.0                ha95c52a_0    conda-forge

and finally, the output of dpkg -l | grep libglib:

ii  libglib-object-introspection-perl                                       0.044-2                                             amd64        Perl bindings for gobject-introspection libraries
ii  libglib-perl                                                            3:1.326-1build1                                     amd64        interface to the GLib and GObject libraries
ii  libglib2.0-0:amd64                                                      2.56.4-0ubuntu0.18.04.8                             amd64        GLib library of C routines
ii  libglib2.0-bin                                                          2.56.4-0ubuntu0.18.04.8                             amd64        Programs for the GLib library
ii  libglib2.0-cil                                                          2.12.40-2                                           amd64        CLI binding for the GLib utility library 2.12
ii  libglib2.0-cil-dev                                                      2.12.40-2                                           amd64        CLI binding for the GLib utility library 2.12
ii  libglib2.0-data                                                         2.56.4-0ubuntu0.18.04.8                             all          Common files for GLib library
ii  libglib2.0-dev:amd64                                                    2.56.4-0ubuntu0.18.04.8                             amd64        Development files for the GLib library
ii  libglib2.0-dev-bin                                                      2.56.4-0ubuntu0.18.04.8                             amd64        Development utilities for the GLib library
ii  libglib2.0-doc                                                          2.56.4-0ubuntu0.18.04.8                             all          Documentation files for the GLib library
ii  libglib2.0-tests                                                        2.56.4-0ubuntu0.18.04.8                             amd64        GLib library of C routines - installed tests
ii  libglibmm-2.4-1v5:amd64                                                 2.56.0-1                                            amd64        C++ wrapper for the GLib toolkit (shared libraries)
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godot11 commented Sep 7, 2021 •
edited

As a workaround, getting rid of the conflicting module in anaconda as

mv ~/anaconda3/envs/simex/lib/libgio-2.0.so.0 ~/anaconda3/envs/simex/lib/libgio-2.0.so.0.backup

solved it for now, but I'm not sure if this hack doesn't break anything else...

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