Something Wrong with Prerequisites

[Qi Xu]

When i follow the official document to conduct prerequisites, i have encontered two problems:

1. when i execute commands make install-dependencies on the console, sometimes it will terminated because of the fail to obtain corresponding version of packages.
2. when i installed all dependencies and execute make presubmit, it will fail in analysis/test_plotting.py::test_pariwise_unique_coverage_heatmap_plot , and partial error message like this:

analysis/test_plotting.py::test_pariwise_unique_coverage_heatmap_plot Fatal Python error: Aborted

Current thread 0x00007fa19f2f6000 (most recent call first):
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/matplotlib/backends/backend_qt.py", line 143 in _create_qApp
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/matplotlib/backends/backend_qt.py", line 204 in __init__
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/matplotlib/backend_bases.py", line 2858 in create_with_canvas
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/matplotlib/backend_bases.py", line 1742 in new_manager
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/matplotlib/backend_bases.py", line 3579 in new_figure_manager_given_figure
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/matplotlib/backend_bases.py", line 3574 in new_figure_manager
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/matplotlib/pyplot.py", line 384 in new_figure_manager
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/matplotlib/pyplot.py", line 840 in figure
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/matplotlib/_api/deprecation.py", line 454 in wrapper
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/matplotlib/pyplot.py", line 1501 in subplots
  File "/home/xuqi/Desktop/fuzzbench/analysis/plotting.py", line 126 in _write_plot_to_image
  File "/home/xuqi/Desktop/fuzzbench/analysis/plotting.py", line 565 in write_pairwise_unique_coverage_heatmap_plot
  File "/home/xuqi/Desktop/fuzzbench/analysis/test_plotting.py", line 33 in test_pariwise_unique_coverage_heatmap_plot
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/_pytest/python.py", line 192 in pytest_pyfunc_call
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/pluggy/_callers.py", line 80 in _multicall
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/pluggy/_manager.py", line 112 in _hookexec
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/pluggy/_hooks.py", line 433 in __call__
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/_pytest/python.py", line 1761 in runtest
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/_pytest/runner.py", line 166 in pytest_runtest_call
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/pluggy/_callers.py", line 80 in _multicall
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/pluggy/_manager.py", line 112 in _hookexec
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/pluggy/_hooks.py", line 433 in __call__
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/_pytest/runner.py", line 259 in <lambda>
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/_pytest/runner.py", line 338 in from_call
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/_pytest/runner.py", line 258 in call_runtest_hook
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/_pytest/runner.py", line 219 in call_and_report
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/_pytest/runner.py", line 130 in runtestprotocol
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/_pytest/runner.py", line 111 in pytest_runtest_protocol
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/pluggy/_callers.py", line 80 in _multicall
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/pluggy/_manager.py", line 112 in _hookexec
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/pluggy/_hooks.py", line 433 in __call__
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/_pytest/main.py", line 347 in pytest_runtestloop
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/pluggy/_callers.py", line 80 in _multicall
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/pluggy/_manager.py", line 112 in _hookexec
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/pluggy/_hooks.py", line 433 in __call__
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/_pytest/main.py", line 322 in _main
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/_pytest/main.py", line 268 in wrap_session
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/_pytest/main.py", line 315 in pytest_cmdline_main
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/pluggy/_callers.py", line 80 in _multicall
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/pluggy/_manager.py", line 112 in _hookexec
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/pluggy/_hooks.py", line 433 in __call__
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/_pytest/config/__init__.py", line 164 in main
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/_pytest/config/__init__.py", line 187 in console_main
  File "/home/xuqi/Desktop/fuzzbench/.venv/lib/python3.10/site-packages/pytest/__main__.py", line 5 in <module>
  File "/usr/lib/python3.10/runpy.py", line 86 in _run_code
  File "/usr/lib/python3.10/runpy.py", line 196 in _run_module_as_main

Extension modules: sqlalchemy.cimmutabledict, greenlet._greenlet, sqlalchemy.cprocessors, sqlalchemy.cresultproxy, google.protobuf.pyext._message, grpc._cython.cygrpc, charset_normalizer.md, _cffi_backend, yaml._yaml, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.ccalendar, pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.strptime, pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, pandas._libs.tslibs.timestamps, pandas._libs.properties, pandas._libs.tslibs.offsets, pandas._libs.tslibs.parsing, pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, pandas._libs.interval, pandas._libs.tslib, pandas._libs.lib, pandas._libs.hashing, pandas._libs.ops, bottleneck.move, bottleneck.nonreduce, bottleneck.nonreduce_axis, bottleneck.reduce, pandas._libs.arrays, pandas._libs.index, pandas._libs.join, pandas._libs.sparse, pandas._libs.reduction, pandas._libs.indexing, pandas._libs.internals, pandas._libs.writers, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.groupby, pandas._libs.testing, pandas._libs.parsers, pandas._libs.json, psutil._psutil_linux, psutil._psutil_posix, scipy._lib._ccallback_c, numpy.linalg.lapack_lite, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._isolve._iterative, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg._cythonized_array_utils, scipy.linalg._flinalg, scipy.linalg._solve_toeplitz, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_lapack, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.ndimage._nd_image, _ni_label, scipy.ndimage._ni_label, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize.__nnls, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.optimize._direct, scipy.integrate._odepack, scipy.integrate._quadpack, scipy.integrate._vode, scipy.integrate._dop, scipy.integrate._lsoda, scipy.special.cython_special, scipy.stats._stats, scipy.stats.beta_ufunc, scipy.stats._boost.beta_ufunc, scipy.stats.binom_ufunc, scipy.stats._boost.binom_ufunc, scipy.stats.nbinom_ufunc, scipy.stats._boost.nbinom_ufunc, scipy.stats.hypergeom_ufunc, scipy.stats._boost.hypergeom_ufunc, scipy.stats.ncf_ufunc, scipy.stats._boost.ncf_ufunc, scipy.interpolate._fitpack, scipy.interpolate.dfitpack, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.stats._biasedurn, scipy.stats._levy_stable.levyst, scipy._lib._uarray._uarray, scipy.stats._hypotests_pythran, scipy.stats._statlib, scipy.stats._mvn, scipy.stats._sobol, scipy.stats._qmc_cy, scipy.stats.unuran_wrapper, scipy.stats._unuran.unuran_wrapper, matplotlib._c_internal_utils, PIL._imaging, matplotlib._path, kiwisolver._cext, matplotlib._image, scipy.cluster._vq, scipy.cluster._hierarchy, scipy.cluster._optimal_leaf_ordering, Orange.data._variable, Orange.data._contingency, Orange.data._valuecount, sklearn.__check_build._check_build, sklearn.utils.murmurhash, sklearn.utils._isfinite, sklearn.utils._openmp_helpers, sklearn.utils.sparsefuncs_fast, Orange.data._io, PyQt5.QtCore, PyQt5.QtGui, PyQt5.QtWidgets, PyQt5.QtSvg, PyQt5.QtTest, markupsafe._speedups (total: 185)
ERROR: test failed, see errors above.
Failed checks: test
Failed.
make: *** [Makefile:60: presubmit] Error 1

I have solved the above two problems, methods as follows:

1. When terminated, I delete the .venv floder and retry the make install-dependencies command. Multiple repetitions are needed before all dependencies are installed.
2. About the presubmit test fail, run sudo apt undate && sudo apt install qtbase5-dev can fix it. This problem is similar to #1223.

My environmemt:

Ubuntu 22.04.1
Python 3.10.6