Open AnnabelPerry opened 2 years ago
Hi @AnnabelPerry! First, SimBA has no SQL dependencies or currently store data in SQL format, and not sure why it would try to connect to SQL server. If you see those error again: terminate your session, and make sure you are installing SimBA in a fresh conda environment.
The rest of the errors, however, seems very similar to the errors reported by another user this morning, who is also working in Linux or MacOS. https://github.com/sgoldenlab/simba/issues/154
Can you try to install simba with pip install simba-uw-tf-dev --no-deps
and see if that fixes it? It seems related to MacOS/Linus and the installation of wxpython. Also make sur you are running python 3.6.10
Thank you for your rapid response! So I'd actually tried re-installing SimBA with no dependencies a couple days ago. It installed properly, but I encountered an issue in the GUI where it would fail with an error when I tried to crop videos. I tried replicating the error just now, but it appears to have installed successfully this time. Here's what I did: I removed the old environment and reran these steps (with the no dependencies flag):
conda create -n simbaenv python=3.6.10
conda activate simbaenv
pip install simba-uw-tf-dev --no-deps
pip uninstall shapely
conda install -c conda-forge shapely
I then ran the simba
command, getting this error:
Traceback (most recent call last):
File "/home/blackmonlab/anaconda3/envs/simbaenv/bin/simba", line 5, in
from simba.SimBA import main
File "/home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages/simba/SimBA.py", line 6, in
import seaborn as sns
ModuleNotFoundError: No module named 'seaborn'
I ran pip install seaborn
, getting this error:
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
simba-uw-tf-dev 0.88.8 requires cefpython3==66.0, which is not installed.
simba-uw-tf-dev 0.88.8 requires dash==1.14.0, which is not installed.
simba-uw-tf-dev 0.88.8 requires dash-color-picker==0.0.1, which is not installed.
simba-uw-tf-dev 0.88.8 requires dash-colorscales==0.0.4, which is not installed.
simba-uw-tf-dev 0.88.8 requires dash-core-components==1.10.2, which is not installed.
simba-uw-tf-dev 0.88.8 requires dash-html-components==1.0.3, which is not installed.
simba-uw-tf-dev 0.88.8 requires dtreeviz==0.8.1, which is not installed.
simba-uw-tf-dev 0.88.8 requires eli5==0.10.1, which is not installed.
simba-uw-tf-dev 0.88.8 requires graphviz==0.11, which is not installed.
simba-uw-tf-dev 0.88.8 requires h5py==2.9.0, which is not installed.
simba-uw-tf-dev 0.88.8 requires imblearn==0.0, which is not installed.
simba-uw-tf-dev 0.88.8 requires imgaug==0.4.0, which is not installed.
simba-uw-tf-dev 0.88.8 requires imutils==0.5.2, which is not installed.
simba-uw-tf-dev 0.88.8 requires numba==0.48.0, which is not installed.
simba-uw-tf-dev 0.88.8 requires numexpr==2.6.9, which is not installed.
simba-uw-tf-dev 0.88.8 requires opencv-python==3.4.5.20, which is not installed.
simba-uw-tf-dev 0.88.8 requires plotly==4.9.0, which is not installed.
simba-uw-tf-dev 0.88.8 requires pyarrow==0.17.1, which is not installed.
simba-uw-tf-dev 0.88.8 requires pyyaml==5.3.1, which is not installed.
simba-uw-tf-dev 0.88.8 requires scikit-image==0.14.2, which is not installed.
simba-uw-tf-dev 0.88.8 requires scikit-learn==0.22.2, which is not installed.
simba-uw-tf-dev 0.88.8 requires shap==0.35.0, which is not installed.
simba-uw-tf-dev 0.88.8 requires statsmodels==0.9.0, which is not installed.
simba-uw-tf-dev 0.88.8 requires tables==3.6.1, which is not installed.
simba-uw-tf-dev 0.88.8 requires tabulate==0.8.3, which is not installed.
simba-uw-tf-dev 0.88.8 requires tqdm==4.30.0, which is not installed.
simba-uw-tf-dev 0.88.8 requires wxpython==4.0.4, which is not installed.
simba-uw-tf-dev 0.88.8 requires xgboost==0.90, which is not installed.
simba-uw-tf-dev 0.88.8 requires yellowbrick==0.9.1, which is not installed.
simba-uw-tf-dev 0.88.8 requires matplotlib==3.0.3, but you have matplotlib 3.3.4 which is incompatible.
simba-uw-tf-dev 0.88.8 requires numpy==1.18.1, but you have numpy 1.19.5 which is incompatible.
simba-uw-tf-dev 0.88.8 requires pandas==0.25.3, but you have pandas 1.1.5 which is incompatible.
simba-uw-tf-dev 0.88.8 requires Pillow==5.4.1, but you have pillow 8.4.0 which is incompatible.
simba-uw-tf-dev 0.88.8 requires scipy==1.1.0, but you have scipy 1.5.4 which is incompatible.
simba-uw-tf-dev 0.88.8 requires seaborn==0.9.0, but you have seaborn 0.11.2 which is incompatible.
simba-uw-tf-dev 0.88.8 requires shapely==1.7, but you have shapely 1.7.1 which is incompatible.
I pip installed all the requested package versions. All except wxpython
installed without error. pip install wxpython==4.0.4
yielded the error at the bottom of the post (incredibly lengthy, so I included it outside the flow of the text so you could see the rest of my message)
I then ran the simba
command, successfully entering the GUI. I have yet to encounter any issues preprocessing videos, but if the wxpython
error becomes a problem I'll open a new issue! Thanks again for the help!
pip install wxpython==4.0.4
error:
Collecting wxpython==4.0.4
Using cached wxPython-4.0.4.tar.gz (68.8 MB)
Requirement already satisfied: six in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from wxpython==4.0.4) (1.16.0)
Requirement already satisfied: Pillow in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from wxpython==4.0.4) (5.4.1)
Building wheels for collected packages: wxpython
Building wheel for wxpython (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /home/blackmonlab/anaconda3/envs/simbaenv/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-2l9g9bkk/wxpython_2695da00068440fd9b9c0b88c3250ba0/setup.py'"'"'; __file__='"'"'/tmp/pip-install-2l9g9bkk/wxpython_2695da00068440fd9b9c0b88c3250ba0/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-ee4j772p
cwd: /tmp/pip-install-2l9g9bkk/wxpython_2695da00068440fd9b9c0b88c3250ba0/
Complete output (525 lines):
/home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages/setuptools/dist.py:720: UserWarning: Usage of dash-separated 'license-file' will not be supported in future versions. Please use the underscore name 'license_file' instead
% (opt, underscore_opt)
/home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages/setuptools/dist.py:294: DistDeprecationWarning: use_2to3 is ignored.
warnings.warn(f"{attr} is ignored.", DistDeprecationWarning)
running bdist_wheel
running build
WARNING: Building this way assumes that all generated files have been
generated already. If that is not the case then use build.py directly
to generate the source and perform the build stage. You can use
--skip-build with the bdist_* or install commands to avoid this
message and the wxWidgets and Phoenix build steps in the future.
"/home/blackmonlab/anaconda3/envs/simbaenv/bin/python" -u build.py build
Will build using: "/home/blackmonlab/anaconda3/envs/simbaenv/bin/python"
3.6.10 |Anaconda, Inc.| (default, May 8 2020, 02:54:21)
[GCC 7.3.0]
Python's architecture is 64bit
cfg.VERSION: 4.0.4
Running command: build
Running command: build_wx
wxWidgets build options: ['--wxpython', '--unicode', '--gtk3']
Configure options: ['--enable-unicode', '--with-gtk=3', '--with-opengl', '--enable-sound', '--enable-graphics_ctx', '--enable-mediactrl', '--enable-display', '--enable-geometry', '--enable-debug_flag', '--enable-optimise', '--disable-debugreport', '--enable-uiactionsim', '--enable-autoidman', '--with-sdl']
/tmp/pip-install-2l9g9bkk/wxpython_2695da00068440fd9b9c0b88c3250ba0/ext/wxWidgets/configure --enable-unicode --with-gtk=3 --with-opengl --enable-sound --enable-graphics_ctx --enable-mediactrl --enable-display --enable-geometry --enable-debug_flag --enable-optimise --disable-debugreport --enable-uiactionsim --enable-autoidman --with-sdl
checking build system type... x86_64-pc-linux-gnu
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checking for SDL - version >= 1.2.0... no
*** The sdl-config script installed by SDL could not be found
*** If SDL was installed in PREFIX, make sure PREFIX/bin is in
*** your path, or set the SDL_CONFIG environment variable to the
*** full path to sdl-config.
checking for GTKPRINT... yes
checking for LIBNOTIFY... checking for LIBNOTIFY... configure: WARNING: libnotify not found, wxNotificationMessage will use generic implementation.
checking for complete xlocale... no
checking for sys/epoll.h... yes
checking for gettimeofday... yes
checking whether gettimeofday takes two arguments... yes
checking for timezone variable in <time.h>... timezone
checking for localtime... yes
checking for tm_gmtoff in struct tm... yes
checking for setpriority... yes
checking for socket... yes
checking what is the type of the third argument of getsockname... socklen_t
checking what is the type of the fifth argument of getsockopt... socklen_t
checking for linux/joystick.h... yes
checking for python... /home/blackmonlab/anaconda3/envs/simbaenv/bin/python
checking for WEBKIT... configure: WARNING: webkit2gtk not found, falling back to webkitgtk
checking for WEBKIT... configure: WARNING: webkitgtk not found.
configure: WARNING: WebKit not available, disabling wxWebView
checking for CAIRO... yes
checking for cairo_push_group... yes
checking for GST... configure: WARNING: GStreamer 1.0 not available, falling back to 0.10
checking for GST... configure: WARNING: GStreamer 0.10 not available, falling back to 0.8
configure: WARNING: wxMediaCtrl can't be built because GStreamer not available
configure: error: wxMediaCtrl was explicitly requested but can't be built.
Fix the problems reported above or don't use --enable-mediactrl configure option.
Error running configure
ERROR: failed building wxWidgets
Traceback (most recent call last):
File "build.py", line 1321, in cmd_build_wx
wxbuild.main(wxDir(), build_options)
File "/tmp/pip-install-2l9g9bkk/wxpython_2695da00068440fd9b9c0b88c3250ba0/buildtools/build_wxwidgets.py", line 375, in main
"Error running configure")
File "/tmp/pip-install-2l9g9bkk/wxpython_2695da00068440fd9b9c0b88c3250ba0/buildtools/build_wxwidgets.py", line 85, in exitIfError
raise builder.BuildError(msg)
buildtools.builder.BuildError: Error running configure
Finished command: build_wx (0m8.126s)
Finished command: build (0m8.126s)
Command '"/home/blackmonlab/anaconda3/envs/simbaenv/bin/python" -u build.py build' failed with exit code 1.
----------------------------------------
ERROR: Failed building wheel for wxpython
Running setup.py clean for wxpython
Failed to build wxpython
Installing collected packages: wxpython
Running setup.py install for wxpython ... error
ERROR: Command errored out with exit status 1:
command: /home/blackmonlab/anaconda3/envs/simbaenv/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-2l9g9bkk/wxpython_2695da00068440fd9b9c0b88c3250ba0/setup.py'"'"'; __file__='"'"'/tmp/pip-install-2l9g9bkk/wxpython_2695da00068440fd9b9c0b88c3250ba0/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-_jggwalf/install-record.txt --single-version-externally-managed --compile --install-headers /home/blackmonlab/anaconda3/envs/simbaenv/include/python3.6m/wxpython
cwd: /tmp/pip-install-2l9g9bkk/wxpython_2695da00068440fd9b9c0b88c3250ba0/
Complete output (525 lines):
/home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages/setuptools/dist.py:720: UserWarning: Usage of dash-separated 'license-file' will not be supported in future versions. Please use the underscore name 'license_file' instead
% (opt, underscore_opt)
/home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages/setuptools/dist.py:294: DistDeprecationWarning: use_2to3 is ignored.
warnings.warn(f"{attr} is ignored.", DistDeprecationWarning)
running install
running build
WARNING: Building this way assumes that all generated files have been
generated already. If that is not the case then use build.py directly
to generate the source and perform the build stage. You can use
--skip-build with the bdist_* or install commands to avoid this
message and the wxWidgets and Phoenix build steps in the future.
"/home/blackmonlab/anaconda3/envs/simbaenv/bin/python" -u build.py build
Will build using: "/home/blackmonlab/anaconda3/envs/simbaenv/bin/python"
3.6.10 |Anaconda, Inc.| (default, May 8 2020, 02:54:21)
[GCC 7.3.0]
Python's architecture is 64bit
cfg.VERSION: 4.0.4
Running command: build
Running command: build_wx
wxWidgets build options: ['--wxpython', '--unicode', '--gtk3']
Configure options: ['--enable-unicode', '--with-gtk=3', '--with-opengl', '--enable-sound', '--enable-graphics_ctx', '--enable-mediactrl', '--enable-display', '--enable-geometry', '--enable-debug_flag', '--enable-optimise', '--disable-debugreport', '--enable-uiactionsim', '--enable-autoidman', '--with-sdl']
/tmp/pip-install-2l9g9bkk/wxpython_2695da00068440fd9b9c0b88c3250ba0/ext/wxWidgets/configure --enable-unicode --with-gtk=3 --with-opengl --enable-sound --enable-graphics_ctx --enable-mediactrl --enable-display --enable-geometry --enable-debug_flag --enable-optimise --disable-debugreport --enable-uiactionsim --enable-autoidman --with-sdl
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for --disable-gui... no
checking for --enable-monolithic... no
checking for --enable-plugins... no
checking for --without-subdirs... no
checking for --enable-official_build... no
checking for --disable-all-features... no
checking for --enable-universal... no
checking for --enable-nanox... no
checking for --enable-gpe... no
checking for toolkit... gtk
checking for --with-libpng... yes
checking for --with-libjpeg... yes
checking for --with-libtiff... yes
checking for --without-libjbig... no
checking for --without-liblzma... no
checking for --with-libxpm... yes
checking for --with-libiconv... yes
checking for --with-libmspack... no
checking for --without-gtkprint... no
checking for --with-gnomevfs... no
checking for --with-libnotify... yes
checking for --with-hildon... no
checking for --with-opengl... yes
checking for --with-dmalloc... no
checking for --with-sdl... yes
checking for --with-regex... yes
checking for --with-zlib... yes
checking for --with-expat... yes
checking for --with-macosx-sdk...
checking for --with-macosx-version-min...
checking for --enable-debug... default
checking for --disable-debug_flag... no
checking for --enable-debug_info... no
checking for --enable-debug_gdb... no
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checking for --enable-std_string... yes
checking for --enable-std_string_conv_in_wxstring... no
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checking for --enable-ftp... yes
checking for --enable-http... yes
checking for --enable-fileproto... yes
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checking for --enable-ipc... yes
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checking for --enable-apple_ieee... yes
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checking for --enable-catch_segvs... yes
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checking for --enable-fs_archive... yes
checking for --enable-fs_inet... yes
checking for --enable-fs_zip... yes
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checking for --enable-arttango... auto
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checking for --enable-wizarddlg... yes
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checking for --enable-miniframe... yes
checking for --enable-tooltips... yes
checking for --enable-splines... yes
checking for --enable-mousewheel... yes
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checking for --enable-busyinfo... yes
checking for --enable-hotkey... auto
checking for --enable-joystick... yes
checking for --enable-metafile... auto
checking for --enable-dragimage... yes
checking for --enable-accessibility... no
checking for --enable-uiactionsim... yes
checking for --enable-dctransform... yes
checking for --enable-webviewwebkit... yes
checking for --enable-palette... yes
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checking for --enable-wxdib... yes
checking for --enable-webviewie... yes
checking for --enable-autoidman... yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether we are using the Intel C compiler... no
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking whether gcc needs -traditional... no
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checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether we are using the Intel C++ compiler... no
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checking for ANSI C header files... yes
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checking for an ANSI C-conforming const... yes
checking for inline... inline
checking size of short... 2
checking size of void *... 8
checking size of int... 4
checking size of long... 8
checking size of size_t... 8
checking size of long long... 8
checking size of wchar_t... 4
checking for va_copy... yes
checking whether the compiler supports variadic macros... yes
checking for _FILE_OFFSET_BITS value needed for large files... 64
checking if large file support is available... yes
checking for _LARGEFILE_SOURCE value needed for large files... no
checking whether byte ordering is bigendian... no
checking for iostream... yes
checking if C++ compiler supports the explicit keyword... yes
checking for std::wstring in <string>... yes
checking for std::istream... yes
checking for std::ostream... yes
checking how to run the C++ preprocessor... g++ -E
checking type_traits usability... yes
checking type_traits presence... yes
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checking for __sync_fetch_and_add and __sync_sub_and_fetch builtins... yes
checking for libraries directories... /usr/lib/x86_64-linux-gnu /usr/lib
checking for cos... no
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checking for sin... yes
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checking if floating point functions link with -lm... yes
checking for strtoull... yes
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
configure: WARNING: Defaulting to the builtin regex library for Unicode build.
checking for zlib.h >= 1.1.4... yes
checking for zlib.h... (cached) yes
checking for deflate in -lz... yes
checking for png.h > 0.90... yes
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checking for png_sig_cmp in -lpng... yes
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checking for jpeg_read_header in -ljpeg... yes
checking for tiffio.h... yes
checking for TIFFError in -ltiff... yes
checking for expat.h... yes
checking if expat.h is valid C++ header... yes
checking for XML_ParserCreate in -lexpat... yes
checking for GTK+ version...
checking for pkg-config... /usr/bin/pkg-config
checking for GTK+ - version >= 3.0.0... yes (version 3.22.30)
checking for X11/Xlib.h... yes
checking for X11/XKBlib.h... yes
checking for Xxf86vm... yes
checking for X11/extensions/xf86vmode.h... yes
checking for SM... yes
checking for OpenGL headers... found in /usr/include
checking for GL/gl.h... yes
checking for GL/glu.h... yes
checking for GL... yes
checking for GLU... yes
checking if the linker accepts --version-script... yes
checking for symbols visibility support... yes
checking for broken libstdc++ visibility... no
checking for mode_t... yes
checking for off_t... yes
checking for pid_t... yes
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checking for ssize_t... yes
checking if size_t is unsigned int... no
checking if size_t is unsigned long... yes
checking if wchar_t is separate type... yes
checking for pw_gecos in struct passwd... yes
checking for wcslen... yes
checking for wcsftime... yes
checking for strnlen... yes
checking for wcsdup... yes
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checking for wcscasecmp... yes
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checking for vsnprintf... yes
checking for vsscanf... yes
checking for vsnprintf declaration... yes
checking if vsnprintf declaration is broken... no
checking for snprintf declaration... yes
checking if snprintf supports positional arguments... yes
checking for vsscanf declaration... yes
checking if vsscanf() declaration is broken... no
checking for putws... no
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checking if iconv needs const... no
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checking for sa_handler type... int
checking for backtrace() in <execinfo.h>... checking for library containing backtrace... none required
yes
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checking for mkstemp... yes
checking for statfs... yes
checking for statfs declaration... yes
checking for fcntl... yes
checking for setenv... yes
checking for unsetenv... yes
checking for nanosleep... yes
checking for uname... yes
checking for strtok_r... yes
checking for inet_addr... yes
checking for inet_aton... yes
checking for fdopen... yes
checking for sysconf... yes
checking for getpwuid_r... yes
checking for getgrgid_r... yes
checking whether pthreads work with -pthread... yes
checking if more special flags are required for pthreads... no
checking for pthread_setconcurrency... yes
checking for pthread_cleanup_push/pop... yes
checking for sched.h... yes
checking for sched_yield... yes
checking for pthread_attr_getschedpolicy... yes
checking for pthread_attr_setschedparam... yes
checking for sched_get_priority_max... yes
checking for pthread_cancel... yes
checking for pthread_mutex_timedlock... yes
checking for pthread_attr_setstacksize... yes
checking for pthread_mutexattr_t... yes
checking for pthread_mutexattr_settype declaration... yes
checking for abi::__forced_unwind() in <cxxabi.h>... yes
checking for localtime_r... yes
checking for gmtime_r... yes
checking how many arguments gethostbyname_r() takes... six
checking how many arguments getservbyname_r() takes... six
checking for dlopen... no
checking for dlopen in -ldl... yes
checking for dlerror... no
checking for dlerror in -ldl... yes
checking for sys/inotify.h... yes
checking for SNDCTL_DSP_SPEED in sys/soundcard.h... yes
checking for SDL... configure: SDL 2.0 not available. Falling back to 1.2.
checking for sdl-config... no
checking for SDL - version >= 1.2.0... no
*** The sdl-config script installed by SDL could not be found
*** If SDL was installed in PREFIX, make sure PREFIX/bin is in
*** your path, or set the SDL_CONFIG environment variable to the
*** full path to sdl-config.
checking for GTKPRINT... yes
checking for LIBNOTIFY... checking for LIBNOTIFY... configure: WARNING: libnotify not found, wxNotificationMessage will use generic implementation.
checking for complete xlocale... no
checking for sys/epoll.h... yes
checking for gettimeofday... yes
checking whether gettimeofday takes two arguments... yes
checking for timezone variable in <time.h>... timezone
checking for localtime... yes
checking for tm_gmtoff in struct tm... yes
checking for setpriority... yes
checking for socket... yes
checking what is the type of the third argument of getsockname... socklen_t
checking what is the type of the fifth argument of getsockopt... socklen_t
checking for linux/joystick.h... yes
checking for python... /home/blackmonlab/anaconda3/envs/simbaenv/bin/python
checking for WEBKIT... configure: WARNING: webkit2gtk not found, falling back to webkitgtk
checking for WEBKIT... configure: WARNING: webkitgtk not found.
configure: WARNING: WebKit not available, disabling wxWebView
checking for CAIRO... yes
checking for cairo_push_group... yes
checking for GST... configure: WARNING: GStreamer 1.0 not available, falling back to 0.10
checking for GST... configure: WARNING: GStreamer 0.10 not available, falling back to 0.8
configure: WARNING: wxMediaCtrl can't be built because GStreamer not available
configure: error: wxMediaCtrl was explicitly requested but can't be built.
Fix the problems reported above or don't use --enable-mediactrl configure option.
Error running configure
ERROR: failed building wxWidgets
Traceback (most recent call last):
File "build.py", line 1321, in cmd_build_wx
wxbuild.main(wxDir(), build_options)
File "/tmp/pip-install-2l9g9bkk/wxpython_2695da00068440fd9b9c0b88c3250ba0/buildtools/build_wxwidgets.py", line 375, in main
"Error running configure")
File "/tmp/pip-install-2l9g9bkk/wxpython_2695da00068440fd9b9c0b88c3250ba0/buildtools/build_wxwidgets.py", line 85, in exitIfError
raise builder.BuildError(msg)
buildtools.builder.BuildError: Error running configure
Finished command: build_wx (0m7.750s)
Finished command: build (0m7.751s)
Command '"/home/blackmonlab/anaconda3/envs/simbaenv/bin/python" -u build.py build' failed with exit code 1.
----------------------------------------
ERROR: Command errored out with exit status 1: /home/blackmonlab/anaconda3/envs/simbaenv/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-2l9g9bkk/wxpython_2695da00068440fd9b9c0b88c3250ba0/setup.py'"'"'; __file__='"'"'/tmp/pip-install-2l9g9bkk/wxpython_2695da00068440fd9b9c0b88c3250ba0/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-_jggwalf/install-record.txt --single-version-externally-managed --compile --install-headers /home/blackmonlab/anaconda3/envs/simbaenv/include/python3.6m/wxpython Check the logs for full command output.
Hi @AnnabelPerry , I just had this same issue this week. It seems wxpython is still a pain to work with. My recollection was that conda installing wxpython might have helped. See issue here;
I am trying to install simba on Ubuntu 18.04 I used the following commands to install simba:
When I initially ran
pip install simba-uw-tf-dev
, I got the error at the bottom of this post (it's very long, so I did not include it within text). I assumed this was the forewarned shapely error and continued.When I ran
sudo apt install simba
, I successfully encountered a purple GUI asking me to name and assign a password to a mysql server. However, after entering the requested information, I reached the following error message:I clicked "abort", deactivated my conda environment, and attempted install mysql:
sudo apt-get install mysql-server
This reopened the purple GUI and the password was requested After entering the password, I got the following error:I reentered conda environment and tried to run simba, getting the following error:
Error in configuration filePermission denied
So, I instead ran
sudo simba
and got following error:Access denied for user 'mirrors'@'localhost' (using password: YES)
So I tried deactivating the environment, removing it, then running back through the environment creation and installation steps listed at the top of this post. I still get the
filePermission denied
error when I runsimba
andsudo apt install simba
yields the following message:I'm not entirely sure where to go from here. Help would be greatly appreciated
Original install error: