error when running epic2-df example

[smartgamer]

Hi,

I recently ran the epic2-df example but got an error.

Below is the output:

$ epic2-df -fdrc 1 -tk /home/user/anaconda3/lib/python3.8/site-packages/epic2/examples/test.bed.gz -tw /home/user/anaconda3/lib/python3.8/site-packages/epic2/examples/control.bed.gz -ok deleteme_ko.txt -ow deleteme_wt.txt > deleteme.txt Running epic2 on KO. Traceback (most recent call last): File "/home/user/anaconda3/bin/epic2-df", line 332, in bins_counts_ko = _main(args) File "/home/user/anaconda3/lib/python3.8/site-packages/epic2/main.py", line 35, in _main effective_genome_length, chromsizes = egl_and_chromsizes(args) File "epic2/src/genome_info.pyx", line 315, in epic2.src.genome_info.egl_and_chromsizes File "epic2/src/genome_info.pyx", line 93, in epic2.src.genome_info.find_readlength KeyError: 'guess_bampe'

Thanks,

[endrebak]

Which version are you using?

Endre

On Saturday, October 24, 2020, Charlie notifications@github.com wrote:

Below is the output:

$ epic2-df -fdrc 1 -tk /home/user/anaconda3/lib/ python3.8/site-packages/epic2/examples/test.bed.gz -tw /home/user/anaconda3/lib/python3.8/site-packages/epic2/examples/control.bed.gz -ok deleteme_ko.txt -ow deleteme_wt.txt > deleteme.txt Running epic2 on KO. Traceback (most recent call last): File "/home/user/anaconda3/bin/epic2-df", line 332, in bins_counts_ko = _main(args) File "/home/user/anaconda3/lib/python3.8/site-packages/epic2/main.py", line 35, in _main effective_genome_length, chromsizes = egl_and_chromsizes(args) File "epic2/src/genome_info.pyx", line 315, in epic2.src.genome_info.egl_and_chromsizes File "epic2/src/genome_info.pyx", line 93, in epic2.src.genomeinfo.find readlength KeyError: 'guess_bampe'

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[smartgamer]

The current version. I installed it yesterday.

Charles

On Oct 24, 2020, at 3:30 PM, Endre Bakken Stovner notifications@github.com wrote:



Which version are you using?

Endre

On Saturday, October 24, 2020, Charlie notifications@github.com wrote:

Below is the output:

$ epic2-df -fdrc 1 -tk /home/user/anaconda3/lib/ python3.8/site-packages/epic2/examples/test.bed.gz -tw /home/user/anaconda3/lib/python3.8/site-packages/epic2/examples/control.bed.gz -ok deleteme_ko.txt -ow deleteme_wt.txt > deleteme.txt Running epic2 on KO. Traceback (most recent call last): File "/home/user/anaconda3/bin/epic2-df", line 332, in bins_counts_ko = _main(args) File "/home/user/anaconda3/lib/python3.8/site-packages/epic2/main.py", line 35, in _main effective_genome_length, chromsizes = egl_and_chromsizes(args) File "epic2/src/genome_info.pyx", line 315, in epic2.src.genome_info.egl_and_chromsizes File "epic2/src/genome_info.pyx", line 93, in epic2.src.genomeinfo.find readlength KeyError: 'guess_bampe'

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[endrebak]

I've attempted a fix on the master branch now. If you git clone and run python setup.py install you can see if it works. I've been unable to test it myself, but will try tomorrow.

[endrebak]

Thanks for reporting btw 👍

[smartgamer]

I used epic2 a while ago and didn't have any issues. So, I don't know why it doesn't work this time.

[smartgamer]

When I try to run python setup.py install, I got an error: "gcc: error: epic2/src/gzstream.cpp: No such file or directory error: command 'gcc' failed with exit status 1 "

[endrebak]

I am getting the same error. I asked here: https://stackoverflow.com/questions/64529594/how-do-i-use-a-c-header-file-in-a-setuptools-extension

It might take some reading to fix it. Will try more tonight after work.

On Mon, Oct 26, 2020 at 2:04 AM Charlie notifications@github.com wrote:

When I try to run python setup.py install, I got an error: "gcc: error: epic2/src/gzstream.cpp: No such file or directory error: command 'gcc' failed with exit status 1 "

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[smartgamer]

I also tried to change the file name to .cpp, but got the same error as you reported at stackoverflow.

[endrebak]

This might take some time to fix. I do not know where to learn the necessary theory or a more suitable place to ask. I could also switch the reader to pandas. The speed gains in read_csv have been impressive. But that would also take some time and might introduce bugs.

On Mon, Oct 26, 2020 at 9:01 AM Charlie notifications@github.com wrote:

I also tried to change the file name to .cpp, but got the same error as you reported at stackoverflow.

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[endrebak]

I got an answer, but now am getting a different error: https://stackoverflow.com/questions/64542557/why-am-i-getting-name-mangling-issues-in-cython-when-using-a-c-header

I am completely flustered by these new errors. Dunno why they arose.

[endrebak]

I think the simplest fix is to shell out and call gunzip from the command line with bash process substitution and read it as a regular file.

[smartgamer]

No problem. Thanks for the update.

Charles

On Oct 26, 2020, at 3:41 PM, Endre Bakken Stovner notifications@github.com wrote:



I think the simplest fix is to shell out and call gunzip from the command line with bash process substitution and read it as a regular file.

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[smartgamer]

I think the simplest fix is to shell out and call gunzip from the command line with bash process substitution and read it as a regular file.

Can you describe how to do it exactly? I'm not familiar with Cython and C++. Trying to learn it.

Thank you.

[endrebak]

Oh, sorry. That was a note for myself. I have attempted a fix now. It turns out I was missing a C++ file.

If you try git clone epic2 and python setup.py install, does it work now? Thanks for testing :)

[smartgamer]

Oh, sorry. That was a note for myself. I have attempted a fix now. It turns out I was missing a C++ file.

If you try git clone epic2 and python setup.py install, does it work now? Thanks for testing :)

Here's the error I got with the new clone:

[29/40] Cythonizing pandas/_libs/tslibs/parsing.pyx Traceback (most recent call last): File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 154, in save_modules yield saved File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 195, in setup_context yield File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 263, in run_setup _execfile(setup_script, ns) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 45, in _execfile exec(code, globals, locals) File "/tmp/easy_install-4u6i_fh9/pandas-1.1.3/setup.py", line 792, in File "/tmp/easy_install-4u6i_fh9/pandas-1.1.3/setup.py", line 762, in setup_package File "/tmp/easy_install-4u6i_fh9/pandas-1.1.3/setup.py", line 541, in maybe_cythonize File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Build/Dependencies.py", line 1102, in cythonize cythonize_one(*args) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Build/Dependencies.py", line 1208, in cythonize_one result = compile_single(pyx_file, options, full_module_name=full_module_name) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Main.py", line 727, in compile_single return run_pipeline(source, options, full_module_name) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Main.py", line 515, in run_pipeline err, enddata = Pipeline.run_pipeline(pipeline, source) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Pipeline.py", line 355, in run_pipeline data = run(phase, data) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Pipeline.py", line 335, in run return phase(data) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Pipeline.py", line 52, in generate_pyx_code_stage module_node.process_implementation(options, result) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ModuleNode.py", line 143, in process_implementation self.generate_c_code(env, options, result) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ModuleNode.py", line 385, in generate_c_code self.body.generate_function_definitions(env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 442, in generate_function_definitions stat.generate_function_definitions(env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 442, in generate_function_definitions stat.generate_function_definitions(env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 3174, in generate_function_definitions FuncDefNode.generate_function_definitions(self, env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 1981, in generate_function_definitions self.generate_function_body(env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 1743, in generate_function_body self.body.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 448, in generate_execution_code stat.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/UtilNodes.py", line 326, in generate_execution_code self.body.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 6706, in generate_execution_code self.body.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 448, in generate_execution_code stat.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 6276, in generate_execution_code self.else_clause.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 448, in generate_execution_code stat.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 7219, in generate_execution_code self.body.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 448, in generate_execution_code stat.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 5147, in generate_execution_code self.expr.generate_evaluation_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ExprNodes.py", line 5875, in generate_evaluation_code self.allocate_temp_result(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ExprNodes.py", line 721, in allocate_temp_result elif not (self.result_is_used or type.is_memoryviewslice or self.is_c_result_required()): File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ExprNodes.py", line 5841, in is_c_result_required if not func_type.exception_value or func_type.exception_check == '+': AttributeError: 'BuiltinObjectType' object has no attribute 'exception_value'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/user/Downloads/epic2/setup.py", line 118, in setup( File "/home/user/anaconda3/envs/NGS/lib/python3.9/distutils/core.py", line 148, in setup dist.run_commands() File "/home/user/anaconda3/envs/NGS/lib/python3.9/distutils/dist.py", line 966, in run_commands self.run_command(cmd) File "/home/user/anaconda3/envs/NGS/lib/python3.9/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/install.py", line 67, in run self.do_egg_install() File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/install.py", line 117, in do_egg_install cmd.run(show_deprecation=False) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 425, in run self.easy_install(spec, not self.no_deps) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 667, in easy_install return self.install_item(None, spec, tmpdir, deps, True) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 714, in install_item self.process_distribution(spec, dist, deps) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 758, in process_distribution distros = WorkingSet([]).resolve( File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/pkg_resources/init.py", line 779, in resolve dist = best[req.key] = env.best_match( File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/pkg_resources/init.py", line 1064, in best_match return self.obtain(req, installer) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/pkg_resources/init.py", line 1076, in obtain return installer(requirement) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 686, in easy_install return self.install_item(spec, dist.location, tmpdir, deps) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 712, in install_item dists = self.install_eggs(spec, download, tmpdir) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 897, in install_eggs return self.build_and_install(setup_script, setup_base) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 1167, in build_and_install self.run_setup(setup_script, setup_base, args) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 1151, in run_setup run_setup(setup_script, args) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 266, in run_setup raise File "/home/user/anaconda3/envs/NGS/lib/python3.9/contextlib.py", line 135, in exit self.gen.throw(type, value, traceback) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 195, in setup_context yield File "/home/user/anaconda3/envs/NGS/lib/python3.9/contextlib.py", line 135, in exit self.gen.throw(type, value, traceback) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 166, in save_modules saved_exc.resume() File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 141, in resume six.reraise(type, exc, self._tb) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/_vendor/six.py", line 685, in reraise raise value.with_traceback(tb) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 154, in save_modules yield saved File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 195, in setup_context yield File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 263, in run_setup _execfile(setup_script, ns) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 45, in _execfile exec(code, globals, locals) File "/tmp/easy_install-4u6i_fh9/pandas-1.1.3/setup.py", line 792, in File "/tmp/easy_install-4u6i_fh9/pandas-1.1.3/setup.py", line 762, in setup_package File "/tmp/easy_install-4u6i_fh9/pandas-1.1.3/setup.py", line 541, in maybe_cythonize File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Build/Dependencies.py", line 1102, in cythonize cythonize_one(*args) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Build/Dependencies.py", line 1208, in cythonize_one result = compile_single(pyx_file, options, full_module_name=full_module_name) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Main.py", line 727, in compile_single return run_pipeline(source, options, full_module_name) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Main.py", line 515, in run_pipeline err, enddata = Pipeline.run_pipeline(pipeline, source) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Pipeline.py", line 355, in run_pipeline data = run(phase, data) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Pipeline.py", line 335, in run return phase(data) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Pipeline.py", line 52, in generate_pyx_code_stage module_node.process_implementation(options, result) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ModuleNode.py", line 143, in process_implementation self.generate_c_code(env, options, result) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ModuleNode.py", line 385, in generate_c_code self.body.generate_function_definitions(env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 442, in generate_function_definitions stat.generate_function_definitions(env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 442, in generate_function_definitions stat.generate_function_definitions(env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 3174, in generate_function_definitions FuncDefNode.generate_function_definitions(self, env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 1981, in generate_function_definitions self.generate_function_body(env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 1743, in generate_function_body self.body.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 448, in generate_execution_code stat.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/UtilNodes.py", line 326, in generate_execution_code self.body.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 6706, in generate_execution_code self.body.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 448, in generate_execution_code stat.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 6276, in generate_execution_code self.else_clause.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 448, in generate_execution_code stat.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 7219, in generate_execution_code self.body.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 448, in generate_execution_code stat.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 5147, in generate_execution_code self.expr.generate_evaluation_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ExprNodes.py", line 5875, in generate_evaluation_code self.allocate_temp_result(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ExprNodes.py", line 721, in allocate_temp_result elif not (self.result_is_used or type.is_memoryviewslice or self.is_c_result_required()): File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ExprNodes.py", line 5841, in is_c_result_required if not func_type.exception_value or func_type.exception_check == '+': AttributeError: 'BuiltinObjectType' object has no attribute 'exception_value'

[endrebak]

Thanks. What if you do pip install —-upgrade Cython and try again?

On Monday, October 26, 2020, Charlie notifications@github.com wrote:

Oh, sorry. That was a note for myself. I have attempted a fix now. It turns out I was missing a C++ file.

If you try git clone epic2 and python setup.py install, does it work now? Thanks for testing :)

Here's the error I got with the new clone:

[29/40] Cythonizing pandas/_libs/tslibs/parsing.pyx Traceback (most recent call last): File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/sandbox.py", line 154, in save_modules yield saved File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/sandbox.py", line 195, in setup_context yield File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/sandbox.py", line 263, in run_setup _execfile(setup_script, ns) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/sandbox.py", line 45, in _execfile exec(code, globals, locals) File "/tmp/easy_install-4u6i_fh9/pandas-1.1.3/setup.py", line 792, in File "/tmp/easy_install-4u6i_fh9/pandas-1.1.3/setup.py", line 762, in setup_package File "/tmp/easy_install-4u6i_fh9/pandas-1.1.3/setup.py", line 541, in maybe_cythonize File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Build/Dependencies.py", line 1102, in cythonize cythonize_one(*args) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Build/Dependencies.py", line 1208, in cythonize_one result = compile_single(pyx_file, options, full_module_name=fullmodule name) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Main.py", line 727, in compile_single return run_pipeline(source, options, full_module_name) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Main.py", line 515, in run_pipeline err, enddata = Pipeline.run_pipeline(pipeline, source) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Pipeline.py", line 355, in run_pipeline data = run(phase, data) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Pipeline.py", line 335, in run return phase(data) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Pipeline.py", line 52, in generate_pyx_code_stage module_node.process_implementation(options, result) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/ModuleNode.py", line 143, in process_implementation self.generate_c_code(env, options, result) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/ModuleNode.py", line 385, in generate_c_code self.body.generate_function_definitions(env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 442, in generate_function_definitions stat.generate_function_definitions(env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 442, in generate_function_definitions stat.generate_function_definitions(env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 3174, in generate_function_definitions FuncDefNode.generate_function_definitions(self, env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 1981, in generate_function_definitions self.generate_function_body(env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 1743, in generate_function_body self.body.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 448, in generate_execution_code stat.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/UtilNodes.py", line 326, in generate_execution_code self.body.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 6706, in generate_execution_code self.body.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 448, in generate_execution_code stat.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 6276, in generate_execution_code self.else_clause.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 448, in generate_execution_code stat.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 7219, in generate_execution_code self.body.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 448, in generate_execution_code stat.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 5147, in generate_execution_code self.expr.generate_evaluation_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/ExprNodes.py", line 5875, in generate_evaluation_code self.allocate_temp_result(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/ExprNodes.py", line 721, in allocate_temp_result elif not (self.result_is_used or type.is_memoryviewslice or self.is_c_result_required()): File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/ExprNodes.py", line 5841, in is_c_result_required if not func_type.exception_value or func_type.exception_check == '+': AttributeError: 'BuiltinObjectType' object has no attribute 'exception_value'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/user/Downloads/epic2/setup.py", line 118, in setup( File "/home/user/anaconda3/envs/NGS/lib/python3.9/distutils/core.py", line 148, in setup dist.run_commands() File "/home/user/anaconda3/envs/NGS/lib/python3.9/distutils/dist.py", line 966, in run_commands self.run_command(cmd) File "/home/user/anaconda3/envs/NGS/lib/python3.9/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/command/install.py", line 67, in run self.do_egg_install() File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/command/install.py", line 117, in do_egg_install cmd.run(show_deprecation=False) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/command/easy_install.py", line 425, in run self.easy_install(spec, not self.no_deps) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/command/easy_install.py", line 667, in easy_install return self.install_item(None, spec, tmpdir, deps, True) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/command/easy_install.py", line 714, in install_item self.process_distribution(spec, dist, deps) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/command/easy_install.py", line 758, in process_distribution distros = WorkingSet([]).resolve( File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/pkg_resources/init.py", line 779, in resolve dist = best[req.key] = env.best_match( File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/pkg_resources/init.py", line 1064, in best_match return self.obtain(req, installer) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/pkg_resources/init.py", line 1076, in obtain return installer(requirement) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/command/easy_install.py", line 686, in easy_install return self.install_item(spec, dist.location, tmpdir, deps) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/command/easy_install.py", line 712, in install_item dists = self.install_eggs(spec, download, tmpdir) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/command/easy_install.py", line 897, in install_eggs return self.build_and_install(setup_script, setup_base) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/command/easy_install.py", line 1167, in build_and_install self.run_setup(setup_script, setup_base, args) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/command/easy_install.py", line 1151, in run_setup run_setup(setup_script, args) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/sandbox.py", line 266, in run_setup raise File "/home/user/anaconda3/envs/NGS/lib/python3.9/contextlib.py", line 135, in exit self.gen.throw(type, value, traceback) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/sandbox.py", line 195, in setup_context yield File "/home/user/anaconda3/envs/NGS/lib/python3.9/contextlib.py", line 135, in exit self.gen.throw(type, value, traceback) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/sandbox.py", line 166, in save_modules saved_exc.resume() File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/sandbox.py", line 141, in resume six.reraise(type, exc, self._tb) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/_vendor/six.py", line 685, in reraise raise value.with_traceback(tb) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/sandbox.py", line 154, in save_modules yield saved File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/sandbox.py", line 195, in setup_context yield File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/sandbox.py", line 263, in run_setup _execfile(setup_script, ns) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/sandbox.py", line 45, in _execfile exec(code, globals, locals) File "/tmp/easy_install-4u6i_fh9/pandas-1.1.3/setup.py", line 792, in File "/tmp/easy_install-4u6i_fh9/pandas-1.1.3/setup.py", line 762, in setup_package File "/tmp/easy_install-4u6i_fh9/pandas-1.1.3/setup.py", line 541, in maybe_cythonize File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Build/Dependencies.py", line 1102, in cythonize cythonize_one(*args) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Build/Dependencies.py", line 1208, in cythonize_one result = compile_single(pyx_file, options, full_module_name=fullmodule name) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Main.py", line 727, in compile_single return run_pipeline(source, options, full_module_name) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Main.py", line 515, in run_pipeline err, enddata = Pipeline.run_pipeline(pipeline, source) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Pipeline.py", line 355, in run_pipeline data = run(phase, data) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Pipeline.py", line 335, in run return phase(data) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Pipeline.py", line 52, in generate_pyx_code_stage module_node.process_implementation(options, result) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/ModuleNode.py", line 143, in process_implementation self.generate_c_code(env, options, result) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/ModuleNode.py", line 385, in generate_c_code self.body.generate_function_definitions(env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 442, in generate_function_definitions stat.generate_function_definitions(env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 442, in generate_function_definitions stat.generate_function_definitions(env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 3174, in generate_function_definitions FuncDefNode.generate_function_definitions(self, env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 1981, in generate_function_definitions self.generate_function_body(env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 1743, in generate_function_body self.body.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 448, in generate_execution_code stat.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/UtilNodes.py", line 326, in generate_execution_code self.body.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 6706, in generate_execution_code self.body.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 448, in generate_execution_code stat.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 6276, in generate_execution_code self.else_clause.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 448, in generate_execution_code stat.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 7219, in generate_execution_code self.body.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 448, in generate_execution_code stat.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 5147, in generate_execution_code self.expr.generate_evaluation_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/ExprNodes.py", line 5875, in generate_evaluation_code self.allocate_temp_result(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/ExprNodes.py", line 721, in allocate_temp_result elif not (self.result_is_used or type.is_memoryviewslice or self.is_c_result_required()): File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/ExprNodes.py", line 5841, in is_c_result_required if not func_type.exception_value or func_type.exception_check == '+': AttributeError: 'BuiltinObjectType' object has no attribute 'exception_value'

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[smartgamer]

Should I use pip or pip3? Is this project based on python 2 or 3?

Charles

On Oct 27, 2020, at 3:03 AM, Endre Bakken Stovner notifications@github.com wrote:



Thanks. What if you do pip install —-upgrade Cython and try again?

On Monday, October 26, 2020, Charlie notifications@github.com wrote:

Oh, sorry. That was a note for myself. I have attempted a fix now. It turns out I was missing a C++ file.

If you try git clone epic2 and python setup.py install, does it work now? Thanks for testing :)

Here's the error I got with the new clone:

[29/40] Cythonizing pandas/_libs/tslibs/parsing.pyx Traceback (most recent call last): File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/sandbox.py", line 154, in save_modules yield saved File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/sandbox.py", line 195, in setup_context yield File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/sandbox.py", line 263, in run_setup _execfile(setup_script, ns) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/sandbox.py", line 45, in _execfile exec(code, globals, locals) File "/tmp/easy_install-4u6i_fh9/pandas-1.1.3/setup.py", line 792, in File "/tmp/easy_install-4u6i_fh9/pandas-1.1.3/setup.py", line 762, in setup_package File "/tmp/easy_install-4u6i_fh9/pandas-1.1.3/setup.py", line 541, in maybe_cythonize File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Build/Dependencies.py", line 1102, in cythonize cythonize_one(*args) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Build/Dependencies.py", line 1208, in cythonize_one result = compile_single(pyx_file, options, full_module_name=fullmodule name) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Main.py", line 727, in compile_single return run_pipeline(source, options, full_module_name) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Main.py", line 515, in run_pipeline err, enddata = Pipeline.run_pipeline(pipeline, source) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Pipeline.py", line 355, in run_pipeline data = run(phase, data) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Pipeline.py", line 335, in run return phase(data) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Pipeline.py", line 52, in generate_pyx_code_stage module_node.process_implementation(options, result) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/ModuleNode.py", line 143, in process_implementation self.generate_c_code(env, options, result) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/ModuleNode.py", line 385, in generate_c_code self.body.generate_function_definitions(env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 442, in generate_function_definitions stat.generate_function_definitions(env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 442, in generate_function_definitions stat.generate_function_definitions(env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 3174, in generate_function_definitions FuncDefNode.generate_function_definitions(self, env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 1981, in generate_function_definitions self.generate_function_body(env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 1743, in generate_function_body self.body.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 448, in generate_execution_code stat.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/UtilNodes.py", line 326, in generate_execution_code self.body.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 6706, in generate_execution_code self.body.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 448, in generate_execution_code stat.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 6276, in generate_execution_code self.else_clause.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 448, in generate_execution_code stat.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 7219, in generate_execution_code self.body.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 448, in generate_execution_code stat.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 5147, in generate_execution_code self.expr.generate_evaluation_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/ExprNodes.py", line 5875, in generate_evaluation_code self.allocate_temp_result(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/ExprNodes.py", line 721, in allocate_temp_result elif not (self.result_is_used or type.is_memoryviewslice or self.is_c_result_required()): File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/ExprNodes.py", line 5841, in is_c_result_required if not func_type.exception_value or func_type.exception_check == '+': AttributeError: 'BuiltinObjectType' object has no attribute 'exception_value'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/user/Downloads/epic2/setup.py", line 118, in setup( File "/home/user/anaconda3/envs/NGS/lib/python3.9/distutils/core.py", line 148, in setup dist.run_commands() File "/home/user/anaconda3/envs/NGS/lib/python3.9/distutils/dist.py", line 966, in run_commands self.run_command(cmd) File "/home/user/anaconda3/envs/NGS/lib/python3.9/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/command/install.py", line 67, in run self.do_egg_install() File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/command/install.py", line 117, in do_egg_install cmd.run(show_deprecation=False) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/command/easy_install.py", line 425, in run self.easy_install(spec, not self.no_deps) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/command/easy_install.py", line 667, in easy_install return self.install_item(None, spec, tmpdir, deps, True) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/command/easy_install.py", line 714, in install_item self.process_distribution(spec, dist, deps) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/command/easy_install.py", line 758, in process_distribution distros = WorkingSet([]).resolve( File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/pkg_resources/init.py", line 779, in resolve dist = best[req.key] = env.best_match( File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/pkg_resources/init.py", line 1064, in best_match return self.obtain(req, installer) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/pkg_resources/init.py", line 1076, in obtain return installer(requirement) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/command/easy_install.py", line 686, in easy_install return self.install_item(spec, dist.location, tmpdir, deps) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/command/easy_install.py", line 712, in install_item dists = self.install_eggs(spec, download, tmpdir) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/command/easy_install.py", line 897, in install_eggs return self.build_and_install(setup_script, setup_base) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/command/easy_install.py", line 1167, in build_and_install self.run_setup(setup_script, setup_base, args) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/command/easy_install.py", line 1151, in run_setup run_setup(setup_script, args) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/sandbox.py", line 266, in run_setup raise File "/home/user/anaconda3/envs/NGS/lib/python3.9/contextlib.py", line 135, in exit self.gen.throw(type, value, traceback) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/sandbox.py", line 195, in setup_context yield File "/home/user/anaconda3/envs/NGS/lib/python3.9/contextlib.py", line 135, in exit self.gen.throw(type, value, traceback) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/sandbox.py", line 166, in save_modules saved_exc.resume() File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/sandbox.py", line 141, in resume six.reraise(type, exc, self._tb) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/_vendor/six.py", line 685, in reraise raise value.with_traceback(tb) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/sandbox.py", line 154, in save_modules yield saved File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/sandbox.py", line 195, in setup_context yield File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/sandbox.py", line 263, in run_setup _execfile(setup_script, ns) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/setuptools/sandbox.py", line 45, in _execfile exec(code, globals, locals) File "/tmp/easy_install-4u6i_fh9/pandas-1.1.3/setup.py", line 792, in File "/tmp/easy_install-4u6i_fh9/pandas-1.1.3/setup.py", line 762, in setup_package File "/tmp/easy_install-4u6i_fh9/pandas-1.1.3/setup.py", line 541, in maybe_cythonize File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Build/Dependencies.py", line 1102, in cythonize cythonize_one(*args) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Build/Dependencies.py", line 1208, in cythonize_one result = compile_single(pyx_file, options, full_module_name=fullmodule name) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Main.py", line 727, in compile_single return run_pipeline(source, options, full_module_name) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Main.py", line 515, in run_pipeline err, enddata = Pipeline.run_pipeline(pipeline, source) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Pipeline.py", line 355, in run_pipeline data = run(phase, data) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Pipeline.py", line 335, in run return phase(data) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Pipeline.py", line 52, in generate_pyx_code_stage module_node.process_implementation(options, result) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/ModuleNode.py", line 143, in process_implementation self.generate_c_code(env, options, result) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/ModuleNode.py", line 385, in generate_c_code self.body.generate_function_definitions(env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 442, in generate_function_definitions stat.generate_function_definitions(env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 442, in generate_function_definitions stat.generate_function_definitions(env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 3174, in generate_function_definitions FuncDefNode.generate_function_definitions(self, env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 1981, in generate_function_definitions self.generate_function_body(env, code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 1743, in generate_function_body self.body.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 448, in generate_execution_code stat.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/UtilNodes.py", line 326, in generate_execution_code self.body.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 6706, in generate_execution_code self.body.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 448, in generate_execution_code stat.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 6276, in generate_execution_code self.else_clause.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 448, in generate_execution_code stat.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 7219, in generate_execution_code self.body.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 448, in generate_execution_code stat.generate_execution_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/Nodes.py", line 5147, in generate_execution_code self.expr.generate_evaluation_code(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/ExprNodes.py", line 5875, in generate_evaluation_code self.allocate_temp_result(code) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/ExprNodes.py", line 721, in allocate_temp_result elif not (self.result_is_used or type.is_memoryviewslice or self.is_c_result_required()): File "/home/user/anaconda3/envs/NGS/lib/python3.9/site- packages/Cython/Compiler/ExprNodes.py", line 5841, in is_c_result_required if not func_type.exception_value or func_type.exception_check == '+': AttributeError: 'BuiltinObjectType' object has no attribute 'exception_value'

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[smartgamer]

Hi,

When I tried pip install --upgrade Cython, I got a message: Requirement already up-to-date: Cython in /home/upsman/anaconda3/envs/myNGS/lib/python3.9/site-packages (0.29.21)

When I tried the new installation: python setup.py install, I got this message including the errors:

Installing epic2 script to /home/user/anaconda3/envs/NGS/bin

Installed /home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/epic2-0.0.48-py3.9-linux-x86_64.egg Processing dependencies for epic2==0.0.48 Searching for pandas Reading https://pypi.org/simple/pandas/ Downloading https://files.pythonhosted.org/packages/1b/e5/552ba65835ab43e12b299458fea94ee23886125b8b8aabc91edb03f2ba65/pandas-1.1.3.tar.gz#sha256=babbeda2f83b0686c9ad38d93b10516e68cdcd5771007eb80a763e98aaf44613 Best match: pandas 1.1.3 Processing pandas-1.1.3.tar.gz Writing /tmp/easy_install-7jsz5meu/pandas-1.1.3/setup.cfg Running pandas-1.1.3/setup.py -q bdist_egg --dist-dir /tmp/easy_install-7jsz5meu/pandas-1.1.3/egg-dist-tmp-0bcx55b3 Compiling pandas/_libs/algos.pyx because it changed. Compiling pandas/_libs/groupby.pyx because it changed. Compiling pandas/_libs/hashing.pyx because it changed. Compiling pandas/_libs/hashtable.pyx because it changed. Compiling pandas/_libs/index.pyx because it changed. Compiling pandas/_libs/indexing.pyx because it changed. Compiling pandas/_libs/internals.pyx because it changed. Compiling pandas/_libs/interval.pyx because it changed. Compiling pandas/_libs/join.pyx because it changed. Compiling pandas/_libs/lib.pyx because it changed. Compiling pandas/_libs/missing.pyx because it changed. Compiling pandas/_libs/parsers.pyx because it changed. Compiling pandas/_libs/reduction.pyx because it changed. Compiling pandas/_libs/ops.pyx because it changed. Compiling pandas/_libs/ops_dispatch.pyx because it changed. Compiling pandas/_libs/properties.pyx because it changed. Compiling pandas/_libs/reshape.pyx because it changed. Compiling pandas/_libs/sparse.pyx because it changed. Compiling pandas/_libs/tslib.pyx because it changed. Compiling pandas/_libs/tslibs/base.pyx because it changed. Compiling pandas/_libs/tslibs/ccalendar.pyx because it changed. Compiling pandas/_libs/tslibs/dtypes.pyx because it changed. Compiling pandas/_libs/tslibs/conversion.pyx because it changed. Compiling pandas/_libs/tslibs/fields.pyx because it changed. Compiling pandas/_libs/tslibs/nattype.pyx because it changed. Compiling pandas/_libs/tslibs/np_datetime.pyx because it changed. Compiling pandas/_libs/tslibs/offsets.pyx because it changed. Compiling pandas/_libs/tslibs/parsing.pyx because it changed. Compiling pandas/_libs/tslibs/period.pyx because it changed. Compiling pandas/_libs/tslibs/strptime.pyx because it changed. Compiling pandas/_libs/tslibs/timedeltas.pyx because it changed. Compiling pandas/_libs/tslibs/timestamps.pyx because it changed. Compiling pandas/_libs/tslibs/timezones.pyx because it changed. Compiling pandas/_libs/tslibs/tzconversion.pyx because it changed. Compiling pandas/_libs/tslibs/vectorized.pyx because it changed. Compiling pandas/_libs/testing.pyx because it changed. Compiling pandas/_libs/window/aggregations.pyx because it changed. Compiling pandas/_libs/window/indexers.pyx because it changed. Compiling pandas/_libs/writers.pyx because it changed. Compiling pandas/io/sas/sas.pyx because it changed. [ 1/40] Cythonizing pandas/_libs/algos.pyx Traceback (most recent call last): File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 2218, in visit_FuncDefNode node.body = node.body.analyse_expressions(node.local_scope) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 435, in analyse_expressions self.stats = [stat.analyse_expressions(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 435, in self.stats = [stat.analyse_expressions(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 6683, in analyse_expressions self.target = self.target.analyse_target_types(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ExprNodes.py", line 7504, in analyse_target_types coerced_unpacked_item = unpacked_item.coerce_to(arg.type, env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ExprNodes.py", line 952, in coerce_to src = PyTypeTestNode(src, dst_type, env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ExprNodes.py", line 13021, in init assert dst_type.is_extension_type or dst_type.is_builtin_type, "PyTypeTest on non extension type" AssertionError: PyTypeTest on non extension type

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 154, in save_modules yield saved File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 195, in setup_context yield File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 263, in run_setup _execfile(setup_script, ns) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 45, in _execfile exec(code, globals, locals) File "/tmp/easy_install-7jsz5meu/pandas-1.1.3/setup.py", line 792, in File "/tmp/easy_install-7jsz5meu/pandas-1.1.3/setup.py", line 762, in setup_package File "/tmp/easy_install-7jsz5meu/pandas-1.1.3/setup.py", line 541, in maybe_cythonize File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Build/Dependencies.py", line 1102, in cythonize cythonize_one(*args) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Build/Dependencies.py", line 1208, in cythonize_one result = compile_single(pyx_file, options, full_module_name=full_module_name) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Main.py", line 727, in compile_single return run_pipeline(source, options, full_module_name) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Main.py", line 515, in run_pipeline err, enddata = Pipeline.run_pipeline(pipeline, source) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Pipeline.py", line 355, in run_pipeline data = run(phase, data) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Pipeline.py", line 335, in run return phase(data) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 1598, in call return super_class.call(root) File "Cython/Compiler/Visitor.py", line 355, in Cython.Compiler.Visitor.EnvTransform.call File "Cython/Compiler/Visitor.py", line 302, in Cython.Compiler.Visitor.CythonTransform.call File "Cython/Compiler/Visitor.py", line 284, in Cython.Compiler.Visitor.VisitorTransform.call File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 1608, in visit_ModuleNode node.analyse_declarations(self.current_env()) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ModuleNode.py", line 124, in analyse_declarations self.body.analyse_declarations(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 431, in analyse_declarations stat.analyse_declarations(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 431, in analyse_declarations stat.analyse_declarations(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 375, in analyse_declarations self.body.analyse_declarations(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 431, in analyse_declarations stat.analyse_declarations(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 2354, in analyse_declarations name_declarator, type = self.declarator.analyse( File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 681, in analyse name_declarator, type = arg_node.analyse( File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 891, in analyse base_type = self.base_type.analyse(env, could_be_name=could_be_name) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 1082, in analyse axes_specs = MemoryView.get_axes_specs(env, self.axes) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/MemoryView.py", line 535, in get_axes_specs cythonscope.load_cythonscope() File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/CythonScope.py", line 126, in load_cythonscope view_utility_scope = MemoryView.view_utility_code.declare_in_scope( File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/UtilityCode.py", line 208, in declare_in_scope tree = self.get_tree(entries_only=True, cython_scope=cython_scope) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/UtilityCode.py", line 185, in get_tree (err, tree) = Pipeline.run_pipeline(pipeline, tree, printtree=False) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Pipeline.py", line 355, in run_pipeline data = run(phase, data) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Pipeline.py", line 335, in run return phase(data) File "Cython/Compiler/Visitor.py", line 302, in Cython.Compiler.Visitor.CythonTransform.call File "Cython/Compiler/Visitor.py", line 284, in Cython.Compiler.Visitor.VisitorTransform.call File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 2213, in visit_ModuleNode self.visitchildren(node) File "Cython/Compiler/Visitor.py", line 247, in Cython.Compiler.Visitor.VisitorTransform.visitchildren File "Cython/Compiler/Visitor.py", line 251, in Cython.Compiler.Visitor.VisitorTransform.visitchildren File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 221, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 312, in Cython.Compiler.Visitor.CythonTransform.visit_Node File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 219, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 312, in Cython.Compiler.Visitor.CythonTransform.visit_Node File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 219, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 312, in Cython.Compiler.Visitor.CythonTransform.visit_Node File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 221, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 312, in Cython.Compiler.Visitor.CythonTransform.visit_Node File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 221, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 312, in Cython.Compiler.Visitor.CythonTransform.visit_Node File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 219, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 188, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 148, in Cython.Compiler.Visitor.TreeVisitor._raise_compiler_error Cython.Compiler.Errors.CompilerCrash: Error compiling Cython file:

... __pyx_memoryview_thread_locks[pyx_memoryview_thread_locks_used], pyx_memoryview_thread_locks[i]) break else: PyThread_free_lock(self.lock)

cdef char *get_item_pointer(memoryview self, object index) except NULL:
    ^

---

View.MemoryView:393:9: Compiler crash in AnalyseExpressionsTransform

ModuleNode.body = StatListNode(View.MemoryView:5:0) StatListNode.stats[18] = StatListNode(View.MemoryView:330:5) StatListNode.stats[0] = CnameDecoratorNode(View.MemoryView:330:5, cname = '__pyx_memoryview') CnameDecoratorNode.node = CClassDefNode(View.MemoryView:330:5, as_name = 'memoryview', class_name = 'memoryview', decorators = [...]/0, module_name = '', visibility = 'private') CClassDefNode.body = StatListNode(View.MemoryView:332:4) StatListNode.stats[2] = CFuncDefNode(View.MemoryView:393:9, args = [...]/2, is_c_class_method = 1, modifiers = [...]/0, visibility = 'private')

Compiler crash traceback from this point on: File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 2218, in visit_FuncDefNode node.body = node.body.analyse_expressions(node.local_scope) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 435, in analyse_expressions self.stats = [stat.analyse_expressions(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 435, in self.stats = [stat.analyse_expressions(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 6683, in analyse_expressions self.target = self.target.analyse_target_types(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ExprNodes.py", line 7504, in analyse_target_types coerced_unpacked_item = unpacked_item.coerce_to(arg.type, env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ExprNodes.py", line 952, in coerce_to src = PyTypeTestNode(src, dst_type, env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ExprNodes.py", line 13021, in init assert dst_type.is_extension_type or dst_type.is_builtin_type, "PyTypeTest on non extension type" AssertionError: PyTypeTest on non extension type

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/user/Downloads/epic2/setup.py", line 118, in setup( File "/home/user/anaconda3/envs/NGS/lib/python3.9/distutils/core.py", line 148, in setup dist.run_commands() File "/home/user/anaconda3/envs/NGS/lib/python3.9/distutils/dist.py", line 966, in run_commands self.run_command(cmd) File "/home/user/anaconda3/envs/NGS/lib/python3.9/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/install.py", line 67, in run self.do_egg_install() File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/install.py", line 117, in do_egg_install cmd.run(show_deprecation=False) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 425, in run self.easy_install(spec, not self.no_deps) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 667, in easy_install return self.install_item(None, spec, tmpdir, deps, True) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 714, in install_item self.process_distribution(spec, dist, deps) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 758, in process_distribution distros = WorkingSet([]).resolve( File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/pkg_resources/init.py", line 779, in resolve dist = best[req.key] = env.best_match( File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/pkg_resources/init.py", line 1064, in best_match return self.obtain(req, installer) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/pkg_resources/init.py", line 1076, in obtain return installer(requirement) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 686, in easy_install return self.install_item(spec, dist.location, tmpdir, deps) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 712, in install_item dists = self.install_eggs(spec, download, tmpdir) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 897, in install_eggs return self.build_and_install(setup_script, setup_base) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 1167, in build_and_install self.run_setup(setup_script, setup_base, args) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 1151, in run_setup run_setup(setup_script, args) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 266, in run_setup raise File "/home/user/anaconda3/envs/NGS/lib/python3.9/contextlib.py", line 135, in exit self.gen.throw(type, value, traceback) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 195, in setup_context yield File "/home/user/anaconda3/envs/NGS/lib/python3.9/contextlib.py", line 135, in exit self.gen.throw(type, value, traceback) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 166, in save_modules saved_exc.resume() File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 141, in resume six.reraise(type, exc, self._tb) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/_vendor/six.py", line 685, in reraise raise value.with_traceback(tb) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 154, in save_modules yield saved File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 195, in setup_context yield File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 263, in run_setup _execfile(setup_script, ns) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 45, in _execfile exec(code, globals, locals) File "/tmp/easy_install-7jsz5meu/pandas-1.1.3/setup.py", line 792, in File "/tmp/easy_install-7jsz5meu/pandas-1.1.3/setup.py", line 762, in setup_package File "/tmp/easy_install-7jsz5meu/pandas-1.1.3/setup.py", line 541, in maybe_cythonize File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Build/Dependencies.py", line 1102, in cythonize cythonize_one(*args) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Build/Dependencies.py", line 1208, in cythonize_one result = compile_single(pyx_file, options, full_module_name=full_module_name) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Main.py", line 727, in compile_single return run_pipeline(source, options, full_module_name) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Main.py", line 515, in run_pipeline err, enddata = Pipeline.run_pipeline(pipeline, source) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Pipeline.py", line 355, in run_pipeline data = run(phase, data) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Pipeline.py", line 335, in run return phase(data) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 1598, in call return super_class.call(root) File "Cython/Compiler/Visitor.py", line 355, in Cython.Compiler.Visitor.EnvTransform.call File "Cython/Compiler/Visitor.py", line 302, in Cython.Compiler.Visitor.CythonTransform.call File "Cython/Compiler/Visitor.py", line 284, in Cython.Compiler.Visitor.VisitorTransform.call File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 1608, in visit_ModuleNode node.analyse_declarations(self.current_env()) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ModuleNode.py", line 124, in analyse_declarations self.body.analyse_declarations(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 431, in analyse_declarations stat.analyse_declarations(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 431, in analyse_declarations stat.analyse_declarations(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 375, in analyse_declarations self.body.analyse_declarations(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 431, in analyse_declarations stat.analyse_declarations(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 2354, in analyse_declarations name_declarator, type = self.declarator.analyse( File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 681, in analyse name_declarator, type = arg_node.analyse( File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 891, in analyse base_type = self.base_type.analyse(env, could_be_name=could_be_name) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 1082, in analyse axes_specs = MemoryView.get_axes_specs(env, self.axes) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/MemoryView.py", line 535, in get_axes_specs cythonscope.load_cythonscope() File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/CythonScope.py", line 126, in load_cythonscope view_utility_scope = MemoryView.view_utility_code.declare_in_scope( File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/UtilityCode.py", line 208, in declare_in_scope tree = self.get_tree(entries_only=True, cython_scope=cython_scope) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/UtilityCode.py", line 185, in get_tree (err, tree) = Pipeline.run_pipeline(pipeline, tree, printtree=False) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Pipeline.py", line 355, in run_pipeline data = run(phase, data) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Pipeline.py", line 335, in run return phase(data) File "Cython/Compiler/Visitor.py", line 302, in Cython.Compiler.Visitor.CythonTransform.call File "Cython/Compiler/Visitor.py", line 284, in Cython.Compiler.Visitor.VisitorTransform.call File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 2213, in visit_ModuleNode self.visitchildren(node) File "Cython/Compiler/Visitor.py", line 247, in Cython.Compiler.Visitor.VisitorTransform.visitchildren File "Cython/Compiler/Visitor.py", line 251, in Cython.Compiler.Visitor.VisitorTransform.visitchildren File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 221, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 312, in Cython.Compiler.Visitor.CythonTransform.visit_Node File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 219, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 312, in Cython.Compiler.Visitor.CythonTransform.visit_Node File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 219, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 312, in Cython.Compiler.Visitor.CythonTransform.visit_Node File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 221, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 312, in Cython.Compiler.Visitor.CythonTransform.visit_Node File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 221, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 312, in Cython.Compiler.Visitor.CythonTransform.visit_Node File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 219, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 188, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 148, in Cython.Compiler.Visitor.TreeVisitor._raise_compiler_error setuptools.sandbox.UnpickleableException: CompilerCrash((, 393, 9), 'AnalyseExpressionsTransform', 'Compiler crash in AnalyseExpressionsTransform\n\nModuleNode.body = StatListNode(View.MemoryView:5:0)\nStatListNode.stats[18] = StatListNode(View.MemoryView:330:5)\nStatListNode.stats[0] = CnameDecoratorNode(View.MemoryView:330:5,\n cname = \'__pyx_memoryview\')\nCnameDecoratorNode.node = CClassDefNode(View.MemoryView:330:5,\n as_name = \'memoryview\',\n class_name = \'memoryview\',\n decorators = [...]/0,\n module_name = \'\',\n visibility = \'private\')\nCClassDefNode.body = StatListNode(View.MemoryView:332:4)\nStatListNode.stats[2] = CFuncDefNode(View.MemoryView:393:9,\n args = [...]/2,\n is_c_class_method = 1,\n modifiers = [...]/0,\n visibility = \'private\')\n\nCompiler crash traceback from this point on:\n File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit\n File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 2218, in visit_FuncDefNode\n node.body = node.body.analyse_expressions(node.local_scope)\n File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 435, in analyse_expressions\n self.stats = [stat.analyse_expressions(env)\n File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 435, in \n self.stats = [stat.analyse_expressions(env)\n File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 6683, in analyse_expressions\n self.target = self.target.analyse_target_types(env)\n File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ExprNodes.py", line 7504, in analyse_target_types\n coerced_unpacked_item = unpacked_item.coerce_to(arg.type, env)\n File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ExprNodes.py", line 952, in coerce_to\n src = PyTypeTestNode(src, dst_type, env)\n File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ExprNodes.py", line 13021, in init\n assert dst_type.is_extension_type or dst_type.is_builtin_type, "PyTypeTest on non extension type"\nAssertionError: PyTypeTest on non extension type', AssertionError('PyTypeTest on non extension type'), <traceback object at 0x7fd10597f600>)

[endrebak]

That is good in a sense, because now the errors are not in epic2. I will try to make it work later.

On Tue, Oct 27, 2020 at 9:37 PM Charlie notifications@github.com wrote:

Hi,

When I tried pip install --upgrade Cython, I got a message: Requirement already up-to-date: Cython in /home/upsman/anaconda3/envs/myNGS/lib/python3.9/site-packages (0.29.21)

When I tried the new installation: python setup.py install, I got this message including the errors:

Installing epic2 script to /home/user/anaconda3/envs/NGS/bin

Installed /home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/epic2-0.0.48-py3.9-linux-x86_64.egg Processing dependencies for epic2==0.0.48 Searching for pandas Reading https://pypi.org/simple/pandas/ Downloading https://files.pythonhosted.org/packages/1b/e5/552ba65835ab43e12b299458fea94ee23886125b8b8aabc91edb03f2ba65/pandas-1.1.3.tar.gz#sha256=babbeda2f83b0686c9ad38d93b10516e68cdcd5771007eb80a763e98aaf44613 Best match: pandas 1.1.3 Processing pandas-1.1.3.tar.gz Writing /tmp/easy_install-7jsz5meu/pandas-1.1.3/setup.cfg Running pandas-1.1.3/setup.py -q bdist_egg --dist-dir /tmp/easy_install-7jsz5meu/pandas-1.1.3/egg-dist-tmp-0bcx55b3 Compiling pandas/_libs/algos.pyx because it changed. Compiling pandas/_libs/groupby.pyx because it changed. Compiling pandas/_libs/hashing.pyx because it changed. Compiling pandas/_libs/hashtable.pyx because it changed. Compiling pandas/_libs/index.pyx because it changed. Compiling pandas/_libs/indexing.pyx because it changed. Compiling pandas/_libs/internals.pyx because it changed. Compiling pandas/_libs/interval.pyx because it changed. Compiling pandas/_libs/join.pyx because it changed. Compiling pandas/_libs/lib.pyx because it changed. Compiling pandas/_libs/missing.pyx because it changed. Compiling pandas/_libs/parsers.pyx because it changed. Compiling pandas/_libs/reduction.pyx because it changed. Compiling pandas/_libs/ops.pyx because it changed. Compiling pandas/_libs/ops_dispatch.pyx because it changed. Compiling pandas/_libs/properties.pyx because it changed. Compiling pandas/_libs/reshape.pyx because it changed. Compiling pandas/_libs/sparse.pyx because it changed. Compiling pandas/_libs/tslib.pyx because it changed. Compiling pandas/_libs/tslibs/base.pyx because it changed. Compiling pandas/_libs/tslibs/ccalendar.pyx because it changed. Compiling pandas/_libs/tslibs/dtypes.pyx because it changed. Compiling pandas/_libs/tslibs/conversion.pyx because it changed. Compiling pandas/_libs/tslibs/fields.pyx because it changed. Compiling pandas/_libs/tslibs/nattype.pyx because it changed. Compiling pandas/_libs/tslibs/np_datetime.pyx because it changed. Compiling pandas/_libs/tslibs/offsets.pyx because it changed. Compiling pandas/_libs/tslibs/parsing.pyx because it changed. Compiling pandas/_libs/tslibs/period.pyx because it changed. Compiling pandas/_libs/tslibs/strptime.pyx because it changed. Compiling pandas/_libs/tslibs/timedeltas.pyx because it changed. Compiling pandas/_libs/tslibs/timestamps.pyx because it changed. Compiling pandas/_libs/tslibs/timezones.pyx because it changed. Compiling pandas/_libs/tslibs/tzconversion.pyx because it changed. Compiling pandas/_libs/tslibs/vectorized.pyx because it changed. Compiling pandas/_libs/testing.pyx because it changed. Compiling pandas/_libs/window/aggregations.pyx because it changed. Compiling pandas/_libs/window/indexers.pyx because it changed. Compiling pandas/_libs/writers.pyx because it changed. Compiling pandas/io/sas/sas.pyx because it changed. [ 1/40] Cythonizing pandas/_libs/algos.pyx Traceback (most recent call last): File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 2218, in visit_FuncDefNode node.body = node.body.analyse_expressions(node.local_scope) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 435, in analyse_expressions self.stats = [stat.analyse_expressions(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 435, in self.stats = [stat.analyse_expressions(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 6683, in analyse_expressions self.target = self.target.analyse_target_types(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ExprNodes.py", line 7504, in analyse_target_types coerced_unpacked_item = unpacked_item.coerce_to(arg.type, env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ExprNodes.py", line 952, in coerce_to src = PyTypeTestNode(src, dst_type, env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ExprNodes.py", line 13021, in init assert dst_type.is_extension_type or dst_type.is_builtin_type, "PyTypeTest on non extension type" AssertionError: PyTypeTest on non extension type

During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 154, in save_modules yield saved File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 195, in setup_context yield File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 263, in run_setup _execfile(setup_script, ns) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 45, in _execfile exec(code, globals, locals) File "/tmp/easy_install-7jsz5meu/pandas-1.1.3/setup.py", line 792, in File "/tmp/easy_install-7jsz5meu/pandas-1.1.3/setup.py", line 762, in setup_package File "/tmp/easy_install-7jsz5meu/pandas-1.1.3/setup.py", line 541, in maybe_cythonize File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Build/Dependencies.py", line 1102, in cythonize cythonize_one(args) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Build/Dependencies.py", line 1208, in cythonize_one result = compile_single(pyx_file, options, full_module_name=full_module_name) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Main.py", line 727, in compile_single return run_pipeline(source, options, full_module_name) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Main.py", line 515, in run_pipeline err, enddata = Pipeline.run_pipeline(pipeline, source) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Pipeline.py", line 355, in run_pipeline data = run(phase, data) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Pipeline.py", line 335, in run return phase(data) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 1598, in call return super_class.call(root) File "Cython/Compiler/Visitor.py", line 355, in Cython.Compiler.Visitor.EnvTransform.call File "Cython/Compiler/Visitor.py", line 302, in Cython.Compiler.Visitor.CythonTransform.call File "Cython/Compiler/Visitor.py", line 284, in Cython.Compiler.Visitor.VisitorTransform.call File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 1608, in visit_ModuleNode node.analyse_declarations(self.current_env()) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ModuleNode.py", line 124, in analyse_declarations self.body.analyse_declarations(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 431, in analyse_declarations stat.analyse_declarations(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 431, in analyse_declarations stat.analyse_declarations(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 375, in analyse_declarations self.body.analyse_declarations(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 431, in analyse_declarations stat.analyse_declarations(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 2354, in analyse_declarations name_declarator, type = self.declarator.analyse( File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 681, in analyse name_declarator, type = arg_node.analyse( File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 891, in analyse base_type = self.base_type.analyse(env, could_be_name=could_be_name) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 1082, in analyse axes_specs = MemoryView.get_axes_specs(env, self.axes) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/MemoryView.py", line 535, in get_axes_specs cythonscope.load_cythonscope() File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/CythonScope.py", line 126, in load_cythonscope view_utility_scope = MemoryView.view_utility_code.declare_in_scope( File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/UtilityCode.py", line 208, in declare_in_scope tree = self.get_tree(entries_only=True, cython_scope=cython_scope) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/UtilityCode.py", line 185, in get_tree (err, tree) = Pipeline.run_pipeline(pipeline, tree, printtree=False) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Pipeline.py", line 355, in run_pipeline data = run(phase, data) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Pipeline.py", line 335, in run return phase(data) File "Cython/Compiler/Visitor.py", line 302, in Cython.Compiler.Visitor.CythonTransform.call File "Cython/Compiler/Visitor.py", line 284, in Cython.Compiler.Visitor.VisitorTransform.call* File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 2213, in visit_ModuleNode self.visitchildren(node) File "Cython/Compiler/Visitor.py", line 247, in Cython.Compiler.Visitor.VisitorTransform.visitchildren File "Cython/Compiler/Visitor.py", line 251, in Cython.Compiler.Visitor.VisitorTransform.visitchildren File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 221, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 312, in Cython.Compiler.Visitor.CythonTransform.visit_Node File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 219, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 312, in Cython.Compiler.Visitor.CythonTransform.visit_Node File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 219, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 312, in Cython.Compiler.Visitor.CythonTransform.visit_Node File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 221, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 312, in Cython.Compiler.Visitor.CythonTransform.visit_Node File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 221, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 312, in Cython.Compiler.Visitor.CythonTransform.visit_Node File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 219, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 188, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 148, in Cython.Compiler.Visitor.TreeVisitor._raise_compiler_error Cython.Compiler.Errors.CompilerCrash: Error compiling Cython file:

... __pyx_memoryview_thread_locks[pyx_memoryview_thread_locks_used], pyx_memoryview_thread_locks[i]) break else: PyThread_free_lock(self.lock)

cdef char *get_item_pointer(memoryview self, object index) except NULL: ^

---

View.MemoryView:393:9: Compiler crash in AnalyseExpressionsTransform

ModuleNode.body = StatListNode(View.MemoryView:5:0) StatListNode.stats[18] = StatListNode(View.MemoryView:330:5) StatListNode.stats[0] = CnameDecoratorNode(View.MemoryView:330:5, cname = '__pyx_memoryview') CnameDecoratorNode.node = CClassDefNode(View.MemoryView:330:5, as_name = 'memoryview', class_name = 'memoryview', decorators = [...]/0, module_name = '', visibility = 'private') CClassDefNode.body = StatListNode(View.MemoryView:332:4) StatListNode.stats[2] = CFuncDefNode(View.MemoryView:393:9, args = [...]/2, is_c_class_method = 1, modifiers = [...]/0, visibility = 'private')

Compiler crash traceback from this point on: File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 2218, in visit_FuncDefNode node.body = node.body.analyse_expressions(node.local_scope) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 435, in analyse_expressions self.stats = [stat.analyse_expressions(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 435, in self.stats = [stat.analyse_expressions(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 6683, in analyse_expressions self.target = self.target.analyse_target_types(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ExprNodes.py", line 7504, in analyse_target_types coerced_unpacked_item = unpacked_item.coerce_to(arg.type, env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ExprNodes.py", line 952, in coerce_to src = PyTypeTestNode(src, dst_type, env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ExprNodes.py", line 13021, in init assert dst_type.is_extension_type or dst_type.is_builtin_type, "PyTypeTest on non extension type" AssertionError: PyTypeTest on non extension type

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/user/Downloads/epic2/setup.py", line 118, in setup( File "/home/user/anaconda3/envs/NGS/lib/python3.9/distutils/core.py", line 148, in setup dist.run_commands() File "/home/user/anaconda3/envs/NGS/lib/python3.9/distutils/dist.py", line 966, in run_commands self.run_command(cmd) File "/home/user/anaconda3/envs/NGS/lib/python3.9/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/install.py", line 67, in run self.do_egg_install() File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/install.py", line 117, in do_egg_install cmd.run(show_deprecation=False) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 425, in run self.easy_install(spec, not self.no_deps) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 667, in easy_install return self.install_item(None, spec, tmpdir, deps, True) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 714, in install_item self.process_distribution(spec, dist, deps) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 758, in process_distribution distros = WorkingSet([]).resolve( File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/pkg_resources/ init.py", line 779, in resolve dist = best[req.key] = env.best_match( File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/pkg_resources/ init.py", line 1064, in best_match return self.obtain(req, installer) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/pkg_resources/ init.py", line 1076, in obtain return installer(requirement) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 686, in easy_install return self.install_item(spec, dist.location, tmpdir, deps) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 712, in install_item dists = self.install_eggs(spec, download, tmpdir) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 897, in install_eggs return self.build_and_install(setup_script, setup_base) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 1167, in build_and_install self.run_setup(setup_script, setup_base, args) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 1151, in run_setup run_setup(setup_script, args) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 266, in run_setup raise File "/home/user/anaconda3/envs/NGS/lib/python3.9/contextlib.py", line 135, in exit self.gen.throw(type, value, traceback) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 195, in setup_context yield File "/home/user/anaconda3/envs/NGS/lib/python3.9/contextlib.py", line 135, in exit self.gen.throw(type, value, traceback) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 166, in save_modules saved_exc.resume() File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 141, in resume six.reraise(type, exc, self._tb) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/_vendor/six.py", line 685, in reraise raise value.with_traceback(tb) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 154, in save_modules yield saved File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 195, in setup_context yield File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 263, in run_setup _execfile(setup_script, ns) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/setuptools/sandbox.py", line 45, in _execfile exec(code, globals, locals) File "/tmp/easy_install-7jsz5meu/pandas-1.1.3/setup.py", line 792, in File "/tmp/easy_install-7jsz5meu/pandas-1.1.3/setup.py", line 762, in setup_package File "/tmp/easy_install-7jsz5meu/pandas-1.1.3/setup.py", line 541, in maybe_cythonize File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Build/Dependencies.py", line 1102, in cythonize cythonize_one(args) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Build/Dependencies.py", line 1208, in cythonize_one result = compile_single(pyx_file, options, full_module_name=full_module_name) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Main.py", line 727, in compile_single return run_pipeline(source, options, full_module_name) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Main.py", line 515, in run_pipeline err, enddata = Pipeline.run_pipeline(pipeline, source) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Pipeline.py", line 355, in run_pipeline data = run(phase, data) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Pipeline.py", line 335, in run return phase(data) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 1598, in call return super_class.call(root) File "Cython/Compiler/Visitor.py", line 355, in Cython.Compiler.Visitor.EnvTransform.call File "Cython/Compiler/Visitor.py", line 302, in Cython.Compiler.Visitor.CythonTransform.call File "Cython/Compiler/Visitor.py", line 284, in Cython.Compiler.Visitor.VisitorTransform.call File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 1608, in visit_ModuleNode node.analyse_declarations(self.current_env()) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ModuleNode.py", line 124, in analyse_declarations self.body.analyse_declarations(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 431, in analyse_declarations stat.analyse_declarations(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 431, in analyse_declarations stat.analyse_declarations(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 375, in analyse_declarations self.body.analyse_declarations(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 431, in analyse_declarations stat.analyse_declarations(env) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 2354, in analyse_declarations name_declarator, type = self.declarator.analyse( File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 681, in analyse name_declarator, type = arg_node.analyse( File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 891, in analyse base_type = self.base_type.analyse(env, could_be_name=could_be_name) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 1082, in analyse axes_specs = MemoryView.get_axes_specs(env, self.axes) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/MemoryView.py", line 535, in get_axes_specs cythonscope.load_cythonscope() File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/CythonScope.py", line 126, in load_cythonscope view_utility_scope = MemoryView.view_utility_code.declare_in_scope( File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/UtilityCode.py", line 208, in declare_in_scope tree = self.get_tree(entries_only=True, cython_scope=cython_scope) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/UtilityCode.py", line 185, in get_tree (err, tree) = Pipeline.run_pipeline(pipeline, tree, printtree=False) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Pipeline.py", line 355, in run_pipeline data = run(phase, data) File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Pipeline.py", line 335, in run return phase(data) File "Cython/Compiler/Visitor.py", line 302, in Cython.Compiler.Visitor.CythonTransform.call File "Cython/Compiler/Visitor.py", line 284, in Cython.Compiler.Visitor.VisitorTransform.call File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 2213, in visit_ModuleNode self.visitchildren(node) File "Cython/Compiler/Visitor.py", line 247, in Cython.Compiler.Visitor.VisitorTransform.visitchildren File "Cython/Compiler/Visitor.py", line 251, in Cython.Compiler.Visitor.VisitorTransform.visitchildren File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 221, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 312, in Cython.Compiler.Visitor.CythonTransform.visit_Node File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 219, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 312, in Cython.Compiler.Visitor.CythonTransform.visit_Node File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 219, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 312, in Cython.Compiler.Visitor.CythonTransform.visit_Node File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 221, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 312, in Cython.Compiler.Visitor.CythonTransform.visit_Node File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 221, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 312, in Cython.Compiler.Visitor.CythonTransform.visit_Node File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children File "Cython/Compiler/Visitor.py", line 219, in Cython.Compiler.Visitor.TreeVisitor._visitchildren File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild File "Cython/Compiler/Visitor.py", line 188, in Cython.Compiler.Visitor.TreeVisitor._visit File "Cython/Compiler/Visitor.py", line 148, in Cython.Compiler.Visitor.TreeVisitor._raise_compiler_error setuptools.sandbox.UnpickleableException: CompilerCrash((StringSourceDescriptor:View.MemoryView, 393, 9), 'AnalyseExpressionsTransform', 'Compiler crash in AnalyseExpressionsTransform\n\nModuleNode.body = StatListNode(View.MemoryView:5:0)\nStatListNode.stats[18] = StatListNode(View.MemoryView:330:5)\nStatListNode.stats[0] = CnameDecoratorNode(View.MemoryView:330:5,\n cname = '__pyx_memoryview')\nCnameDecoratorNode.node = CClassDefNode(View.MemoryView:330:5,\n as_name = 'memoryview',\n class_name = 'memoryview',\n decorators = [...]/0,\n module_name = '',\n visibility = 'private')\nCClassDefNode.body = StatListNode(View.MemoryView:332:4)\nStatListNode.stats[2] = CFuncDefNode(View.MemoryView:393:9,\n args = [...]/2,\n is_c_class_method = 1,\n modifiers = [...]/0,\n visibility = 'private')\n\nCompiler crash traceback from this point on:\n File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit\n File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 2218, in visit_FuncDefNode\n node.body = node.body.analyse_expressions(node.local_scope)\n File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 435, in analyse_expressions\n self.stats = [stat.analyse_expressions(env)\n File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 435, in \n self.stats = [stat.analyse_expressions(env)\n File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/Nodes.py", line 6683, in analyse_expressions\n self.target = self.target.analyse_target_types(env)\n File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ExprNodes.py", line 7504, in analyse_target_types\n coerced_unpacked_item = unpacked_item.coerce_to(arg.type, env)\n File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ExprNodes.py", line 952, in coerce_to\n src = PyTypeTestNode(src, dst_type, env)\n File "/home/user/anaconda3/envs/NGS/lib/python3.9/site-packages/Cython/Compiler/ExprNodes.py", line 13021, in init*\n assert dst_type.is_extension_type or dst_type.is_builtin_type, "PyTypeTest on non extension type"\nAssertionError: PyTypeTest on non extension type', AssertionError('PyTypeTest on non extension type'), <traceback object at 0x7fd10597f600>)

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