installation issue
Opened this issue · 4 comments
Subhayan18 commented
Hi,
new to python, so I'm probably doing something stupid. I have installed pyclone-vi and $pyclone-vi --help is responsive.
(pyclone-vi) D:\pyclone-vi>pyclone-vi --help
Usage: pyclone-vi [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
Commands:
fit Fit PyClone-VI model to data.
write-results-file Write the results of a fitted model to file.
But $pyclone-vi fit is throwing an error that I can't figure out.
(pyclone-vi) D:\pyclone-vi>pyclone-vi fit -i examples/tracerx.tsv -o tracerx.h5 -c 40 -d beta-binomial -r 10
Traceback (most recent call last):
File "C:\Users\Subhayan\miniconda3\envs\pyclone-vi\Scripts\pyclone-vi-script.py", line 33, in <module>
sys.exit(load_entry_point('pyclone-vi==0.1.1', 'console_scripts', 'pyclone-vi')())
File "C:\Users\Subhayan\miniconda3\envs\pyclone-vi\lib\site-packages\click\core.py", line 829, in __call__
return self.main(*args, **kwargs)
File "C:\Users\Subhayan\miniconda3\envs\pyclone-vi\lib\site-packages\click\core.py", line 782, in main
rv = self.invoke(ctx)
File "C:\Users\Subhayan\miniconda3\envs\pyclone-vi\lib\site-packages\click\core.py", line 1259, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "C:\Users\Subhayan\miniconda3\envs\pyclone-vi\lib\site-packages\click\core.py", line 1066, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "C:\Users\Subhayan\miniconda3\envs\pyclone-vi\lib\site-packages\click\core.py", line 610, in invoke
return callback(*args, **kwargs)
File "C:\Users\Subhayan\miniconda3\envs\pyclone-vi\lib\site-packages\pyclone_vi\cli.py", line 113, in fit
pyclone_vi.run.fit(**kwargs)
File "C:\Users\Subhayan\miniconda3\envs\pyclone-vi\lib\site-packages\pyclone_vi\run.py", line 29, in fit
log_p_data, mutations, samples = load_data(in_file, density, num_grid_points, precision=precision)
File "C:\Users\Subhayan\miniconda3\envs\pyclone-vi\lib\site-packages\pyclone_vi\data.py", line 11, in load_data
data, mutations, samples = load_pyclone_data(file_name)
File "C:\Users\Subhayan\miniconda3\envs\pyclone-vi\lib\site-packages\pyclone_vi\data.py", line 86, in load_pyclone_data
SampleDataPoint(a, b, cn, mu, log_pi, row['tumour_content'])
File "C:\Users\Subhayan\miniconda3\envs\pyclone-vi\lib\site-packages\numba\experimental\jitclass\base.py", line 122, in __call__
return cls._ctor(*bind.args[1:], **bind.kwargs)
File "C:\Users\Subhayan\miniconda3\envs\pyclone-vi\lib\site-packages\numba\core\dispatcher.py", line 420, in _compile_for_args
error_rewrite(e, 'typing')
File "C:\Users\Subhayan\miniconda3\envs\pyclone-vi\lib\site-packages\numba\core\dispatcher.py", line 361, in error_rewrite
raise e.with_traceback(None)
numba.core.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend)
Internal error at <numba.core.typeinfer.CallConstraint object at 0x000001DEBEAF65E0>.
Failed in nopython mode pipeline (step: nopython mode backend)
Can only insert i64* at [4] in {i8*, i8*, i64, i64, i64*, [2 x i64], [2 x i64]}: got i32*
File "C:\Users\Subhayan\miniconda3\envs\pyclone-vi\lib\site-packages\pyclone_vi\data.py", line 184:
def __init__(self, a, b, cn, mu, log_pi, t):
<source elided>
self.b = b
self.cn = cn
^
During: lowering "(self).cn = cn" at C:\Users\Subhayan\miniconda3\envs\pyclone-vi\lib\site-packages\pyclone_vi\data.py (184)
During: resolving callee type: jitclass.SampleDataPoint#1debdcb0370<a:int64,b:int64,cn:array(int64, 2d, A),mu:array(float64, 2d, A),log_pi:array(float64, 1d, A),t:float64>
During: typing of call at <string> (3)
Enable logging at debug level for details.
File "<string>", line 3:
<source missing, REPL/exec in use?>
Sorry I had to include the whole traceback as I don't understand what is going on in there. Does it show an issue?
Thx!
/Subhayan
aroth85 commented
Can you post the output of conda list from inside the environment. Best guess is the numba package needs an update, but not certain.
Subhayan18 commented
the numba version is 0.46.0
# Name Version Build Channel
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.1 py_0 conda-forge
backports_abc 0.5 py_1 conda-forge
blas 1.0 mkl
certifi 2019.11.28 py27h8c360ce_1 conda-forge
cycler 0.10.0 py_2 conda-forge
enum34 1.1.10 py27h8c360ce_1 conda-forge
freetype 2.10.1 h4d385ea_0 conda-forge
funcsigs 1.0.2 py_3 conda-forge
functools32 3.2.3.2 py_3 conda-forge
futures 3.3.0 py27h8c360ce_1 conda-forge
icc_rt 2019.0.0 h0cc432a_1
intel-openmp 2021.2.0 h57928b3_616 conda-forge
kiwisolver 1.1.0 py27h6c69bd3_1 conda-forge
libblas 3.9.0 8_mkl conda-forge
libcblas 3.9.0 8_mkl conda-forge
liblapack 3.9.0 8_mkl conda-forge
libpng 1.6.37 h7a46e7a_0 conda-forge
llvmlite 0.30.0 py27hc56fc5f_0
matplotlib-base 2.2.5 py27h6595424_1 conda-forge
mkl 2020.4 hb70f87d_311 conda-forge
numba 0.46.0 py27h0e003f4_1 conda-forge
numpy 1.16.5 py27h0d21db5_0 conda-forge
pandas 0.24.2 py27h0e003f4_0 conda-forge
patsy 0.5.1 py_0 conda-forge
pip 20.1.1 pyh9f0ad1d_0 conda-forge
pyclone 0.13.1 py_0 bioconda
pydp 0.2.4 py_0 bioconda
pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge
python 2.7.15 h2880e7c_1011_cpython conda-forge
python-dateutil 2.8.1 py_0 conda-forge
python_abi 2.7 1_cp27m conda-forge
pytz 2020.1 pyh9f0ad1d_0 conda-forge
pyyaml 5.3.1 py27h462b5f4_0 conda-forge
scipy 1.2.1 py27h4c3ab11_0
seaborn 0.9.0 py_2 conda-forge
setuptools 44.0.0 py27_0 conda-forge
singledispatch 3.6.1 pyh44b312d_0 conda-forge
six 1.15.0 pyh9f0ad1d_0 conda-forge
statsmodels 0.10.2 py27h83e69c8_0 conda-forge
tornado 5.1.1 py27h0c8e037_1000 conda-forge
vc 9 h7299396_1
vs2008_runtime 9.0.30729.6161 0 conda-forge
vs2015_runtime 14.28.29325 h5e1d092_4 conda-forge
wheel 0.36.2 pyhd3deb0d_0 conda-forge
wincertstore 0.2 py27_1003 conda-forge
yaml 0.2.2 h0c8e037_1 conda-forge
zlib 1.2.11 h3cc03e0_1006 conda-forge
p.s. I was able to execute original PyClone without a hitch with these libraries.
Thanks a lot for trying to help.
aroth85 commented
I see. PyClone and PyClone-VI need different dependencies. The latter has been fully updated to Python 3. Could you create a new conda environment following the instructions on the main page and see if that helps
sarahVanAlsten commented
I seem to be having the same issue as the user above:
(pyclone-vi) C:\Users\Owner\Documents\UNC\Research\pyclone>pyclone-vi fit -i examples\tracerx.tsv -o tracerx.h5 -c 40 -d beta-binomial -r 10
Traceback (most recent call last):
File "C:\Users\Owner\miniconda3\envs\pyclone-vi\lib\runpy.py", line 196, in _run_module_as_main
return _run_code(code, main_globals, None,
File "C:\Users\Owner\miniconda3\envs\pyclone-vi\lib\runpy.py", line 86, in _run_code
exec(code, run_globals)
File "C:\Users\Owner\miniconda3\envs\pyclone-vi\Scripts\pyclone-vi.exe\__main__.py", line 7, in <module>
File "C:\Users\Owner\miniconda3\envs\pyclone-vi\lib\site-packages\click\core.py", line 1130, in __call__
return self.main(*args, **kwargs)
File "C:\Users\Owner\miniconda3\envs\pyclone-vi\lib\site-packages\click\core.py", line 1055, in main
rv = self.invoke(ctx)
File "C:\Users\Owner\miniconda3\envs\pyclone-vi\lib\site-packages\click\core.py", line 1657, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "C:\Users\Owner\miniconda3\envs\pyclone-vi\lib\site-packages\click\core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "C:\Users\Owner\miniconda3\envs\pyclone-vi\lib\site-packages\click\core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "C:\Users\Owner\miniconda3\envs\pyclone-vi\lib\site-packages\pyclone_vi\cli.py", line 113, in fit
pyclone_vi.run.fit(**kwargs)
File "C:\Users\Owner\miniconda3\envs\pyclone-vi\lib\site-packages\pyclone_vi\run.py", line 29, in fit
log_p_data, mutations, samples = load_data(in_file, density, num_grid_points, precision=precision)
File "C:\Users\Owner\miniconda3\envs\pyclone-vi\lib\site-packages\pyclone_vi\data.py", line 11, in load_data
data, mutations, samples = load_pyclone_data(file_name)
File "C:\Users\Owner\miniconda3\envs\pyclone-vi\lib\site-packages\pyclone_vi\data.py", line 86, in load_pyclone_data
SampleDataPoint(a, b, cn, mu, log_pi, row['tumour_content'])
File "C:\Users\Owner\miniconda3\envs\pyclone-vi\lib\site-packages\numba\experimental\jitclass\base.py", line 124, in __call__
return cls._ctor(*bind.args[1:], **bind.kwargs)
File "C:\Users\Owner\miniconda3\envs\pyclone-vi\lib\site-packages\numba\core\dispatcher.py", line 468, in _compile_for_args
error_rewrite(e, 'typing')
File "C:\Users\Owner\miniconda3\envs\pyclone-vi\lib\site-packages\numba\core\dispatcher.py", line 409, in error_rewrite
raise e.with_traceback(None)
numba.core.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend)
Internal error at <numba.core.typeinfer.CallConstraint object at 0x0000028DF003ADA0>.
←[1m←[1mFailed in nopython mode pipeline (step: native lowering)
←[1m←[1mCan only insert i64* at [4] in {i8*, i8*, i64, i64, i64*, [2 x i64], [2 x i64]}: got i32*
←[1m
File "..\..\..\..\miniconda3\envs\pyclone-vi\lib\site-packages\pyclone_vi\data.py", line 184:←[0m
←[1m def __init__(self, a, b, cn, mu, log_pi, t):
<source elided>
self.b = b
←[1m self.cn = cn
←[0m ←[1m^←[0m←[0m
←[0m
←[0m←[1mDuring: lowering "(self).cn = cn" at C:\Users\Owner\miniconda3\envs\pyclone-vi\lib\site-packages\pyclone_vi\data.py (184)←[0m
←[0m←[1mDuring: resolving callee type: jitclass.SampleDataPoint#28dedc34be0<a:int64,b:int64,cn:array(int64, 2d, A),mu:array(float64, 2d, A),log_pi:array(float64, 1d, A),t:float64>←[0m
←[0m←[1mDuring: typing of call at <string> (3)
←[0m
Enable logging at debug level for details.
←[1m
File "<string>", line 3:←[0m
←[1m<source missing, REPL/exec in use?>←[0m]Looking at the conda list command, as far as I can tell my Python and dependencies are up to date, so I'm not sure
(pyclone-vi) C:\Users\Owner\Documents\UNC\Research\pyclone>conda list
# packages in environment at C:\Users\Owner\miniconda3\envs\pyclone-vi:
#
# Name Version Build Channel
bzip2 1.0.8 h8ffe710_4 conda-forge
ca-certificates 2022.9.24 h5b45459_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
click 8.1.3 py310h5588dad_0 conda-forge
colorama 0.4.5 pyhd8ed1ab_0 conda-forge
h5py 3.7.0 nompi_py310h425bae0_101 conda-forge
hdf5 1.12.2 nompi_h57737ce_100 conda-forge
intel-openmp 2022.1.0 h57928b3_3787 conda-forge
krb5 1.19.3 hc8ab02b_0 conda-forge
libblas 3.9.0 16_win64_mkl conda-forge
libcblas 3.9.0 16_win64_mkl conda-forge
libcurl 7.83.1 h789b8ee_0 conda-forge
libffi 3.4.2 h8ffe710_5 conda-forge
liblapack 3.9.0 16_win64_mkl conda-forge
libsqlite 3.39.3 hcfcfb64_0 conda-forge
libssh2 1.10.0 h9a1e1f7_3 conda-forge
libzlib 1.2.12 hcfcfb64_3 conda-forge
llvmlite 0.39.1 py310hb84602e_0 conda-forge
m2w64-gcc-libgfortran 5.3.0 6 conda-forge
m2w64-gcc-libs 5.3.0 7 conda-forge
m2w64-gcc-libs-core 5.3.0 7 conda-forge
m2w64-gmp 6.1.0 2 conda-forge
m2w64-libwinpthread-git 5.0.0.4634.697f757 2 conda-forge
mkl 2022.1.0 h6a75c08_874 conda-forge
msys2-conda-epoch 20160418 1 conda-forge
numba 0.56.2 py310h19bcfe9_0 conda-forge
numpy 1.23.3 py310h4a8f9c9_0 conda-forge
openssl 3.0.5 hcfcfb64_2 conda-forge
pandas 1.5.0 py310h1c4a608_0 conda-forge
pip 22.2.2 pyhd8ed1ab_0 conda-forge
pyclone-vi 0.1.1 pypi_0 pypi
python 3.10.6 hcf16a7b_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python_abi 3.10 2_cp310 conda-forge
pytz 2022.2.1 pyhd8ed1ab_0 conda-forge
scipy 1.9.1 py310h578b7cb_0 conda-forge
setuptools 65.4.0 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
tbb 2021.6.0 h91493d7_0 conda-forge
tk 8.6.12 h8ffe710_0 conda-forge
tzdata 2022d h191b570_0 conda-forge
ucrt 10.0.20348.0 h57928b3_0 conda-forge
vc 14.2 hb210afc_7 conda-forge
vs2015_runtime 14.29.30139 h890b9b1_7 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h8d14728_0 conda-forgeMy best guess is somehow an incompatible type is trying to be entered into the array, but I'm not sure of next steps to work around it.
Thanks so much!