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AttributeError: 'PolyCollection' object has no property 'stat_func'
See original GitHub issueGood afternoon,
I’m having issues installing and running NanoPlot. I installed NanoPlot with conda create -n nanoplot_env -c bioconda nanoplot, and I am getting the following error:
$ NanoPlot -t 4 --fastq G3-combined.fastq --plots hex dot --N50 -o G3_combined_nanoplot
/usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/_collections_abc.py:702: MatplotlibDeprecationWarning: The global colormaps dictionary is no longer considered public API.
return len(self._mapping)
/usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/_collections_abc.py:720: MatplotlibDeprecationWarning: The global colormaps dictionary is no longer considered public API.
yield from self._mapping
/usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/seaborn/distributions.py:2557: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `histplot` (an axes-level function for histograms).
warnings.warn(msg, FutureWarning)
If you read this then NanoPlot 1.32.1 has crashed :-(
Please try updating NanoPlot and see if that helps...
If not, please report this issue at https://github.com/wdecoster/NanoPlot/issues
If you could include the log file that would be really helpful.
Thanks!
Traceback (most recent call last):
File "/usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/bin/NanoPlot", line 10, in <module>
sys.exit(main())
File "/usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/nanoplot/NanoPlot.py", line 101, in main
plots = make_plots(datadf, settings)
File "/usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/nanoplot/NanoPlot.py", line 169, in make_plots
plot_settings=plot_settings)
File "/usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/nanoplotter/nanoplotter_main.py", line 135, in scatter
height=10)
File "/usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/seaborn/_decorators.py", line 46, in inner_f
return f(**kwargs)
File "/usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/seaborn/axisgrid.py", line 2189, in jointplot
grid.plot_joint(plt.hexbin, **joint_kws)
File "/usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/seaborn/axisgrid.py", line 1736, in plot_joint
func(self.x, self.y, **kwargs)
File "/usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/matplotlib/pyplot.py", line 2673, in hexbin
**({"data": data} if data is not None else {}), **kwargs)
File "/usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/matplotlib/__init__.py", line 1447, in inner
return func(ax, *map(sanitize_sequence, args), **kwargs)
File "/usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/matplotlib/axes/_axes.py", line 4853, in hexbin
collection.update(kwargs)
File "/usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/matplotlib/artist.py", line 996, in update
raise AttributeError(f"{type(self).__name__!r} object "
AttributeError: 'PolyCollection' object has no property 'stat_func'
I tried updating:
$ conda update nanoplot
Collecting package metadata (current_repodata.json): done
Solving environment: done
# All requested packages already installed.
so I tried updating with pip:
$ pip install NanoPlot --upgrade
Requirement already satisfied: NanoPlot in /local/ifs2_projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages (1.32.1)
Collecting NanoPlot
Using cached NanoPlot-1.33.1-py3-none-any.whl
Requirement already satisfied: pandas>=0.22.0 in /local/ifs2_projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages (from NanoPlot) (1.2.0)
Requirement already satisfied: numpy in /local/ifs2_projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages (from NanoPlot) (1.19.5)
Requirement already satisfied: pyarrow in /local/ifs2_projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages (from NanoPlot) (0.11.1)
Requirement already satisfied: biopython in /local/ifs2_projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages (from NanoPlot) (1.78)
Requirement already satisfied: nanomath>=1.0.0 in /local/ifs2_projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages (from NanoPlot) (1.2.0)
Requirement already satisfied: matplotlib>=3.1.3 in /local/ifs2_projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages (from NanoPlot) (3.3.3)
Requirement already satisfied: python-dateutil in /local/ifs2_projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages (from NanoPlot) (2.8.1)
Requirement already satisfied: plotly>=4.9.0 in /local/ifs2_projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages (from NanoPlot) (4.14.3)
Requirement already satisfied: pysam>0.10.0.0 in /local/ifs2_projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages (from NanoPlot) (0.15.3)
Requirement already satisfied: scipy in /local/ifs2_projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages (from NanoPlot) (1.6.0)
Requirement already satisfied: nanoget>=1.14.0 in /local/ifs2_projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages (from NanoPlot) (1.15.0)
Collecting pauvre==0.2.0
Using cached pauvre-0.2-py3-none-any.whl
Requirement already satisfied: scikit-learn in /local/ifs2_projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages (from pauvre==0.2.0->NanoPlot) (0.24.0)
Collecting seaborn==0.10.1
Using cached seaborn-0.10.1-py3-none-any.whl (215 kB)
Requirement already satisfied: cycler>=0.10 in /local/ifs2_projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages (from matplotlib>=3.1.3->NanoPlot) (0.10.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /local/ifs2_projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages (from matplotlib>=3.1.3->NanoPlot) (1.3.1)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 in /local/ifs2_projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages (from matplotlib>=3.1.3->NanoPlot) (2.4.7)
Requirement already satisfied: pillow>=6.2.0 in /local/ifs2_projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages (from matplotlib>=3.1.3->NanoPlot) (8.1.0)
Requirement already satisfied: six in /local/ifs2_projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages (from cycler>=0.10->matplotlib>=3.1.3->NanoPlot) (1.15.0)
Requirement already satisfied: pytz>=2017.3 in /local/ifs2_projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages (from pandas>=0.22.0->NanoPlot) (2020.5)
Requirement already satisfied: retrying>=1.3.3 in /local/ifs2_projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages (from plotly>=4.9.0->NanoPlot) (1.3.3)
Collecting kaleido
Using cached kaleido-0.1.0-py2.py3-none-manylinux1_x86_64.whl (74.6 MB)
Collecting Python-Deprecated
Using cached Python_Deprecated-1.1.0-py2.py3-none-any.whl
Requirement already satisfied: threadpoolctl>=2.0.0 in /local/ifs2_projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages (from scikit-learn->pauvre==0.2.0->NanoPlot) (2.1.0)
Requirement already satisfied: joblib>=0.11 in /local/ifs2_projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages (from scikit-learn->pauvre==0.2.0->NanoPlot) (1.0.0)
Installing collected packages: Python-Deprecated, seaborn, pauvre, kaleido, NanoPlot
Attempting uninstall: seaborn
Found existing installation: seaborn 0.11.1
Uninstalling seaborn-0.11.1:
Successfully uninstalled seaborn-0.11.1
Attempting uninstall: pauvre
Found existing installation: pauvre 0.1924
Uninstalling pauvre-0.1924:
Successfully uninstalled pauvre-0.1924
Attempting uninstall: NanoPlot
Found existing installation: NanoPlot 1.32.1
Uninstalling NanoPlot-1.32.1:
Successfully uninstalled NanoPlot-1.32.1
Successfully installed NanoPlot-1.33.1 Python-Deprecated-1.1.0 kaleido-0.1.0 pauvre-0.2 seaborn-0.10.1
This appeared to work, but now I get glibc errors:
$ NanoPlot -t 4 --fastq G3-combined.fastq --plots hex dot --N50 -o G3_combined_nanoplot
If you read this then NanoPlot 1.33.1 has crashed :-(
Please try updating NanoPlot and see if that helps...
If not, please report this issue at https://github.com/wdecoster/NanoPlot/issues
If you could include the log file that would be really helpful.
Thanks!
Traceback (most recent call last):
File "/usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/bin/NanoPlot", line 8, in <module>
sys.exit(main())
File "/usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/nanoplot/NanoPlot.py", line 101, in main
plots = make_plots(datadf, settings)
File "/usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/nanoplot/NanoPlot.py", line 155, in make_plots
title=settings["title"])
File "/usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/nanoplotter/nanoplotter_main.py", line 324, in length_plots
plots.append(dynamic_histogram(array=array, name=name, path=path, title=title, color=color))
File "/usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/nanoplotter/nanoplotter_main.py", line 347, in dynamic_histogram
dynhist.save()
File "/usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/nanoplotter/plot.py", line 42, in save
self.save_static()
File "/usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/nanoplotter/plot.py", line 58, in save_static
pio.write_image(self.fig, self.path.replace('html', 'png'), engine="kaleido")
File "/usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/plotly/io/_kaleido.py", line 252, in write_image
engine=engine,
File "/usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/plotly/io/_kaleido.py", line 132, in to_image
fig_dict, format=format, width=width, height=height, scale=scale
File "/usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/kaleido/scopes/plotly.py", line 104, in transform
figure, format=format, width=width, height=height, scale=scale
File "/usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/kaleido/scopes/base.py", line 280, in _perform_transform
self._ensure_kaleido()
File "/usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/kaleido/scopes/base.py", line 188, in _ensure_kaleido
raise ValueError(message)
ValueError: Failed to start Kaleido subprocess. Error stream:
./bin/kaleido: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by ./bin/kaleido)
./bin/kaleido: /lib64/libc.so.6: version `GLIBC_2.15' not found (required by ./bin/kaleido)
./bin/kaleido: /lib64/libc.so.6: version `GLIBC_2.16' not found (required by ./bin/kaleido)
./bin/kaleido: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/kaleido/executable/lib/libnss3.so)
./bin/kaleido: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/kaleido/executable/lib/libnssutil3.so)
./bin/kaleido: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/kaleido/executable/lib/libnspr4.so)
./bin/kaleido: /lib64/libc.so.6: version `GLIBC_2.15' not found (required by /usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/kaleido/executable/lib/libnspr4.so)
./bin/kaleido: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by /usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/kaleido/executable/lib/libnspr4.so)
./bin/kaleido: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/kaleido/executable/lib/libexpat.so.1)
./bin/kaleido: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/kaleido/executable/lib/libplc4.so)
./bin/kaleido: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot_env/lib/python3.7/site-packages/kaleido/executable/lib/libplds4.so)
So I tried creating a blank conda environment, and then installed pip with conda install pip and then tried pip install NanoPlot, and I got a whole bunch of red text ending with:
In file included from /usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot3_env/include/python3.9/unicodeobject.h:1026:0,
from /usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot3_env/include/python3.9/Python.h:97,
from numpy/random/mtrand/mtrand.c:4:
/usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot3_env/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
^~~~~~~~~~~~~~~~~~~~~~~~~~
error: Command "gcc -pthread -B /usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot3_env/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot3_env/include -fPIC -O2 -isystem /usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot3_env/include -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE=1 -D_LARGEFILE64_SOURCE=1 -Inumpy/core/include -Ibuild/src.linux-x86_64-3.9/numpy/core/include/numpy -Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot3_env/include/python3.9 -Ibuild/src.linux-x86_64-3.9/numpy/core/src/common -Ibuild/src.linux-x86_64-3.9/numpy/core/src/npymath -Ibuild/src.linux-x86_64-3.9/numpy/core/src/common -Ibuild/src.linux-x86_64-3.9/numpy/core/src/npymath -c numpy/random/mtrand/mtrand.c -o build/temp.linux-x86_64-3.9/numpy/random/mtrand/mtrand.o -MMD -MF build/temp.linux-x86_64-3.9/numpy/random/mtrand/mtrand.o.d" failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot3_env/bin/python3.9 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/local/ifs3_scratch/MISC/jobaker/TMP/pip-install-3645_4qd/numpy_4366d5ecce854be49b8470bdbec914e0/setup.py'"'"'; __file__='"'"'/local/ifs3_scratch/MISC/jobaker/TMP/pip-install-3645_4qd/numpy_4366d5ecce854be49b8470bdbec914e0/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /local/ifs3_scratch/MISC/jobaker/TMP/pip-record-hoo8_dyb/install-record.txt --single-version-externally-managed --prefix /local/ifs3_scratch/MISC/jobaker/TMP/pip-build-env-550hbjgc/overlay --compile --install-headers /local/ifs3_scratch/MISC/jobaker/TMP/pip-build-env-550hbjgc/overlay/include/python3.9/numpy Check the logs for full command output.
----------------------------------------
ERROR: Command errored out with exit status 1: /usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot3_env/bin/python3.9 /usr/local/projdata/0718/projects/jon/conda_envs/envs/nanoplot3_env/lib/python3.9/site-packages/pip install --ignore-installed --no-user --prefix /local/ifs3_scratch/MISC/jobaker/TMP/pip-build-env-550hbjgc/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- 'cython >= 0.29' 'numpy==1.14.5; python_version<'"'"'3.7'"'"'' 'numpy==1.16.0; python_version>='"'"'3.7'"'"'' setuptools setuptools_scm wheel Check the logs for full command output.
Any help would be fantastic. Thanks a lot,
Jon
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- State:
- Created 3 years ago
- Comments:6 (4 by maintainers)
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In case it comes up I just installed NanoPlot using Conda and ran into the same ‘stat_func’ error and did resolve it simply by downgrading seaborn with
conda install seaborn==0.10.1.I’m sorry for that, but good to hear that you could solve it. I can’t get a new version on bioconda due to some incompatibilities, unfortunately.