Closed Heather1999 closed 6 months ago
WardDeb
commented
7 months ago Hi,
I cannot reproduce this error.
Could you give some more information on the OS you use, and ideally the full stdout from the build ? Does this also occur if you run pip install deeptools directly ?
Heather1999
commented
7 months ago Hi, Thank you for responding. The OS I use: Distributor ID: Ubuntu Description: Ubuntu 20.04.3 LTS Release: 20.04
Yes, it still occur when I run pip install deeptools.
The full stdout: Building wheels for collected packages: deeptoolsintervals, py2bit Building wheel for deeptoolsintervals (setup.py) ... error error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [130 lines of output]
/home/sealight1999/miniconda3/lib/python3.11/site-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'classifier'
warnings.warn(msg)
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-cpython-311
creating build/lib.linux-x86_64-cpython-311/deeptoolsintervals
copying deeptoolsintervals/enrichment.py -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals
copying deeptoolsintervals/init.py -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals
copying deeptoolsintervals/parse.py -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals
running egg_info
writing deeptoolsintervals.egg-info/PKG-INFO
writing dependency_links to deeptoolsintervals.egg-info/dependency_links.txt
writing top-level names to deeptoolsintervals.egg-info/top_level.txt
reading manifest file 'deeptoolsintervals.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'deeptoolsintervals/tree.*'
adding license file 'LICENSE'
writing manifest file 'deeptoolsintervals.egg-info/SOURCES.txt'
/home/sealight1999/miniconda3/lib/python3.11/site-packages/setuptools/command/build_py.py:204: _Warning: Package 'deeptoolsintervals.test' is absent from the packages configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'deeptoolsintervals.test' as an importable package[^1],
but it is absent from setuptools' `packages` configuration.
This leads to an ambiguous overall configuration. If you want to distribute this
package, please make sure that 'deeptoolsintervals.test' is explicitly added
to the `packages` configuration field.
Alternatively, you can also rely on setuptools' discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
If you don't want 'deeptoolsintervals.test' to be distributed and are
already explicitly excluding 'deeptoolsintervals.test' via
`find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
you can try to use `exclude_package_data`, or `include-package-data=False` in
combination with a more fine grained `package-data` configuration.
You can read more about "package data files" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/datafiles.html
[^1]: For Python, any directory (with suitable naming) can be imported,
even if it does not contain any `.py` files.
On the other hand, currently there is no concept of package data
directory, all directories are treated like packages.
********************************************************************************
!!
check.warn(importable)
/home/sealight1999/miniconda3/lib/python3.11/site-packages/setuptools/command/build_py.py:204: _Warning: Package 'deeptoolsintervals.tree' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'deeptoolsintervals.tree' as an importable package[^1],
but it is absent from setuptools' `packages` configuration.
This leads to an ambiguous overall configuration. If you want to distribute this
package, please make sure that 'deeptoolsintervals.tree' is explicitly added
to the `packages` configuration field.
Alternatively, you can also rely on setuptools' discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
If you don't want 'deeptoolsintervals.tree' to be distributed and are
already explicitly excluding 'deeptoolsintervals.tree' via
`find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
you can try to use `exclude_package_data`, or `include-package-data=False` in
combination with a more fine grained `package-data` configuration.
You can read more about "package data files" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/datafiles.html
[^1]: For Python, any directory (with suitable naming) can be imported,
even if it does not contain any `.py` files.
On the other hand, currently there is no concept of package data
directory, all directories are treated like packages.
********************************************************************************
!!
check.warn(importable)
creating build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test
copying deeptoolsintervals/test/GRCh38.84.2.gtf.gz -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test
copying deeptoolsintervals/test/GRCh38.84.bed -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test
copying deeptoolsintervals/test/GRCh38.84.bed12.bz2 -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test
copying deeptoolsintervals/test/GRCh38.84.bed2 -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test
copying deeptoolsintervals/test/GRCh38.84.bed6 -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test
copying deeptoolsintervals/test/GRCh38.84.gtf.gz -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test
copying deeptoolsintervals/test/GRCh38.84.labels.bed -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test
copying deeptoolsintervals/test/noOverlaps.bed -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test
copying deeptoolsintervals/test/strands.bed -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test
creating build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree
copying deeptoolsintervals/tree/findOverlaps.c -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree
copying deeptoolsintervals/tree/gtf.c -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree
copying deeptoolsintervals/tree/gtf.h -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree
copying deeptoolsintervals/tree/hashTable.c -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree
copying deeptoolsintervals/tree/kseq.h -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree
copying deeptoolsintervals/tree/kstring.h -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree
copying deeptoolsintervals/tree/murmur3.c -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree
copying deeptoolsintervals/tree/murmur3.h -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree
copying deeptoolsintervals/tree/tree.c -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree
copying deeptoolsintervals/tree/tree.h -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree
running build_ext
building 'deeptoolsintervals.tree' extension
creating build/temp.linux-x86_64-cpython-311
creating build/temp.linux-x86_64-cpython-311/deeptoolsintervals
creating build/temp.linux-x86_64-cpython-311/deeptoolsintervals/tree
/home/sealight1999/miniconda3/bin/x86_64-conda_cos6-linux-gnu-gcc -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/sealight1999/miniconda3/include -fPIC -O2 -isystem /home/sealight1999/miniconda3/include -fPIC -I/home/sealight1999/miniconda3/include/python3.11 -I/home/sealight1999/miniconda3/include/python3.11 -c deeptoolsintervals/tree/findOverlaps.c -o build/temp.linux-x86_64-cpython-311/deeptoolsintervals/tree/findOverlaps.o
error: command '/home/sealight1999/miniconda3/bin/x86_64-conda_cos6-linux-gnu-gcc' failed: No such file or directory
[end of output]note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for deeptoolsintervals Running setup.py clean for deeptoolsintervals Building wheel for py2bit (setup.py) ... error error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully. │ exit code: 1 ╰─> [40 lines of output] /home/sealight1999/miniconda3/lib/python3.11/site-packages/setuptools/dist.py:498: SetuptoolsDeprecationWarning: Invalid dash-separated options !!
********************************************************************************
Usage of dash-separated 'description-file' will not be supported in future
versions. Please use the underscore name 'description_file' instead.
This deprecation is overdue, please update your project and remove deprecated
calls to avoid build errors in the future.
See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
********************************************************************************
!!
opt = self.warn_dash_deprecation(opt, section)
/home/sealight1999/miniconda3/lib/python3.11/site-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'classifier'
warnings.warn(msg)
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-cpython-311
creating build/lib.linux-x86_64-cpython-311/py2bitTest
copying py2bitTest/test.py -> build/lib.linux-x86_64-cpython-311/py2bitTest
copying py2bitTest/__init__.py -> build/lib.linux-x86_64-cpython-311/py2bitTest
running egg_info
writing py2bit.egg-info/PKG-INFO
writing dependency_links to py2bit.egg-info/dependency_links.txt
writing top-level names to py2bit.egg-info/top_level.txt
reading manifest file 'py2bit.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE.txt'
writing manifest file 'py2bit.egg-info/SOURCES.txt'
copying py2bitTest/foo.2bit -> build/lib.linux-x86_64-cpython-311/py2bitTest
running build_ext
building 'py2bit' extension
creating build/temp.linux-x86_64-cpython-311
creating build/temp.linux-x86_64-cpython-311/lib2bit
/home/sealight1999/miniconda3/bin/x86_64-conda_cos6-linux-gnu-gcc -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/sealight1999/miniconda3/include -fPIC -O2 -isystem /home/sealight1999/miniconda3/include -fPIC -Ilib2bit -I/home/sealight1999/miniconda3/include/python3.11 -I/home/sealight1999/miniconda3/include/python3.11 -c lib2bit/2bit.c -o build/temp.linux-x86_64-cpython-311/lib2bit/2bit.o
error: command '/home/sealight1999/miniconda3/bin/x86_64-conda_cos6-linux-gnu-gcc' failed: No such file or directory
[end of output]note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for py2bit Running setup.py clean for py2bit Failed to build deeptoolsintervals py2bit ERROR: Could not build wheels for deeptoolsintervals, py2bit, which is required to install pyproject.toml-based projects
WardDeb
commented
7 months ago I think your issue stems from here:
error: command '/home/sealight1999/miniconda3/bin/x86_64-conda_cos6-linux-gnu-gcc' failed: No such file or directory
Could you try to first create a separate env (installing packages in your base is not really recommended):
conda create -n deeptools python=3.11.5
conda activate deeptools
conda install -c conda-forge gcc
pip install deeptoolsThank you for taking the time to review my problem:)
After building conda environment, I still get the following error:
` pip install deeptools
Collecting deeptools
Using cached deepTools-3.5.4.post1-py3-none-any.whl.metadata (3.8 kB)
Collecting numpy>=1.9.0 (from deeptools)
Downloading numpy-1.26.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.0/61.0 kB 1.1 MB/s eta 0:00:00
Collecting scipy>=0.17.0 (from deeptools)
Using cached scipy-1.12.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
Collecting matplotlib>=3.5.0 (from deeptools)
Downloading matplotlib-3.8.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB)
Collecting pysam>=0.14.0 (from deeptools)
Downloading pysam-0.22.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (1.5 kB)
Collecting numpydoc>=0.5 (from deeptools)
Using cached numpydoc-1.6.0-py3-none-any.whl.metadata (4.2 kB)
Collecting pyBigWig>=0.2.1 (from deeptools)
Using cached pyBigWig-0.3.22-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB)
Collecting py2bit>=0.2.0 (from deeptools)
Using cached py2bit-0.3.0.tar.gz (16 kB)
Preparing metadata (setup.py) ... done
Collecting plotly>=4.9 (from deeptools)
Using cached plotly-5.19.0-py3-none-any.whl.metadata (7.0 kB)
Collecting deeptoolsintervals>=0.1.8 (from deeptools)
Using cached deeptoolsintervals-0.1.9.tar.gz (41 kB)
Preparing metadata (setup.py) ... done
Collecting importlib-metadata (from deeptools)
Using cached importlib_metadata-7.0.1-py3-none-any.whl.metadata (4.9 kB)
Collecting contourpy>=1.0.1 (from matplotlib>=3.5.0->deeptools)
Downloading contourpy-1.2.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB)
Collecting cycler>=0.10 (from matplotlib>=3.5.0->deeptools)
Using cached cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
Collecting fonttools>=4.22.0 (from matplotlib>=3.5.0->deeptools)
Downloading fonttools-4.49.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (159 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 159.1/159.1 kB 2.7 MB/s eta 0:00:00
Collecting kiwisolver>=1.3.1 (from matplotlib>=3.5.0->deeptools)
Downloading kiwisolver-1.4.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.4 kB)
Collecting packaging>=20.0 (from matplotlib>=3.5.0->deeptools)
Using cached packaging-23.2-py3-none-any.whl.metadata (3.2 kB)
Collecting pillow>=8 (from matplotlib>=3.5.0->deeptools)
Downloading pillow-10.2.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (9.7 kB)
Collecting pyparsing>=2.3.1 (from matplotlib>=3.5.0->deeptools)
Using cached pyparsing-3.1.1-py3-none-any.whl.metadata (5.1 kB)
Collecting python-dateutil>=2.7 (from matplotlib>=3.5.0->deeptools)
Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
Collecting sphinx>=5 (from numpydoc>=0.5->deeptools)
Using cached sphinx-7.2.6-py3-none-any.whl.metadata (5.9 kB)
Collecting Jinja2>=2.10 (from numpydoc>=0.5->deeptools)
Using cached Jinja2-3.1.3-py3-none-any.whl.metadata (3.3 kB)
Collecting tabulate>=0.8.10 (from numpydoc>=0.5->deeptools)
Using cached tabulate-0.9.0-py3-none-any.whl (35 kB)
Collecting tenacity>=6.2.0 (from plotly>=4.9->deeptools)
Using cached tenacity-8.2.3-py3-none-any.whl.metadata (1.0 kB)
Collecting zipp>=0.5 (from importlib-metadata->deeptools)
Using cached zipp-3.17.0-py3-none-any.whl.metadata (3.7 kB)
Collecting MarkupSafe>=2.0 (from Jinja2>=2.10->numpydoc>=0.5->deeptools)
Downloading MarkupSafe-2.1.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB)
Collecting six>=1.5 (from python-dateutil>=2.7->matplotlib>=3.5.0->deeptools)
Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting sphinxcontrib-applehelp (from sphinx>=5->numpydoc>=0.5->deeptools)
Using cached sphinxcontrib_applehelp-1.0.8-py3-none-any.whl.metadata (2.3 kB)
Collecting sphinxcontrib-devhelp (from sphinx>=5->numpydoc>=0.5->deeptools)
Using cached sphinxcontrib_devhelp-1.0.6-py3-none-any.whl.metadata (2.3 kB)
Collecting sphinxcontrib-jsmath (from sphinx>=5->numpydoc>=0.5->deeptools)
Using cached sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB)
Collecting sphinxcontrib-htmlhelp>=2.0.0 (from sphinx>=5->numpydoc>=0.5->deeptools)
Using cached sphinxcontrib_htmlhelp-2.0.5-py3-none-any.whl.metadata (2.3 kB)
Collecting sphinxcontrib-serializinghtml>=1.1.9 (from sphinx>=5->numpydoc>=0.5->deeptools)
Using cached sphinxcontrib_serializinghtml-1.1.10-py3-none-any.whl.metadata (2.4 kB)
Collecting sphinxcontrib-qthelp (from sphinx>=5->numpydoc>=0.5->deeptools)
Using cached sphinxcontrib_qthelp-1.0.7-py3-none-any.whl.metadata (2.2 kB)
Collecting Pygments>=2.14 (from sphinx>=5->numpydoc>=0.5->deeptools)
Using cached pygments-2.17.2-py3-none-any.whl.metadata (2.6 kB)
Collecting docutils<0.21,>=0.18.1 (from sphinx>=5->numpydoc>=0.5->deeptools)
Using cached docutils-0.20.1-py3-none-any.whl.metadata (2.8 kB)
Collecting snowballstemmer>=2.0 (from sphinx>=5->numpydoc>=0.5->deeptools)
Using cached snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB)
Collecting babel>=2.9 (from sphinx>=5->numpydoc>=0.5->deeptools)
Using cached Babel-2.14.0-py3-none-any.whl.metadata (1.6 kB)
Collecting alabaster<0.8,>=0.7 (from sphinx>=5->numpydoc>=0.5->deeptools)
Using cached alabaster-0.7.16-py3-none-any.whl.metadata (2.9 kB)
Collecting imagesize>=1.3 (from sphinx>=5->numpydoc>=0.5->deeptools)
Using cached imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB)
Collecting requests>=2.25.0 (from sphinx>=5->numpydoc>=0.5->deeptools)
Using cached requests-2.31.0-py3-none-any.whl.metadata (4.6 kB)
Collecting charset-normalizer<4,>=2 (from requests>=2.25.0->sphinx>=5->numpydoc>=0.5->deeptools)
Downloading charset_normalizer-3.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB)
Collecting idna<4,>=2.5 (from requests>=2.25.0->sphinx>=5->numpydoc>=0.5->deeptools)
Using cached idna-3.6-py3-none-any.whl.metadata (9.9 kB)
Collecting urllib3<3,>=1.21.1 (from requests>=2.25.0->sphinx>=5->numpydoc>=0.5->deeptools)
Downloading urllib3-2.2.1-py3-none-any.whl.metadata (6.4 kB)
Collecting certifi>=2017.4.17 (from requests>=2.25.0->sphinx>=5->numpydoc>=0.5->deeptools)
Using cached certifi-2024.2.2-py3-none-any.whl.metadata (2.2 kB)
Using cached deepTools-3.5.4.post1-py3-none-any.whl (215 kB)
Downloading matplotlib-3.8.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.6 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.6/11.6 MB 33.0 MB/s eta 0:00:00
Downloading numpy-1.26.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.3 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 18.3/18.3 MB 30.3 MB/s eta 0:00:00
Using cached numpydoc-1.6.0-py3-none-any.whl (61 kB)
Using cached plotly-5.19.0-py3-none-any.whl (15.7 MB)
Using cached pyBigWig-0.3.22-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (213 kB)
Downloading pysam-0.22.0-cp311-cp311-manylinux_2_28_x86_64.whl (25.1 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 25.1/25.1 MB 23.1 MB/s eta 0:00:00
Using cached scipy-1.12.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (38.4 MB)
Using cached importlib_metadata-7.0.1-py3-none-any.whl (23 kB)
Downloading contourpy-1.2.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (313 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 313.4/313.4 kB 4.7 MB/s eta 0:00:00
Using cached cycler-0.12.1-py3-none-any.whl (8.3 kB)
Downloading fonttools-4.49.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.9 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.9/4.9 MB 35.4 MB/s eta 0:00:00
Using cached Jinja2-3.1.3-py3-none-any.whl (133 kB)
Downloading kiwisolver-1.4.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.4 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.4/1.4 MB 33.0 MB/s eta 0:00:00
Using cached packaging-23.2-py3-none-any.whl (53 kB)
Downloading pillow-10.2.0-cp311-cp311-manylinux_2_28_x86_64.whl (4.5 MB)
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Building wheels for collected packages: deeptoolsintervals, py2bit
Building wheel for deeptoolsintervals (setup.py) ... error
error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [130 lines of output]
/home/sealight1999/miniconda3/envs/deeptools/lib/python3.11/site-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'classifier'
warnings.warn(msg)
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-cpython-311
creating build/lib.linux-x86_64-cpython-311/deeptoolsintervals
copying deeptoolsintervals/enrichment.py -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals
copying deeptoolsintervals/init.py -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals
copying deeptoolsintervals/parse.py -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals
running egg_info
writing deeptoolsintervals.egg-info/PKG-INFO
writing dependency_links to deeptoolsintervals.egg-info/dependency_links.txt
writing top-level names to deeptoolsintervals.egg-info/top_level.txt
reading manifest file 'deeptoolsintervals.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'deeptoolsintervals/tree.*'
adding license file 'LICENSE'
writing manifest file 'deeptoolsintervals.egg-info/SOURCES.txt'
/home/sealight1999/miniconda3/envs/deeptools/lib/python3.11/site-packages/setuptools/command/build_py.py:204: _Warning: Package 'deeptoolsintervals.test' is absent from the packages configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'deeptoolsintervals.test' as an importable package[^1],
but it is absent from setuptools' `packages` configuration.
This leads to an ambiguous overall configuration. If you want to distribute this
package, please make sure that 'deeptoolsintervals.test' is explicitly added
to the `packages` configuration field.
Alternatively, you can also rely on setuptools' discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
If you don't want 'deeptoolsintervals.test' to be distributed and are
already explicitly excluding 'deeptoolsintervals.test' via
`find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
you can try to use `exclude_package_data`, or `include-package-data=False` in
combination with a more fine grained `package-data` configuration.
You can read more about "package data files" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/datafiles.html
[^1]: For Python, any directory (with suitable naming) can be imported,
even if it does not contain any `.py` files.
On the other hand, currently there is no concept of package data
directory, all directories are treated like packages.
********************************************************************************
!!
check.warn(importable)
/home/sealight1999/miniconda3/envs/deeptools/lib/python3.11/site-packages/setuptools/command/build_py.py:204: _Warning: Package 'deeptoolsintervals.tree' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'deeptoolsintervals.tree' as an importable package[^1],
but it is absent from setuptools' `packages` configuration.
This leads to an ambiguous overall configuration. If you want to distribute this
package, please make sure that 'deeptoolsintervals.tree' is explicitly added
to the `packages` configuration field.
Alternatively, you can also rely on setuptools' discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
If you don't want 'deeptoolsintervals.tree' to be distributed and are
already explicitly excluding 'deeptoolsintervals.tree' via
`find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
you can try to use `exclude_package_data`, or `include-package-data=False` in
combination with a more fine grained `package-data` configuration.
You can read more about "package data files" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/datafiles.html
[^1]: For Python, any directory (with suitable naming) can be imported,
even if it does not contain any `.py` files.
On the other hand, currently there is no concept of package data
directory, all directories are treated like packages.
********************************************************************************
!!
check.warn(importable)
creating build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test
copying deeptoolsintervals/test/GRCh38.84.2.gtf.gz -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test
copying deeptoolsintervals/test/GRCh38.84.bed -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test
copying deeptoolsintervals/test/GRCh38.84.bed12.bz2 -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test
copying deeptoolsintervals/test/GRCh38.84.bed2 -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test
copying deeptoolsintervals/test/GRCh38.84.bed6 -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test
copying deeptoolsintervals/test/GRCh38.84.gtf.gz -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test
copying deeptoolsintervals/test/GRCh38.84.labels.bed -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test
copying deeptoolsintervals/test/noOverlaps.bed -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test
copying deeptoolsintervals/test/strands.bed -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test
creating build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree
copying deeptoolsintervals/tree/findOverlaps.c -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree
copying deeptoolsintervals/tree/gtf.c -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree
copying deeptoolsintervals/tree/gtf.h -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree
copying deeptoolsintervals/tree/hashTable.c -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree
copying deeptoolsintervals/tree/kseq.h -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree
copying deeptoolsintervals/tree/kstring.h -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree
copying deeptoolsintervals/tree/murmur3.c -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree
copying deeptoolsintervals/tree/murmur3.h -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree
copying deeptoolsintervals/tree/tree.c -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree
copying deeptoolsintervals/tree/tree.h -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree
running build_ext
building 'deeptoolsintervals.tree' extension
creating build/temp.linux-x86_64-cpython-311
creating build/temp.linux-x86_64-cpython-311/deeptoolsintervals
creating build/temp.linux-x86_64-cpython-311/deeptoolsintervals/tree
/home/sealight1999/miniconda3/bin/x86_64-conda_cos6-linux-gnu-gcc -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/sealight1999/miniconda3/envs/deeptools/include -fPIC -O2 -isystem /home/sealight1999/miniconda3/envs/deeptools/include -fPIC -I/home/sealight1999/miniconda3/envs/deeptools/include/python3.11 -I/home/sealight1999/miniconda3/envs/deeptools/include/python3.11 -c deeptoolsintervals/tree/findOverlaps.c -o build/temp.linux-x86_64-cpython-311/deeptoolsintervals/tree/findOverlaps.o
error: command '/home/sealight1999/miniconda3/bin/x86_64-conda_cos6-linux-gnu-gcc' failed: No such file or directory
[end of output]note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for deeptoolsintervals Running setup.py clean for deeptoolsintervals Building wheel for py2bit (setup.py) ... error error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully. │ exit code: 1 ╰─> [40 lines of output] /home/sealight1999/miniconda3/envs/deeptools/lib/python3.11/site-packages/setuptools/dist.py:498: SetuptoolsDeprecationWarning: Invalid dash-separated options !!
********************************************************************************
Usage of dash-separated 'description-file' will not be supported in future
versions. Please use the underscore name 'description_file' instead.
This deprecation is overdue, please update your project and remove deprecated
calls to avoid build errors in the future.
See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
********************************************************************************
!!
opt = self.warn_dash_deprecation(opt, section)
/home/sealight1999/miniconda3/envs/deeptools/lib/python3.11/site-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'classifier'
warnings.warn(msg)
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-cpython-311
creating build/lib.linux-x86_64-cpython-311/py2bitTest
copying py2bitTest/test.py -> build/lib.linux-x86_64-cpython-311/py2bitTest
copying py2bitTest/__init__.py -> build/lib.linux-x86_64-cpython-311/py2bitTest
running egg_info
writing py2bit.egg-info/PKG-INFO
writing dependency_links to py2bit.egg-info/dependency_links.txt
writing top-level names to py2bit.egg-info/top_level.txt
reading manifest file 'py2bit.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE.txt'
writing manifest file 'py2bit.egg-info/SOURCES.txt'
copying py2bitTest/foo.2bit -> build/lib.linux-x86_64-cpython-311/py2bitTest
running build_ext
building 'py2bit' extension
creating build/temp.linux-x86_64-cpython-311
creating build/temp.linux-x86_64-cpython-311/lib2bit
/home/sealight1999/miniconda3/bin/x86_64-conda_cos6-linux-gnu-gcc -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/sealight1999/miniconda3/envs/deeptools/include -fPIC -O2 -isystem /home/sealight1999/miniconda3/envs/deeptools/include -fPIC -Ilib2bit -I/home/sealight1999/miniconda3/envs/deeptools/include/python3.11 -I/home/sealight1999/miniconda3/envs/deeptools/include/python3.11 -c lib2bit/2bit.c -o build/temp.linux-x86_64-cpython-311/lib2bit/2bit.o
error: command '/home/sealight1999/miniconda3/bin/x86_64-conda_cos6-linux-gnu-gcc' failed: No such file or directory
[end of output]note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for py2bit Running setup.py clean for py2bit Failed to build deeptoolsintervals py2bit ERROR: Could not build wheels for deeptoolsintervals, py2bit, which is required to install pyproject.toml-based projects` I think it is identical to the one I get before and ChatGPT did not offer any new insight.. Do you think anything else caused this problem? Thank you!
WardDeb
commented
7 months ago It's still complaining about not finding gcc:
error: command '/home/sealight1999/miniconda3/bin/x86_64-conda_cos6-linux-gnu-gcc' failed: No such file or directory
Could you install gcc in the base env:
conda activate base
conda install -c conda-forge gcc
which x86_64-conda_cos6-linux-gnu-gccand make sure the returned path / executable is appropriate ?
Heather1999
commented
7 months ago Amazing, it was solved!!! Thank you so, so much.
krl513
commented
6 months ago Hi, I am experiencing a similar issue and the proposed solutions here have not resolved it.
I am using Ubuntu 20.04.5 LTS
Attempted steps:
conda create -n deeptools python=3.11.5
conda activate deeptools
conda install -c conda-forge gcc
pip install deeptoolsI get the following error:
~$ pip install deeptools Collecting deeptools Using cached deepTools-3.5.5-py3-none-any.whl.metadata (3.8 kB) Collecting numpy>=1.9.0 (from deeptools) Using cached numpy-1.26.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB) Collecting scipy>=0.17.0 (from deeptools) Using cached scipy-1.13.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB) Collecting matplotlib>=3.5.0 (from deeptools) Using cached matplotlib-3.8.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB) Collecting pysam>=0.14.0 (from deeptools) Using cached pysam-0.22.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (1.5 kB) Collecting numpydoc>=0.5 (from deeptools) Using cached numpydoc-1.7.0-py3-none-any.whl.metadata (4.2 kB) Collecting pyBigWig>=0.2.1 (from deeptools) Using cached pyBigWig-0.3.22-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB) Collecting py2bit>=0.2.0 (from deeptools) Using cached py2bit-0.3.0-cp311-cp311-linux_x86_64.whl Collecting plotly>=4.9 (from deeptools) Using cached plotly-5.20.0-py3-none-any.whl.metadata (7.0 kB) Collecting deeptoolsintervals>=0.1.8 (from deeptools) Using cached deeptoolsintervals-0.1.9.tar.gz (41 kB) Preparing metadata (setup.py) ... done Collecting contourpy>=1.0.1 (from matplotlib>=3.5.0->deeptools) Using cached contourpy-1.2.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB) Collecting cycler>=0.10 (from matplotlib>=3.5.0->deeptools) Using cached cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB) Collecting fonttools>=4.22.0 (from matplotlib>=3.5.0->deeptools) Using cached fonttools-4.50.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (159 kB) Collecting kiwisolver>=1.3.1 (from matplotlib>=3.5.0->deeptools) Using cached kiwisolver-1.4.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.4 kB) Collecting packaging>=20.0 (from matplotlib>=3.5.0->deeptools) Using cached packaging-24.0-py3-none-any.whl.metadata (3.2 kB) Collecting pillow>=8 (from matplotlib>=3.5.0->deeptools) Using cached pillow-10.3.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (9.2 kB) Collecting pyparsing>=2.3.1 (from matplotlib>=3.5.0->deeptools) Using cached pyparsing-3.1.2-py3-none-any.whl.metadata (5.1 kB) Collecting python-dateutil>=2.7 (from matplotlib>=3.5.0->deeptools) Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB) Collecting sphinx>=6 (from numpydoc>=0.5->deeptools) Using cached sphinx-7.2.6-py3-none-any.whl.metadata (5.9 kB) Collecting tabulate>=0.8.10 (from numpydoc>=0.5->deeptools) Using cached tabulate-0.9.0-py3-none-any.whl.metadata (34 kB) Collecting tenacity>=6.2.0 (from plotly>=4.9->deeptools) Using cached tenacity-8.2.3-py3-none-any.whl.metadata (1.0 kB) Collecting six>=1.5 (from python-dateutil>=2.7->matplotlib>=3.5.0->deeptools) Using cached six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB) Collecting sphinxcontrib-applehelp (from sphinx>=6->numpydoc>=0.5->deeptools) Using cached sphinxcontrib_applehelp-1.0.8-py3-none-any.whl.metadata (2.3 kB) Collecting sphinxcontrib-devhelp (from sphinx>=6->numpydoc>=0.5->deeptools) Using cached sphinxcontrib_devhelp-1.0.6-py3-none-any.whl.metadata (2.3 kB) Collecting sphinxcontrib-jsmath (from sphinx>=6->numpydoc>=0.5->deeptools) Using cached sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl.metadata (1.4 kB) Collecting sphinxcontrib-htmlhelp>=2.0.0 (from sphinx>=6->numpydoc>=0.5->deeptools) Using cached sphinxcontrib_htmlhelp-2.0.5-py3-none-any.whl.metadata (2.3 kB) Collecting sphinxcontrib-serializinghtml>=1.1.9 (from sphinx>=6->numpydoc>=0.5->deeptools) Using cached sphinxcontrib_serializinghtml-1.1.10-py3-none-any.whl.metadata (2.4 kB) Collecting sphinxcontrib-qthelp (from sphinx>=6->numpydoc>=0.5->deeptools) Using cached sphinxcontrib_qthelp-1.0.7-py3-none-any.whl.metadata (2.2 kB) Collecting Jinja2>=3.0 (from sphinx>=6->numpydoc>=0.5->deeptools) Using cached Jinja2-3.1.3-py3-none-any.whl.metadata (3.3 kB) Collecting Pygments>=2.14 (from sphinx>=6->numpydoc>=0.5->deeptools) Using cached pygments-2.17.2-py3-none-any.whl.metadata (2.6 kB) Collecting docutils<0.21,>=0.18.1 (from sphinx>=6->numpydoc>=0.5->deeptools) Using cached docutils-0.20.1-py3-none-any.whl.metadata (2.8 kB) Collecting snowballstemmer>=2.0 (from sphinx>=6->numpydoc>=0.5->deeptools) Using cached snowballstemmer-2.2.0-py2.py3-none-any.whl.metadata (6.5 kB) Collecting babel>=2.9 (from sphinx>=6->numpydoc>=0.5->deeptools) Using cached Babel-2.14.0-py3-none-any.whl.metadata (1.6 kB) Collecting alabaster<0.8,>=0.7 (from sphinx>=6->numpydoc>=0.5->deeptools) Using cached alabaster-0.7.16-py3-none-any.whl.metadata (2.9 kB) Collecting imagesize>=1.3 (from sphinx>=6->numpydoc>=0.5->deeptools) Using cached imagesize-1.4.1-py2.py3-none-any.whl.metadata (1.5 kB) Collecting requests>=2.25.0 (from sphinx>=6->numpydoc>=0.5->deeptools) Using cached requests-2.31.0-py3-none-any.whl.metadata (4.6 kB) Collecting MarkupSafe>=2.0 (from Jinja2>=3.0->sphinx>=6->numpydoc>=0.5->deeptools) Using cached MarkupSafe-2.1.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB) Collecting charset-normalizer<4,>=2 (from requests>=2.25.0->sphinx>=6->numpydoc>=0.5->deeptools) Using cached charset_normalizer-3.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB) Collecting idna<4,>=2.5 (from requests>=2.25.0->sphinx>=6->numpydoc>=0.5->deeptools) Using cached idna-3.6-py3-none-any.whl.metadata (9.9 kB) Collecting urllib3<3,>=1.21.1 (from requests>=2.25.0->sphinx>=6->numpydoc>=0.5->deeptools) Using cached urllib3-2.2.1-py3-none-any.whl.metadata (6.4 kB) Collecting certifi>=2017.4.17 (from requests>=2.25.0->sphinx>=6->numpydoc>=0.5->deeptools) Using cached certifi-2024.2.2-py3-none-any.whl.metadata (2.2 kB) Using cached deepTools-3.5.5-py3-none-any.whl (208 kB) Using cached matplotlib-3.8.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.6 MB) Using cached numpy-1.26.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.3 MB) Using cached numpydoc-1.7.0-py3-none-any.whl (62 kB) Using cached plotly-5.20.0-py3-none-any.whl (15.7 MB) Using cached pyBigWig-0.3.22-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (213 kB) Using cached pysam-0.22.0-cp311-cp311-manylinux_2_28_x86_64.whl (25.1 MB) Using cached scipy-1.13.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (38.6 MB) Using cached contourpy-1.2.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (306 kB) Using cached cycler-0.12.1-py3-none-any.whl (8.3 kB) Using cached fonttools-4.50.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.9 MB) Using cached kiwisolver-1.4.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.4 MB) Using cached packaging-24.0-py3-none-any.whl (53 kB) Using cached pillow-10.3.0-cp311-cp311-manylinux_2_28_x86_64.whl (4.5 MB) Using cached pyparsing-3.1.2-py3-none-any.whl (103 kB) Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB) Using cached sphinx-7.2.6-py3-none-any.whl (3.2 MB) Using cached tabulate-0.9.0-py3-none-any.whl (35 kB) Using cached tenacity-8.2.3-py3-none-any.whl (24 kB) Using cached alabaster-0.7.16-py3-none-any.whl (13 kB) Using cached Babel-2.14.0-py3-none-any.whl (11.0 MB) Using cached docutils-0.20.1-py3-none-any.whl (572 kB) Using cached imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB) Using cached Jinja2-3.1.3-py3-none-any.whl (133 kB) Using cached pygments-2.17.2-py3-none-any.whl (1.2 MB) Using cached requests-2.31.0-py3-none-any.whl (62 kB) Using cached six-1.16.0-py2.py3-none-any.whl (11 kB) Using cached snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB) Using cached sphinxcontrib_htmlhelp-2.0.5-py3-none-any.whl (99 kB) Using cached sphinxcontrib_serializinghtml-1.1.10-py3-none-any.whl (92 kB) Using cached sphinxcontrib_applehelp-1.0.8-py3-none-any.whl (120 kB) Using cached sphinxcontrib_devhelp-1.0.6-py3-none-any.whl (83 kB) Using cached sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Using cached sphinxcontrib_qthelp-1.0.7-py3-none-any.whl (89 kB) Using cached certifi-2024.2.2-py3-none-any.whl (163 kB) Using cached charset_normalizer-3.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (140 kB) Using cached idna-3.6-py3-none-any.whl (61 kB) Using cached MarkupSafe-2.1.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (28 kB) Using cached urllib3-2.2.1-py3-none-any.whl (121 kB) Building wheels for collected packages: deeptoolsintervals Building wheel for deeptoolsintervals (setup.py) ... error error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1 ╰─> [137 lines of output] /home/keshav/miniconda3/envs/deeptools/lib/python3.11/site-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'classifier' warnings.warn(msg) running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-cpython-311 creating build/lib.linux-x86_64-cpython-311/deeptoolsintervals copying deeptoolsintervals/enrichment.py -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals copying deeptoolsintervals/parse.py -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals copying deeptoolsintervals/init.py -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals running egg_info writing deeptoolsintervals.egg-info/PKG-INFO writing dependency_links to deeptoolsintervals.egg-info/dependency_links.txt writing top-level names to deeptoolsintervals.egg-info/top_level.txt reading manifest file 'deeptoolsintervals.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'deeptoolsintervals/tree.*' adding license file 'LICENSE' writing manifest file 'deeptoolsintervals.egg-info/SOURCES.txt' /home/keshav/miniconda3/envs/deeptools/lib/python3.11/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'deeptoolsintervals.test' is absent from the
packagesconfiguration. !!******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'deeptoolsintervals.test' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'deeptoolsintervals.test' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'deeptoolsintervals.test' to be distributed and are already explicitly excluding 'deeptoolsintervals.test' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /home/keshav/miniconda3/envs/deeptools/lib/python3.11/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'deeptoolsintervals.tree' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'deeptoolsintervals.tree' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'deeptoolsintervals.tree' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'deeptoolsintervals.tree' to be distributed and are already explicitly excluding 'deeptoolsintervals.tree' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) creating build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test copying deeptoolsintervals/test/GRCh38.84.2.gtf.gz -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test copying deeptoolsintervals/test/GRCh38.84.bed -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test copying deeptoolsintervals/test/GRCh38.84.bed12.bz2 -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test copying deeptoolsintervals/test/GRCh38.84.bed2 -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test copying deeptoolsintervals/test/GRCh38.84.bed6 -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test copying deeptoolsintervals/test/GRCh38.84.gtf.gz -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test copying deeptoolsintervals/test/GRCh38.84.labels.bed -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test copying deeptoolsintervals/test/noOverlaps.bed -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test copying deeptoolsintervals/test/strands.bed -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/test creating build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree copying deeptoolsintervals/tree/findOverlaps.c -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree copying deeptoolsintervals/tree/gtf.c -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree copying deeptoolsintervals/tree/gtf.h -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree copying deeptoolsintervals/tree/hashTable.c -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree copying deeptoolsintervals/tree/kseq.h -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree copying deeptoolsintervals/tree/kstring.h -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree copying deeptoolsintervals/tree/murmur3.c -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree copying deeptoolsintervals/tree/murmur3.h -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree copying deeptoolsintervals/tree/tree.c -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree copying deeptoolsintervals/tree/tree.h -> build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree running build_ext building 'deeptoolsintervals.tree' extension creating build/temp.linux-x86_64-cpython-311 creating build/temp.linux-x86_64-cpython-311/deeptoolsintervals creating build/temp.linux-x86_64-cpython-311/deeptoolsintervals/tree gcc -pthread -B /home/keshav/miniconda3/envs/deeptools/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/keshav/miniconda3/envs/deeptools/include -fPIC -O2 -isystem /home/keshav/miniconda3/envs/deeptools/include -fPIC -I/home/keshav/miniconda3/envs/deeptools/include/python3.11 -I/home/keshav/miniconda3/envs/deeptools/include/python3.11 -c deeptoolsintervals/tree/findOverlaps.c -o build/temp.linux-x86_64-cpython-311/deeptoolsintervals/tree/findOverlaps.o gcc -pthread -B /home/keshav/miniconda3/envs/deeptools/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/keshav/miniconda3/envs/deeptools/include -fPIC -O2 -isystem /home/keshav/miniconda3/envs/deeptools/include -fPIC -I/home/keshav/miniconda3/envs/deeptools/include/python3.11 -I/home/keshav/miniconda3/envs/deeptools/include/python3.11 -c deeptoolsintervals/tree/gtf.c -o build/temp.linux-x86_64-cpython-311/deeptoolsintervals/tree/gtf.o gcc -pthread -B /home/keshav/miniconda3/envs/deeptools/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/keshav/miniconda3/envs/deeptools/include -fPIC -O2 -isystem /home/keshav/miniconda3/envs/deeptools/include -fPIC -I/home/keshav/miniconda3/envs/deeptools/include/python3.11 -I/home/keshav/miniconda3/envs/deeptools/include/python3.11 -c deeptoolsintervals/tree/hashTable.c -o build/temp.linux-x86_64-cpython-311/deeptoolsintervals/tree/hashTable.o gcc -pthread -B /home/keshav/miniconda3/envs/deeptools/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/keshav/miniconda3/envs/deeptools/include -fPIC -O2 -isystem /home/keshav/miniconda3/envs/deeptools/include -fPIC -I/home/keshav/miniconda3/envs/deeptools/include/python3.11 -I/home/keshav/miniconda3/envs/deeptools/include/python3.11 -c deeptoolsintervals/tree/murmur3.c -o build/temp.linux-x86_64-cpython-311/deeptoolsintervals/tree/murmur3.o gcc -pthread -B /home/keshav/miniconda3/envs/deeptools/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/keshav/miniconda3/envs/deeptools/include -fPIC -O2 -isystem /home/keshav/miniconda3/envs/deeptools/include -fPIC -I/home/keshav/miniconda3/envs/deeptools/include/python3.11 -I/home/keshav/miniconda3/envs/deeptools/include/python3.11 -c deeptoolsintervals/tree/tree.c -o build/temp.linux-x86_64-cpython-311/deeptoolsintervals/tree/tree.o gcc -pthread -B /home/keshav/miniconda3/envs/deeptools/compiler_compat -shared -Wl,--allow-shlib-undefined -Wl,-rpath,/home/keshav/miniconda3/envs/deeptools/lib -Wl,-rpath-link,/home/keshav/miniconda3/envs/deeptools/lib -L/home/keshav/miniconda3/envs/deeptools/lib -Wl,--allow-shlib-undefined -Wl,-rpath,/home/keshav/miniconda3/envs/deeptools/lib -Wl,-rpath-link,/home/keshav/miniconda3/envs/deeptools/lib -L/home/keshav/miniconda3/envs/deeptools/lib build/temp.linux-x86_64-cpython-311/deeptoolsintervals/tree/findOverlaps.o build/temp.linux-x86_64-cpython-311/deeptoolsintervals/tree/gtf.o build/temp.linux-x86_64-cpython-311/deeptoolsintervals/tree/hashTable.o build/temp.linux-x86_64-cpython-311/deeptoolsintervals/tree/murmur3.o build/temp.linux-x86_64-cpython-311/deeptoolsintervals/tree/tree.o -L/home/keshav/miniconda3/envs/deeptools/lib -L/home/keshav/miniconda3/envs/deeptools/lib/python3.11/config-3.11-x86_64-linux-gnu -lz -o build/lib.linux-x86_64-cpython-311/deeptoolsintervals/tree.cpython-311-x86_64-linux-gnu.so /home/keshav/miniconda3/envs/deeptools/compiler_compat/ld: cannot find -lz: No such file or directory collect2: error: ld returned 1 exit status error: command '/home/keshav/miniconda3/envs/deeptools/bin/gcc' failed with exit code 1 [end of output]note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for deeptoolsintervals Running setup.py clean for deeptoolsintervals Failed to build deeptoolsintervals ERROR: Could not build wheels for deeptoolsintervals, which is required to install pyproject.toml-based projects
I have also made sure to install gcc in my base environment as suggested in this thread.
I have tried running pip install deeptoolsintervals prior to running pip install deeptools but a similar error arises.
Any help would be much appreciated! Please let me know if I should open a new issue for this. Thank you!
WardDeb
commented
6 months ago This is a different issue it seems:
/home/keshav/miniconda3/envs/deeptools/compiler_compat/ld: cannot find -lz:
Do you have zlib installed on the system (zlib1g-dev in apt) ?
krl513
commented
6 months ago Yes I have run sudo apt-get install zlib1g-dev in my deeptools environment as well as the base conda environment.
This is the output:
Reading package lists... Done Building dependency tree Reading state information... Done zlib1g-dev is already the newest version (1:1.2.11.dfsg-2ubuntu1.5). The following packages were automatically installed and are no longer required: acpi-support aisleriot alsa-base app-install-data-partner apt-config-icons-hidpi apturl apturl-common baobab bluez-cups branding-ubuntu brltty cheese dc deja-dup dmz-cursor-theme duplicity eog espeak-ng-data file-roller fonts-kacst fonts-kacst-one fonts-khmeros-core fonts-lao fonts-liberation2 fonts-lklug-sinhala fonts-noto-cjk fonts-noto-color-emoji fonts-opensymbol fonts-sil-abyssinica fonts-sil-padauk fonts-thai-tlwg fonts-tibetan-machine fonts-tlwg-garuda fonts-tlwg-garuda-ttf fonts-tlwg-kinnari fonts-tlwg-kinnari-ttf fonts-tlwg-laksaman fonts-tlwg-laksaman-ttf fonts-tlwg-loma fonts-tlwg-loma-ttf fonts-tlwg-mono fonts-tlwg-mono-ttf fonts-tlwg-norasi fonts-tlwg-norasi-ttf fonts-tlwg-purisa fonts-tlwg-purisa-ttf fonts-tlwg-sawasdee fonts-tlwg-sawasdee-ttf fonts-tlwg-typewriter fonts-tlwg-typewriter-ttf fonts-tlwg-typist fonts-tlwg-typist-ttf fonts-tlwg-typo fonts-tlwg-typo-ttf fonts-tlwg-umpush fonts-tlwg-umpush-ttf fonts-tlwg-waree fonts-tlwg-waree-ttf g++-8 gamemode gedit gedit-common genisoimage gir1.2-clutter-1.0 gir1.2-clutter-gst-3.0 gir1.2-cogl-1.0 gir1.2-coglpango-1.0 gir1.2-gmenu-3.0 gir1.2-gst-plugins-base-1.0 gir1.2-gstreamer-1.0 gir1.2-gtkclutter-1.0 gir1.2-gtksource-4 gir1.2-gudev-1.0 gir1.2-peas-1.0 gir1.2-rb-3.0 gir1.2-totem-1.0 gir1.2-totemplparser-1.0 gir1.2-udisks-2.0 gnome-accessibility-themes gnome-bluetooth gnome-calculator gnome-calendar gnome-characters gnome-disk-utility gnome-font-viewer gnome-getting-started-docs gnome-initial-setup gnome-logs gnome-mahjongg gnome-mines gnome-power-manager gnome-screenshot gnome-session-canberra gnome-shell-extension-appindicator gnome-shell-extension-desktop-icons gnome-shell-extension-ubuntu-dock gnome-sudoku gnome-system-monitor gnome-themes-extra gnome-themes-extra-data gnome-todo gnome-todo-common gnome-video-effects grilo-plugins-0.3-base gsettings-ubuntu-schemas gstreamer1.0-gtk3 gstreamer1.0-packagekit gstreamer1.0-plugins-base-apps gtk2-engines-murrine gtk2-engines-pixbuf guile-2.2-libs gvfs-bin gvfs-fuse ibus-table inputattach javascript-common kerneloops laptop-detect libabw-0.1-1 libaccinj64-10.1 libamtk-5-0 libamtk-5-common libao-common libao4 libatk-adaptor libatkmm-1.6-1v5 libavahi-ui-gtk3-0 libboost-date-time1.71.0 libboost-filesystem1.71.0 libboost-iostreams1.71.0 libboost-locale1.71.0 libbrlapi0.7 libcairomm-1.0-1v5 libcdr-0.1-1 libclucene-contribs1v5 libclucene-core1v5 libcmis-0.5-5v5 libcolamd2 libcublas10 libcublaslt10 libcudart10.1 libcue2 libcufft10 libcufftw10 libcupsimage2 libcupti-dev libcupti-doc libcupti10.1 libcurand10 libcusolver10 libcusolvermg10 libcusparse10 libdazzle-1.0-0 libdbus-glib-1-2 libdmapsharing-3.0-2 libdotconf0 libe-book-0.1-1 libeot0 libepubgen-0.1-1 libespeak-ng1 libetonyek-0.1-1 libexempi8 libexiv2-27 libexttextcat-2.0-0 libexttextcat-data libfreehand-0.1-1 libfreerdp-client2-2 libfreerdp2-2 libgamemode0 libgamemodeauto0 libgexiv2-2 libglibmm-2.4-1v5 libgnome-games-support-1-3 libgnome-games-support-common libgnome-menu-3-0 libgnome-todo libgom-1.0-0 libgpgmepp6 libgpod-common libgpod4 libgrilo-0.3-0 libgsf-1-114 libgsf-1-common libgtkmm-3.0-1v5 libgtksourceview-4-0 libgtksourceview-4-common libhandy-0.0-0 libjs-jquery libjuh-java libjurt-java liblangtag-common liblangtag1 liblirc-client0 liblua5.3-0 libmessaging-menu0 libmhash2 libminiupnpc17 libmspub-0.1-1 libmwaw-0.3-3 libmythes-1.2-0 libnatpmp1 libncurses5 libneon27-gnutls libnotify-bin libnppc10 libnppial10 libnppicc10 libnppicom10 libnppidei10 libnppif10 libnppig10 libnppim10 libnppist10 libnppisu10 libnppitc10 libnpps10 libnvblas10 libnvgraph10 libnvidia-container-tools libnvidia-container1 libnvjpeg10 libnvrtc10.1 libnvtoolsext1 libnvvm3 libodfgen-0.1-1 liborcus-0.15-0 libpagemaker-0.0-0 libpangomm-1.4-1v5 libpcaudio0 libpeas-1.0-0 libpeas-common libproxy1-plugin-gsettings libproxy1-plugin-networkmanager libqqwing2v5 libraptor2-0 librasqal3 libraw19 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thunderbird-gnome-support totem totem-common totem-plugins tracker tracker-extract tracker-miner-fs transmission-common transmission-gtk ubuntu-desktop-minimal ubuntu-report ubuntu-settings uno-libs-private ure usb-creator-common usb-creator-gtk vino whoopsie x11-apps x11-session-utils xbitmaps xbrlapi xcursor-themes xdg-desktop-portal xdg-desktop-portal-gtk xdg-user-dirs-gtk xinit xorg yaru-theme-gtk yaru-theme-icon yaru-theme-sound Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 251 not upgraded.
WardDeb
commented
6 months ago Note that apt installs are system wide, i.e. it doesn't matter in what conda env you run those.
I'd try two things to continue:
ld doesn't seem to pick up the system wide system libraries, so you could try to include zlib in your deeptools env
conda install -c conda-forge -n deeptools libzlib
Or alternatively (as the gcc version on Ubuntu 20 should be recent enough) an env without gcc should use the one from the system, and thus should be able to pick up the correct headers. Did you receive the same error as the person above, or what prompted you to include gcc in the conda envs ?
krl513
commented
6 months ago I appreciate the tip - I am new to coding in Linux and teaching myself. I was originally receiving an error related to gcc which is why I was including it in the conda envs, but as you saw there were still other issues with the libraries. Including zlib in my deeptools env was not successful.
I was able to resolve this issue -- it seems like it was a conda/pip issue. I first updated conda in my base environment to the most recent version and attempted pip install deeptools again. This install failed due to dependency conflicts arising from pip. I then attempted pip install --upgrade pip . The installed version of pip was already up-to-date but for some reason pip install deeptools was finally successful after these updates. Thank you for your help!!
-ERROR: Could not build wheels for deeptoolsintervals, py2bit, which is required to install pyproject.toml-based projects
I get this error with every possible way.. What could be wrong? thank you!!