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Problem with jcvi installation #553

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filonico opened this issue Mar 22, 2023 · 4 comments
Closed

Problem with jcvi installation #553

filonico opened this issue Mar 22, 2023 · 4 comments

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@filonico
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filonico commented Mar 22, 2023 •
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Hi,
I keep getting an error while installing jcvi, when using both python3 -m pip install jcvi and python3 -m pip install -e ./ in the cloned git repository. The error is the following:

[...]
Building wheels for collected packages: jcvi, ete3, gffutils, pybedtools, docopt, pyBigWig, pysam
  Building wheel for jcvi (pyproject.toml) ... done
  Created wheel for jcvi: filename=jcvi-1.3.3-cp310-cp310-linux_x86_64.whl size=955478 sha256=5e94e6428da39c87026a19e15aec17917f15fbdc2225e6c7b575bfea7fa9af19
  Stored in directory: /home/filipponicolini/.cache/pip/wheels/ea/57/ad/61b2a38c90de2ceef0f758e45fb3e3d63473a11f125d0502ec
  Building wheel for ete3 (setup.py) ... done
  Created wheel for ete3: filename=ete3-3.1.2-py3-none-any.whl size=2273011 sha256=f1a38a533449a170394fd15860003d895c9ef6c3203ba43fde5a2aa4f767ca59
  Stored in directory: /home/filipponicolini/.cache/pip/wheels/2d/57/b0/e3203a462a984f3eed3cedea122a9fe3f23ed67b2b7d7df2bf
  Building wheel for gffutils (setup.py) ... done
  Created wheel for gffutils: filename=gffutils-0.11.1-py3-none-any.whl size=1619347 sha256=85cc12d5566a4bccb66c4561c3e9dd3f4edc4248c6a533a728e8b8659162dd96
  Stored in directory: /home/filipponicolini/.cache/pip/wheels/06/01/2f/ecea8040fe2e2e905351b8027efcca436e23962624e20ed8c3
  Building wheel for pybedtools (setup.py) ... done
  Created wheel for pybedtools: filename=pybedtools-0.9.0-cp310-cp310-linux_x86_64.whl size=12744698 sha256=e05b647c62494e00c9979a89be4ae2ecbe90a439a0e0e535eb7c2cf1ec5212e0
  Stored in directory: /home/filipponicolini/.cache/pip/wheels/50/a7/83/8f6b841c60977cbd76f54f30f5b9e11159150d73a0a8fa42ff
  Building wheel for docopt (setup.py) ... done
  Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13705 sha256=c834ae94a534f585c723a5005df2eeac83f3341f2c55d2b17f76fad8d5439a45
  Stored in directory: /home/filipponicolini/.cache/pip/wheels/fc/ab/d4/5da2067ac95b36618c629a5f93f809425700506f72c9732fac
  Building wheel for pyBigWig (pyproject.toml) ... error
  error: subprocess-exited-with-error
  
  × Building wheel for pyBigWig (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [31 lines of output]
      /tmp/pip-build-env-eojwka3w/overlay/lib/python3.10/site-packages/setuptools/config/pyprojecttoml.py:108: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*.
        warnings.warn(msg, _BetaConfiguration)
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build/lib.linux-x86_64-cpython-310
      creating build/lib.linux-x86_64-cpython-310/pyBigWigTest
      copying pyBigWigTest/__init__.py -> build/lib.linux-x86_64-cpython-310/pyBigWigTest
      copying pyBigWigTest/test.py -> build/lib.linux-x86_64-cpython-310/pyBigWigTest
      running egg_info
      writing pyBigWig.egg-info/PKG-INFO
      writing dependency_links to pyBigWig.egg-info/dependency_links.txt
      writing top-level names to pyBigWig.egg-info/top_level.txt
      listing git files failed - pretending there aren't any
      reading manifest file 'pyBigWig.egg-info/SOURCES.txt'
      reading manifest template 'MANIFEST.in'
      adding license file 'LICENSE.txt'
      writing manifest file 'pyBigWig.egg-info/SOURCES.txt'
      running build_ext
      building 'pyBigWig' extension
      creating build/temp.linux-x86_64-cpython-310
      creating build/temp.linux-x86_64-cpython-310/libBigWig
      /home/filipponicolini/.conda/envs/jcvi_env/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/filipponicolini/.conda/envs/jcvi_env/include -fPIC -O2 -isystem /home/filipponicolini/.conda/envs/jcvi_env/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/filipponicolini/.conda/envs/jcvi_env/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/filipponicolini/.conda/envs/jcvi_env/include -fPIC -DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/home/filipponicolini/.conda/envs/jcvi_env/include/python3.10 -I/tmp/pip-build-env-eojwka3w/overlay/lib/python3.10/site-packages/numpy/core/include -I/home/filipponicolini/.conda/envs/jcvi_env/include/python3.10 -c libBigWig/bwRead.c -o build/temp.linux-x86_64-cpython-310/libBigWig/bwRead.o
      In file included from libBigWig/bigWig.h:4,
                       from libBigWig/bwRead.c:1:
      libBigWig/bigWigIO.h:5:10: fatal error: curl/curl.h: No such file or directory
          5 | #include <curl/curl.h>
            |          ^~~~~~~~~~~~~
      compilation terminated.
      error: command '/home/filipponicolini/.conda/envs/jcvi_env/bin/x86_64-conda-linux-gnu-cc' 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 pyBigWig
  Building wheel for pysam (setup.py) ... done
  Created wheel for pysam: filename=pysam-0.20.0-cp310-cp310-linux_x86_64.whl size=3233169 sha256=93170ca86e12ca1db41d2a076d76c152be5f1ae8279ca0c0691a0e5cc2b95aa4
  Stored in directory: /home/filipponicolini/.cache/pip/wheels/68/d4/5c/c09b53de80bf656ec6de3cbf8e4ad60208f4252e081788dd2b
Successfully built jcvi ete3 gffutils pybedtools docopt pysam
Failed to build pyBigWig
ERROR: Could not build wheels for pyBigWig, which is required to install pyproject.toml-based projects

I also tried to install manually the single python libraries, but (I guess) is still making troubles. I'm working inside a conda environment with python 3.11. Do you have any hint on how to solve the problem?

Thanks a lot!
@tanghaibao
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@filonico

Seems to be missing libcurl, maybe something like yum install libcurl-devel

@filonico
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Dear @tanghaibao, thanks for the response! I managed to install libcurl via conda (unfortunately I don't have root privileges to run yum), but an error keeps showing up:

Collecting pybedtools
  Using cached pybedtools-0.9.0.tar.gz (12.5 MB)
  Preparing metadata (setup.py) ... done
Requirement already satisfied: six in /home/filipponicolini/.conda/envs/jcvi_env/lib/python3.11/site-packages (from pybedtools) (1.16.0)
Requirement already satisfied: pysam in /home/filipponicolini/.conda/envs/jcvi_env/lib/python3.11/site-packages (from pybedtools) (0.20.0)
Building wheels for collected packages: pybedtools
  Building wheel for pybedtools (setup.py) ... error
  error: subprocess-exited-with-error
  
  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [284 lines of output]
      running bdist_wheel
      The [wheel] section is deprecated. Use [bdist_wheel] instead.
      running build
      running build_py
      creating build
      creating build/lib.linux-x86_64-cpython-311
      creating build/lib.linux-x86_64-cpython-311/pybedtools
      copying pybedtools/settings.py -> build/lib.linux-x86_64-cpython-311/pybedtools
      copying pybedtools/genome_registry.py -> build/lib.linux-x86_64-cpython-311/pybedtools
      copying pybedtools/version.py -> build/lib.linux-x86_64-cpython-311/pybedtools
      copying pybedtools/__init__.py -> build/lib.linux-x86_64-cpython-311/pybedtools
      copying pybedtools/bedtool.py -> build/lib.linux-x86_64-cpython-311/pybedtools
      copying pybedtools/paths.py -> build/lib.linux-x86_64-cpython-311/pybedtools
      copying pybedtools/logger.py -> build/lib.linux-x86_64-cpython-311/pybedtools
      copying pybedtools/parallel.py -> build/lib.linux-x86_64-cpython-311/pybedtools
      copying pybedtools/helpers.py -> build/lib.linux-x86_64-cpython-311/pybedtools
      copying pybedtools/filenames.py -> build/lib.linux-x86_64-cpython-311/pybedtools
      copying pybedtools/stats.py -> build/lib.linux-x86_64-cpython-311/pybedtools
      creating build/lib.linux-x86_64-cpython-311/pybedtools/test
      copying pybedtools/test/genomepy_integration.py -> build/lib.linux-x86_64-cpython-311/pybedtools/test
      copying pybedtools/test/regression_tests.py -> build/lib.linux-x86_64-cpython-311/pybedtools/test
      copying pybedtools/test/test_gzip_support.py -> build/lib.linux-x86_64-cpython-311/pybedtools/test
      copying pybedtools/test/test_contrib.py -> build/lib.linux-x86_64-cpython-311/pybedtools/test
      copying pybedtools/test/__init__.py -> build/lib.linux-x86_64-cpython-311/pybedtools/test
      copying pybedtools/test/tfuncs.py -> build/lib.linux-x86_64-cpython-311/pybedtools/test
      copying pybedtools/test/test_helpers.py -> build/lib.linux-x86_64-cpython-311/pybedtools/test
      copying pybedtools/test/test_pathlib.py -> build/lib.linux-x86_64-cpython-311/pybedtools/test
      copying pybedtools/test/test_iter.py -> build/lib.linux-x86_64-cpython-311/pybedtools/test
      copying pybedtools/test/test_1.py -> build/lib.linux-x86_64-cpython-311/pybedtools/test
      copying pybedtools/test/test_len_leak.py -> build/lib.linux-x86_64-cpython-311/pybedtools/test
      copying pybedtools/test/test_issues.py -> build/lib.linux-x86_64-cpython-311/pybedtools/test
      copying pybedtools/test/test_cbedtools.py -> build/lib.linux-x86_64-cpython-311/pybedtools/test
      creating build/lib.linux-x86_64-cpython-311/pybedtools/contrib
      copying pybedtools/contrib/__init__.py -> build/lib.linux-x86_64-cpython-311/pybedtools/contrib
      copying pybedtools/contrib/plotting.py -> build/lib.linux-x86_64-cpython-311/pybedtools/contrib
      copying pybedtools/contrib/bigbed.py -> build/lib.linux-x86_64-cpython-311/pybedtools/contrib
      copying pybedtools/contrib/intersection_matrix.py -> build/lib.linux-x86_64-cpython-311/pybedtools/contrib
      copying pybedtools/contrib/bigwig.py -> build/lib.linux-x86_64-cpython-311/pybedtools/contrib
      copying pybedtools/contrib/venn_maker.py -> build/lib.linux-x86_64-cpython-311/pybedtools/contrib
      copying pybedtools/contrib/long_range_interaction.py -> build/lib.linux-x86_64-cpython-311/pybedtools/contrib
      creating build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/__init__.py -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      running egg_info
      creating pybedtools.egg-info
      writing pybedtools.egg-info/PKG-INFO
      writing dependency_links to pybedtools.egg-info/dependency_links.txt
      writing requirements to pybedtools.egg-info/requires.txt
      writing top-level names to pybedtools.egg-info/top_level.txt
      writing manifest file 'pybedtools.egg-info/SOURCES.txt'
      reading manifest file 'pybedtools.egg-info/SOURCES.txt'
      adding license file 'LICENSE.txt'
      writing manifest file 'pybedtools.egg-info/SOURCES.txt'
      /home/filipponicolini/.conda/envs/jcvi_env/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning:     Installing 'pybedtools.include' as data is deprecated, please list it in `packages`.
          !!
      
      
          ############################
          # Package would be ignored #
          ############################
          Python recognizes 'pybedtools.include' as an importable package,
          but it is not listed in the `packages` configuration of setuptools.
      
          'pybedtools.include' has been automatically added to the distribution only
          because it may contain data files, but this behavior is likely to change
          in future versions of setuptools (and therefore is considered deprecated).
      
          Please make sure that 'pybedtools.include' is included as a package by using
          the `packages` configuration field or the proper discovery methods
          (for example by using `find_namespace_packages(...)`/`find_namespace:`
          instead of `find_packages(...)`/`find:`).
      
          You can read more about "package discovery" and "data files" on setuptools
          documentation page.
      
      
      !!
      
        check.warn(importable)
      copying pybedtools/_Window.pyx -> build/lib.linux-x86_64-cpython-311/pybedtools
      copying pybedtools/cbedtools.cpp -> build/lib.linux-x86_64-cpython-311/pybedtools
      copying pybedtools/cbedtools.pxd -> build/lib.linux-x86_64-cpython-311/pybedtools
      copying pybedtools/cbedtools.pyx -> build/lib.linux-x86_64-cpython-311/pybedtools
      copying pybedtools/featurefuncs.cpp -> build/lib.linux-x86_64-cpython-311/pybedtools
      copying pybedtools/featurefuncs.pyx -> build/lib.linux-x86_64-cpython-311/pybedtools
      creating build/lib.linux-x86_64-cpython-311/pybedtools/include
      copying pybedtools/include/bedFile.cpp -> build/lib.linux-x86_64-cpython-311/pybedtools/include
      copying pybedtools/include/fileType.cpp -> build/lib.linux-x86_64-cpython-311/pybedtools/include
      copying pybedtools/include/gzstream.cpp -> build/lib.linux-x86_64-cpython-311/pybedtools/include
      copying pybedtools/test/data/1000genomes-example.vcf -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/issue_121.bam -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/snps.bed.gz -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/exons.gff -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/small.bam -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/m1.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/gdc.othersort.bam -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/hg19.gff -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/multibamcov_test.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/test_bedpe.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/gdc.sorted.bam.bai -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/gdc.sorted.bam -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/hg38-problem.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/issue319.out.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/genome.fa -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/test.fa.fai -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/hg38-base.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/test_peaks.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/gdc.cram -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/x.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/b.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/gdc.50.200.bam -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/a.igv_script -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/a.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/vcf-stderr-test.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/gdc.1.100.bam -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/expand_test.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/y.bam -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/venn.c.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/democonfig.yaml -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/issue319.vcf.gz -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/small.fastq -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/gdc.gff -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/c.gff -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/test_tsses.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/x.bam -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/a.links.html -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/venn.b.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/gdc.bam -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/gdc.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/mm9.bed12 -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/a.bed.gz.tbi -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/bedpe2.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/tag_test2.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/vcf-stderr-test.vcf -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/issue319.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/gdc.50.200.bam.bai -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/bedpe.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/gdc.1.100.bam.bai -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/gdc.gff.gz -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/test.fa -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/v.vcf -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/d.gff -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/a.bed.gz -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/164.gtf -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/tag_test1.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/reads.bam -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      running build_ext
      building 'pybedtools.cbedtools' extension
      creating build/temp.linux-x86_64-cpython-311
      creating build/temp.linux-x86_64-cpython-311/pybedtools
      creating build/temp.linux-x86_64-cpython-311/pybedtools/include
      /home/filipponicolini/.conda/envs/jcvi_env/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/filipponicolini/.conda/envs/jcvi_env/include -fPIC -O2 -isystem /home/filipponicolini/.conda/envs/jcvi_env/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/filipponicolini/.conda/envs/jcvi_env/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/filipponicolini/.conda/envs/jcvi_env/include -fPIC -Ipybedtools/include/ -I/home/filipponicolini/.conda/envs/jcvi_env/include/python3.11 -c pybedtools/cbedtools.cpp -o build/temp.linux-x86_64-cpython-311/pybedtools/cbedtools.o
      pybedtools/cbedtools.cpp: In function 'int __Pyx_PyBytes_Equals(PyObject*, PyObject*, int)':
      pybedtools/cbedtools.cpp:18681:43: warning: 'PyBytesObject::ob_shash' is deprecated [-Wdeprecated-declarations]
      18681 |             hash1 = ((PyBytesObject*)s1)->ob_shash;
            |                                           ^~~~~~~~
      In file included from /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/bytesobject.h:62,
                       from /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/Python.h:50,
                       from pybedtools/cbedtools.cpp:35:
      /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/cpython/bytesobject.h:7:35: note: declared here
          7 |     Py_DEPRECATED(3.11) Py_hash_t ob_shash;
            |                                   ^~~~~~~~
      pybedtools/cbedtools.cpp:18681:43: warning: 'PyBytesObject::ob_shash' is deprecated [-Wdeprecated-declarations]
      18681 |             hash1 = ((PyBytesObject*)s1)->ob_shash;
            |                                           ^~~~~~~~
      In file included from /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/bytesobject.h:62,
                       from /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/Python.h:50,
                       from pybedtools/cbedtools.cpp:35:
      /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/cpython/bytesobject.h:7:35: note: declared here
          7 |     Py_DEPRECATED(3.11) Py_hash_t ob_shash;
            |                                   ^~~~~~~~
      pybedtools/cbedtools.cpp:18681:43: warning: 'PyBytesObject::ob_shash' is deprecated [-Wdeprecated-declarations]
      18681 |             hash1 = ((PyBytesObject*)s1)->ob_shash;
            |                                           ^~~~~~~~
      In file included from /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/bytesobject.h:62,
                       from /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/Python.h:50,
                       from pybedtools/cbedtools.cpp:35:
      /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/cpython/bytesobject.h:7:35: note: declared here
          7 |     Py_DEPRECATED(3.11) Py_hash_t ob_shash;
            |                                   ^~~~~~~~
      pybedtools/cbedtools.cpp:18682:43: warning: 'PyBytesObject::ob_shash' is deprecated [-Wdeprecated-declarations]
      18682 |             hash2 = ((PyBytesObject*)s2)->ob_shash;
            |                                           ^~~~~~~~
      In file included from /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/bytesobject.h:62,
                       from /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/Python.h:50,
                       from pybedtools/cbedtools.cpp:35:
      /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/cpython/bytesobject.h:7:35: note: declared here
          7 |     Py_DEPRECATED(3.11) Py_hash_t ob_shash;
            |                                   ^~~~~~~~
      pybedtools/cbedtools.cpp:18682:43: warning: 'PyBytesObject::ob_shash' is deprecated [-Wdeprecated-declarations]
      18682 |             hash2 = ((PyBytesObject*)s2)->ob_shash;
            |                                           ^~~~~~~~
      In file included from /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/bytesobject.h:62,
                       from /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/Python.h:50,
                       from pybedtools/cbedtools.cpp:35:
      /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/cpython/bytesobject.h:7:35: note: declared here
          7 |     Py_DEPRECATED(3.11) Py_hash_t ob_shash;
            |                                   ^~~~~~~~
      pybedtools/cbedtools.cpp:18682:43: warning: 'PyBytesObject::ob_shash' is deprecated [-Wdeprecated-declarations]
      18682 |             hash2 = ((PyBytesObject*)s2)->ob_shash;
            |                                           ^~~~~~~~
      In file included from /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/bytesobject.h:62,
                       from /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/Python.h:50,
                       from pybedtools/cbedtools.cpp:35:
      /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/cpython/bytesobject.h:7:35: note: declared here
          7 |     Py_DEPRECATED(3.11) Py_hash_t ob_shash;
            |                                   ^~~~~~~~
      pybedtools/cbedtools.cpp: In function '_PyErr_StackItem* __Pyx_PyErr_GetTopmostException(PyThreadState*)':
      pybedtools/cbedtools.cpp:19126:23: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_type'
      19126 |     while ((exc_info->exc_type == NULL || exc_info->exc_type == Py_None) &&
            |                       ^~~~~~~~
      pybedtools/cbedtools.cpp:19126:53: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_type'
      19126 |     while ((exc_info->exc_type == NULL || exc_info->exc_type == Py_None) &&
            |                                                     ^~~~~~~~
      pybedtools/cbedtools.cpp: In function 'void __Pyx__ExceptionSave(PyThreadState*, PyObject**, PyObject**, PyObject**)':
      pybedtools/cbedtools.cpp:19140:23: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_type'
      19140 |     *type = exc_info->exc_type;
            |                       ^~~~~~~~
      pybedtools/cbedtools.cpp:19142:21: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_traceback'
      19142 |     *tb = exc_info->exc_traceback;
            |                     ^~~~~~~~~~~~~
      pybedtools/cbedtools.cpp: In function 'void __Pyx__ExceptionReset(PyThreadState*, PyObject*, PyObject*, PyObject*)':
      pybedtools/cbedtools.cpp:19156:26: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_type'
      19156 |     tmp_type = exc_info->exc_type;
            |                          ^~~~~~~~
      pybedtools/cbedtools.cpp:19158:24: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_traceback'
      19158 |     tmp_tb = exc_info->exc_traceback;
            |                        ^~~~~~~~~~~~~
      pybedtools/cbedtools.cpp:19159:15: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_type'
      19159 |     exc_info->exc_type = type;
            |               ^~~~~~~~
      pybedtools/cbedtools.cpp:19161:15: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_traceback'
      19161 |     exc_info->exc_traceback = tb;
            |               ^~~~~~~~~~~~~
      pybedtools/cbedtools.cpp: In function 'int __Pyx__GetException(PyThreadState*, PyObject**, PyObject**, PyObject**)':
      pybedtools/cbedtools.cpp:20178:30: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_type'
      20178 |         tmp_type = exc_info->exc_type;
            |                              ^~~~~~~~
      pybedtools/cbedtools.cpp:20180:28: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_traceback'
      20180 |         tmp_tb = exc_info->exc_traceback;
            |                            ^~~~~~~~~~~~~
      pybedtools/cbedtools.cpp:20181:19: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_type'
      20181 |         exc_info->exc_type = local_type;
            |                   ^~~~~~~~
      pybedtools/cbedtools.cpp:20183:19: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_traceback'
      20183 |         exc_info->exc_traceback = local_tb;
            |                   ^~~~~~~~~~~~~
      pybedtools/cbedtools.cpp: In function 'void __Pyx__ExceptionSwap(PyThreadState*, PyObject**, PyObject**, PyObject**)':
      pybedtools/cbedtools.cpp:20828:26: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_type'
      20828 |     tmp_type = exc_info->exc_type;
            |                          ^~~~~~~~
      pybedtools/cbedtools.cpp:20830:24: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_traceback'
      20830 |     tmp_tb = exc_info->exc_traceback;
            |                        ^~~~~~~~~~~~~
      pybedtools/cbedtools.cpp:20831:15: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_type'
      20831 |     exc_info->exc_type = *type;
            |               ^~~~~~~~
      pybedtools/cbedtools.cpp:20833:15: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_traceback'
      20833 |     exc_info->exc_traceback = *tb;
            |               ^~~~~~~~~~~~~
      pybedtools/cbedtools.cpp: In function 'void __Pyx_AddTraceback(const char*, int, int, const char*)':
      pybedtools/cbedtools.cpp:475:62: error: invalid use of incomplete type 'PyFrameObject' {aka 'struct _frame'}
        475 |   #define __Pyx_PyFrame_SetLineNumber(frame, lineno)  (frame)->f_lineno = (lineno)
            |                                                              ^~
      pybedtools/cbedtools.cpp:21511:5: note: in expansion of macro '__Pyx_PyFrame_SetLineNumber'
      21511 |     __Pyx_PyFrame_SetLineNumber(py_frame, py_line);
            |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
      In file included from /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/Python.h:42,
                       from pybedtools/cbedtools.cpp:35:
      /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/pytypedefs.h:22:16: note: forward declaration of 'PyFrameObject' {aka 'struct _frame'}
         22 | typedef struct _frame PyFrameObject;
            |                ^~~~~~
      error: command '/home/filipponicolini/.conda/envs/jcvi_env/bin/x86_64-conda-linux-gnu-cc' 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 pybedtools
  Running setup.py clean for pybedtools
  error: subprocess-exited-with-error
  
  × python setup.py clean did not run successfully.
  │ exit code: 1
  ╰─> [6 lines of output]
      usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
         or: setup.py --help [cmd1 cmd2 ...]
         or: setup.py --help-commands
         or: setup.py cmd --help
      
      error: option --all not recognized
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed cleaning build dir for pybedtools
Failed to build pybedtools
Installing collected packages: pybedtools
  Running setup.py install for pybedtools ... error
  error: subprocess-exited-with-error
  
  × Running setup.py install for pybedtools did not run successfully.
  │ exit code: 1
  ╰─> [164 lines of output]
      running install
      /home/filipponicolini/.conda/envs/jcvi_env/lib/python3.11/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
        warnings.warn(
      running build
      running build_py
      copying pybedtools/version.py -> build/lib.linux-x86_64-cpython-311/pybedtools
      running egg_info
      writing pybedtools.egg-info/PKG-INFO
      writing dependency_links to pybedtools.egg-info/dependency_links.txt
      writing requirements to pybedtools.egg-info/requires.txt
      writing top-level names to pybedtools.egg-info/top_level.txt
      reading manifest file 'pybedtools.egg-info/SOURCES.txt'
      adding license file 'LICENSE.txt'
      writing manifest file 'pybedtools.egg-info/SOURCES.txt'
      /home/filipponicolini/.conda/envs/jcvi_env/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning:     Installing 'pybedtools.include' as data is deprecated, please list it in `packages`.
          !!
      
      
          ############################
          # Package would be ignored #
          ############################
          Python recognizes 'pybedtools.include' as an importable package,
          but it is not listed in the `packages` configuration of setuptools.
      
          'pybedtools.include' has been automatically added to the distribution only
          because it may contain data files, but this behavior is likely to change
          in future versions of setuptools (and therefore is considered deprecated).
      
          Please make sure that 'pybedtools.include' is included as a package by using
          the `packages` configuration field or the proper discovery methods
          (for example by using `find_namespace_packages(...)`/`find_namespace:`
          instead of `find_packages(...)`/`find:`).
      
          You can read more about "package discovery" and "data files" on setuptools
          documentation page.
      
      
      !!
      
        check.warn(importable)
      running build_ext
      building 'pybedtools.cbedtools' extension
      /home/filipponicolini/.conda/envs/jcvi_env/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/filipponicolini/.conda/envs/jcvi_env/include -fPIC -O2 -isystem /home/filipponicolini/.conda/envs/jcvi_env/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/filipponicolini/.conda/envs/jcvi_env/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/filipponicolini/.conda/envs/jcvi_env/include -fPIC -Ipybedtools/include/ -I/home/filipponicolini/.conda/envs/jcvi_env/include/python3.11 -c pybedtools/cbedtools.cpp -o build/temp.linux-x86_64-cpython-311/pybedtools/cbedtools.o
      pybedtools/cbedtools.cpp: In function 'int __Pyx_PyBytes_Equals(PyObject*, PyObject*, int)':
      pybedtools/cbedtools.cpp:18681:43: warning: 'PyBytesObject::ob_shash' is deprecated [-Wdeprecated-declarations]
      18681 |             hash1 = ((PyBytesObject*)s1)->ob_shash;
            |                                           ^~~~~~~~
      In file included from /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/bytesobject.h:62,
                       from /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/Python.h:50,
                       from pybedtools/cbedtools.cpp:35:
      /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/cpython/bytesobject.h:7:35: note: declared here
          7 |     Py_DEPRECATED(3.11) Py_hash_t ob_shash;
            |                                   ^~~~~~~~
      pybedtools/cbedtools.cpp:18681:43: warning: 'PyBytesObject::ob_shash' is deprecated [-Wdeprecated-declarations]
      18681 |             hash1 = ((PyBytesObject*)s1)->ob_shash;
            |                                           ^~~~~~~~
      In file included from /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/bytesobject.h:62,
                       from /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/Python.h:50,
                       from pybedtools/cbedtools.cpp:35:
      /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/cpython/bytesobject.h:7:35: note: declared here
          7 |     Py_DEPRECATED(3.11) Py_hash_t ob_shash;
            |                                   ^~~~~~~~
      pybedtools/cbedtools.cpp:18681:43: warning: 'PyBytesObject::ob_shash' is deprecated [-Wdeprecated-declarations]
      18681 |             hash1 = ((PyBytesObject*)s1)->ob_shash;
            |                                           ^~~~~~~~
      In file included from /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/bytesobject.h:62,
                       from /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/Python.h:50,
                       from pybedtools/cbedtools.cpp:35:
      /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/cpython/bytesobject.h:7:35: note: declared here
          7 |     Py_DEPRECATED(3.11) Py_hash_t ob_shash;
            |                                   ^~~~~~~~
      pybedtools/cbedtools.cpp:18682:43: warning: 'PyBytesObject::ob_shash' is deprecated [-Wdeprecated-declarations]
      18682 |             hash2 = ((PyBytesObject*)s2)->ob_shash;
            |                                           ^~~~~~~~
      In file included from /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/bytesobject.h:62,
                       from /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/Python.h:50,
                       from pybedtools/cbedtools.cpp:35:
      /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/cpython/bytesobject.h:7:35: note: declared here
          7 |     Py_DEPRECATED(3.11) Py_hash_t ob_shash;
            |                                   ^~~~~~~~
      pybedtools/cbedtools.cpp:18682:43: warning: 'PyBytesObject::ob_shash' is deprecated [-Wdeprecated-declarations]
      18682 |             hash2 = ((PyBytesObject*)s2)->ob_shash;
            |                                           ^~~~~~~~
      In file included from /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/bytesobject.h:62,
                       from /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/Python.h:50,
                       from pybedtools/cbedtools.cpp:35:
      /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/cpython/bytesobject.h:7:35: note: declared here
          7 |     Py_DEPRECATED(3.11) Py_hash_t ob_shash;
            |                                   ^~~~~~~~
      pybedtools/cbedtools.cpp:18682:43: warning: 'PyBytesObject::ob_shash' is deprecated [-Wdeprecated-declarations]
      18682 |             hash2 = ((PyBytesObject*)s2)->ob_shash;
            |                                           ^~~~~~~~
      In file included from /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/bytesobject.h:62,
                       from /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/Python.h:50,
                       from pybedtools/cbedtools.cpp:35:
      /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/cpython/bytesobject.h:7:35: note: declared here
          7 |     Py_DEPRECATED(3.11) Py_hash_t ob_shash;
            |                                   ^~~~~~~~
      pybedtools/cbedtools.cpp: In function '_PyErr_StackItem* __Pyx_PyErr_GetTopmostException(PyThreadState*)':
      pybedtools/cbedtools.cpp:19126:23: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_type'
      19126 |     while ((exc_info->exc_type == NULL || exc_info->exc_type == Py_None) &&
            |                       ^~~~~~~~
      pybedtools/cbedtools.cpp:19126:53: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_type'
      19126 |     while ((exc_info->exc_type == NULL || exc_info->exc_type == Py_None) &&
            |                                                     ^~~~~~~~
      pybedtools/cbedtools.cpp: In function 'void __Pyx__ExceptionSave(PyThreadState*, PyObject**, PyObject**, PyObject**)':
      pybedtools/cbedtools.cpp:19140:23: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_type'
      19140 |     *type = exc_info->exc_type;
            |                       ^~~~~~~~
      pybedtools/cbedtools.cpp:19142:21: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_traceback'
      19142 |     *tb = exc_info->exc_traceback;
            |                     ^~~~~~~~~~~~~
      pybedtools/cbedtools.cpp: In function 'void __Pyx__ExceptionReset(PyThreadState*, PyObject*, PyObject*, PyObject*)':
      pybedtools/cbedtools.cpp:19156:26: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_type'
      19156 |     tmp_type = exc_info->exc_type;
            |                          ^~~~~~~~
      pybedtools/cbedtools.cpp:19158:24: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_traceback'
      19158 |     tmp_tb = exc_info->exc_traceback;
            |                        ^~~~~~~~~~~~~
      pybedtools/cbedtools.cpp:19159:15: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_type'
      19159 |     exc_info->exc_type = type;
            |               ^~~~~~~~
      pybedtools/cbedtools.cpp:19161:15: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_traceback'
      19161 |     exc_info->exc_traceback = tb;
            |               ^~~~~~~~~~~~~
      pybedtools/cbedtools.cpp: In function 'int __Pyx__GetException(PyThreadState*, PyObject**, PyObject**, PyObject**)':
      pybedtools/cbedtools.cpp:20178:30: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_type'
      20178 |         tmp_type = exc_info->exc_type;
            |                              ^~~~~~~~
      pybedtools/cbedtools.cpp:20180:28: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_traceback'
      20180 |         tmp_tb = exc_info->exc_traceback;
            |                            ^~~~~~~~~~~~~
      pybedtools/cbedtools.cpp:20181:19: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_type'
      20181 |         exc_info->exc_type = local_type;
            |                   ^~~~~~~~
      pybedtools/cbedtools.cpp:20183:19: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_traceback'
      20183 |         exc_info->exc_traceback = local_tb;
            |                   ^~~~~~~~~~~~~
      pybedtools/cbedtools.cpp: In function 'void __Pyx__ExceptionSwap(PyThreadState*, PyObject**, PyObject**, PyObject**)':
      pybedtools/cbedtools.cpp:20828:26: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_type'
      20828 |     tmp_type = exc_info->exc_type;
            |                          ^~~~~~~~
      pybedtools/cbedtools.cpp:20830:24: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_traceback'
      20830 |     tmp_tb = exc_info->exc_traceback;
            |                        ^~~~~~~~~~~~~
      pybedtools/cbedtools.cpp:20831:15: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_type'
      20831 |     exc_info->exc_type = *type;
            |               ^~~~~~~~
      pybedtools/cbedtools.cpp:20833:15: error: '_PyErr_StackItem' {aka 'struct _err_stackitem'} has no member named 'exc_traceback'
      20833 |     exc_info->exc_traceback = *tb;
            |               ^~~~~~~~~~~~~
      pybedtools/cbedtools.cpp: In function 'void __Pyx_AddTraceback(const char*, int, int, const char*)':
      pybedtools/cbedtools.cpp:475:62: error: invalid use of incomplete type 'PyFrameObject' {aka 'struct _frame'}
        475 |   #define __Pyx_PyFrame_SetLineNumber(frame, lineno)  (frame)->f_lineno = (lineno)
            |                                                              ^~
      pybedtools/cbedtools.cpp:21511:5: note: in expansion of macro '__Pyx_PyFrame_SetLineNumber'
      21511 |     __Pyx_PyFrame_SetLineNumber(py_frame, py_line);
            |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
      In file included from /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/Python.h:42,
                       from pybedtools/cbedtools.cpp:35:
      /home/filipponicolini/.conda/envs/jcvi_env/include/python3.11/pytypedefs.h:22:16: note: forward declaration of 'PyFrameObject' {aka 'struct _frame'}
         22 | typedef struct _frame PyFrameObject;
            |                ^~~~~~
      error: command '/home/filipponicolini/.conda/envs/jcvi_env/bin/x86_64-conda-linux-gnu-cc' failed with exit code 1
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure

× Encountered error while trying to install package.
╰─> pybedtools

note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.

Do you have any further suggestion? Thanks!

@filonico
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Ok I solved the problem. I leave hereafter the solution for those who are encountering similar issues:

  1. Install jcvi dependencies using mamba (please note that installing jcvi dependencies with conda didn't work for me);
  2. install the jcvi package using python python3 -m pip install jcvi;
  3. That's it! It should work.

@benyoung93
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Just adding in my exact install code as the stupid quotes around biopython set me back a day, sighhhhhhh

mamba create -n allmaps_env_v2 -c conda-forge -c bioconda "biopython=1.70" numpy deap networkx matplotlib
mamba activate allmaps_env_v2
python3 -m pip install jcvi
mamba activate allmaps_env_v2
wget https://www.dropbox.com/s/b497bi2b594m6fp/ALLMAPS-testdata.zip
unzip ALLMAPS-testdata.zip
cd ALLMAPS-testdata
sh run.sh

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@tanghaibao @benyoung93 @filonico