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daler / pybedtools

Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
http://daler.github.io/pybedtools
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"python setup.py bdist_wheel did not run successfully" when pip installing with python v3.11 #384

Closed benrhodes26 closed 1 year ago

benrhodes26 commented 1 year ago

As the title says, installing via pip yields an errror (see below).

Downgrading my python to v3.10 fixed the issue, so I assume pybedtools just isnt' currently compatible with python 3.11?

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/helpers.py -> build/lib.linux-x86_64-cpython-311/pybedtools
      copying pybedtools/stats.py -> build/lib.linux-x86_64-cpython-311/pybedtools
      copying pybedtools/genome_registry.py -> build/lib.linux-x86_64-cpython-311/pybedtools
      copying pybedtools/parallel.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/bedtool.py -> build/lib.linux-x86_64-cpython-311/pybedtools
      copying pybedtools/version.py -> build/lib.linux-x86_64-cpython-311/pybedtools
      copying pybedtools/settings.py -> build/lib.linux-x86_64-cpython-311/pybedtools
      copying pybedtools/filenames.py -> build/lib.linux-x86_64-cpython-311/pybedtools
      copying pybedtools/__init__.py -> build/lib.linux-x86_64-cpython-311/pybedtools
      creating 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_helpers.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/test_issues.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_pathlib.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/genomepy_integration.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
      copying pybedtools/test/tfuncs.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/__init__.py -> build/lib.linux-x86_64-cpython-311/pybedtools/test
      creating 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/plotting.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/long_range_interaction.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/bigwig.py -> build/lib.linux-x86_64-cpython-311/pybedtools/contrib
      copying pybedtools/contrib/__init__.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/ben/mambaforge/envs/pyseer_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/CTCF_Mbn2_Bushey_2009.bed -> 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/c.gff -> 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/a.bed.gz -> 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/venn.c.bed -> build/lib.linux-x86_64-cpython-311/pybedtools/test/data
      copying pybedtools/test/data/1000genomes-example.vcf -> 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/m1.bed -> 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/hg38-base.bed -> 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/democonfig.yaml -> 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/gdc.50.200.bam.bai -> 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/genome.fa -> 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/expand_test.bed -> 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/issue319.out.bed -> 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/d.gff -> 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/issue319.bed -> 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/test.fa -> 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/rmsk.hg18.chr21.small.bed.gz -> 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/a.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/CTCF_Kc_Bushey_2009.bed -> 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/gdc.othersort.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/bedpe2.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/snps.bed.gz -> 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/exons.gff -> 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/SuHw_Kc_Bushey_2009.bed -> 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/a.igv_script -> 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/test_bedpe.bed -> 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/b.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/small.bam -> 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/gdc.gff.gz -> 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/issue319.vcf.gz -> 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/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
      copying pybedtools/test/data/gdc.bam -> 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/x.bam -> 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/gdc.gff -> 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/Cp190_Kc_Bushey_2009.bed -> 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/a.links.html -> 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
      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
      gcc -pthread -B /home/ben/mambaforge/envs/pyseer_env/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/ben/mambaforge/envs/pyseer_env/include -fPIC -O2 -isystem /home/ben/mambaforge/envs/pyseer_env/include -fPIC -Ipybedtools/include/ -I/home/ben/mambaforge/envs/pyseer_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/ben/mambaforge/envs/pyseer_env/include/python3.11/bytesobject.h:62,
                       from /home/ben/mambaforge/envs/pyseer_env/include/python3.11/Python.h:50,
                       from pybedtools/cbedtools.cpp:35:
      /home/ben/mambaforge/envs/pyseer_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/ben/mambaforge/envs/pyseer_env/include/python3.11/bytesobject.h:62,
                       from /home/ben/mambaforge/envs/pyseer_env/include/python3.11/Python.h:50,
                       from pybedtools/cbedtools.cpp:35:
      /home/ben/mambaforge/envs/pyseer_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/ben/mambaforge/envs/pyseer_env/include/python3.11/bytesobject.h:62,
                       from /home/ben/mambaforge/envs/pyseer_env/include/python3.11/Python.h:50,
                       from pybedtools/cbedtools.cpp:35:
      /home/ben/mambaforge/envs/pyseer_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/ben/mambaforge/envs/pyseer_env/include/python3.11/bytesobject.h:62,
                       from /home/ben/mambaforge/envs/pyseer_env/include/python3.11/Python.h:50,
                       from pybedtools/cbedtools.cpp:35:
      /home/ben/mambaforge/envs/pyseer_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/ben/mambaforge/envs/pyseer_env/include/python3.11/bytesobject.h:62,
                       from /home/ben/mambaforge/envs/pyseer_env/include/python3.11/Python.h:50,
                       from pybedtools/cbedtools.cpp:35:
      /home/ben/mambaforge/envs/pyseer_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/ben/mambaforge/envs/pyseer_env/include/python3.11/bytesobject.h:62,
                       from /home/ben/mambaforge/envs/pyseer_env/include/python3.11/Python.h:50,
                       from pybedtools/cbedtools.cpp:35:
      /home/ben/mambaforge/envs/pyseer_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/ben/mambaforge/envs/pyseer_env/include/python3.11/Python.h:42,
                       from pybedtools/cbedtools.cpp:35:
      /home/ben/mambaforge/envs/pyseer_env/include/python3.11/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’}
         22 | typedef struct _frame PyFrameObject;
            |                ^~~~~~
      error: command '/usr/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 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
anthony-aylward commented 1 year ago

I am also experiencing this issue on debian bullseye (as well as ubuntu 20.04), both with pybedtools and with another cython project.

dgslos commented 1 year ago

Same here, not installing on python 3.11

maxnewbould-asterinsights commented 1 year ago

Same here

daz10000 commented 1 year ago

And just ran into this wall too..

daler commented 1 year ago

Thank you, everyone, for your patience. Please try version 0.9.1 to see if it works for you on Python 3.11.

anthony-aylward commented 1 year ago

Successfully installed with pip install pybedtools==0.9.1 in a conda environment with python 3.11 on an ubuntu 20.04 system. Thanks @daler , can't wait to see this on bioconda 😄

daz10000 commented 1 year ago

Likewise - it installed correctly on a fresh machine. Much appreciated.

daler commented 1 year ago

Great. Just merged the new recipe, the package should be available in the bioconda channel shortly.