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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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build failure under python 3.11 #387

Closed kbipinkumar closed 1 year ago

kbipinkumar commented 1 year ago

pybedtools is failing to build against python 3.11 and cython 0.29.34 with following error

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/__init__.py -> build/lib.linux-x86_64-cpython-311/pybedtools
copying pybedtools/bedtool.py -> build/lib.linux-x86_64-cpython-311/pybedtools
copying pybedtools/filenames.py -> build/lib.linux-x86_64-cpython-311/pybedtools
copying pybedtools/genome_registry.py -> build/lib.linux-x86_64-cpython-311/pybedtools
copying pybedtools/helpers.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/paths.py -> build/lib.linux-x86_64-cpython-311/pybedtools
copying pybedtools/settings.py -> build/lib.linux-x86_64-cpython-311/pybedtools
copying pybedtools/stats.py -> build/lib.linux-x86_64-cpython-311/pybedtools
copying pybedtools/version.py -> build/lib.linux-x86_64-cpython-311/pybedtools
creating 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/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_1.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/test_contrib.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_helpers.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_len_leak.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/tfuncs.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/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/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/plotting.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
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'
/usr/lib/python3.11/site-packages/setuptools/command/build_py.py:201: _Warning: Package 'pybedtools.include' is absent from the `packages` configuration.
!!

        ********************************************************************************
        ############################
        # Package would be ignored #
        ############################
        Python recognizes 'pybedtools.include' 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 'pybedtools.include' 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 'pybedtools.include' to be distributed and are
        already explicitly excluding 'pybedtools.include' 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)
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/164.gtf -> 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/BEAF_Mbn2_Bushey_2009.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/CTCF_Mbn2_Bushey_2009.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/Cp190_Mbn2_Bushey_2009.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/SuHw_Mbn2_Bushey_2009.bed -> 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/a.bed.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/a.igv_script -> 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/b.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/bedpe2.bed -> 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/d.gff -> 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/dm3-chr2L-5M-invalid.gff.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/expand_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/gdc.1.100.bam.bai -> 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/gdc.50.200.bam.bai -> 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/gdc.cram -> 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/gdc.gff.gz -> 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/gdc.sorted.bam -> 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/genome.fa -> 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/hg38-base.bed -> 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/issue319.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/issue319.vcf.gz -> 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/m1.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/multibamcov_test.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/rmsk.hg18.chr21.small.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/small.bam -> 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/snps.bed.gz -> 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/tag_test2.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/test.fa.fai -> 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/test_peaks.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/v.vcf -> 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/vcf-stderr-test.vcf -> 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/venn.c.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/x.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
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 -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/cbedtools.cpp -o build/temp.linux-x86_64-cpython-311/pybedtools/cbedtools.o
In file included from pybedtools/cbedtools.cpp:731:
pybedtools/include/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
   92 |     for (register short i = 0; i < _binLevels; ++i) {
      |                         ^
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 /usr/include/python3.11/bytesobject.h:62,
                 from /usr/include/python3.11/Python.h:50,
                 from pybedtools/cbedtools.cpp:35:
/usr/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;
      |                                           ^~~~~~~~
/usr/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;
      |                                           ^~~~~~~~
/usr/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;
      |                                           ^~~~~~~~
/usr/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;
      |                                           ^~~~~~~~
/usr/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;
      |                                           ^~~~~~~~
/usr/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 /usr/include/python3.11/Python.h:42:
/usr/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
==> ERROR:(B A failure occurred in build().(B
    Aborting...(B
mgperry commented 1 year ago

I am also experiencing this.

whywhowhat commented 1 year ago

i am also having error : ERROR: Failed building wheel 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.

theAeon commented 1 year ago

cython files need to be recompiled. download the tar.gz and run setup.py cythonize before running setup bdist_wheel

daler commented 1 year ago

@theAeon exactly -- see this line in the tests, python setup.py clean cythonize sdist. In the next release will need to make sure this is straightforward for users installing from PyPI into different versions.

daz10000 commented 11 months ago

Would be nice to get an updated release. The current pip package fails building while it is installing. The downloadable 0.90.0 package has a broken setuptools-17.1.1.zip file that's not a zip file, but a 301 html redirect error. It's a rough install path right now ;)