CODEWITHSUNDEEP
pythonpython-3.xpipbioinformatics
adamk5
adamk5

Reputation: 3

Pip install fails at building wheel at subpackage?

Somewhat a beginner at coding. I was looking to install a package using pip install that I was able to get before I updated my python (currently have Python 2.7.16 and 2.8.0 on my Mac).

The package I am trying to install is called CITE-seq-Count (https://hoohm.github.io/CITE-seq-Count/Installation/)

I have tried their recommended installation:

pip install CITE-seq-Count==1.4.3

and will get this error involving the pysam package. I've tried to individually install pysam but also have the same error. I've seen other people recommend installing on anaconda but I'm not sure if I'd be able to install there and use on the terminal. Thank you for the help!

 Building wheel for pysam (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /Library/Frameworks/Python.framework/Versions/3.8/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/gb/5mct_n_922x_zd87l3gz93xc0000gn/T/pip-install-2lxzoax8/pysam/setup.py'"'"'; __file__='"'"'/private/var/folders/gb/5mct_n_922x_zd87l3gz93xc0000gn/T/pip-install-2lxzoax8/pysam/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/gb/5mct_n_922x_zd87l3gz93xc0000gn/T/pip-wheel-z6kkdnyu --python-tag cp38
       cwd: /private/var/folders/gb/5mct_n_922x_zd87l3gz93xc0000gn/T/pip-install-2lxzoax8/pysam/
  Complete output (277 lines):
  # pysam: no cython available - using pre-compiled C
  # pysam: htslib mode is shared
  # pysam: HTSLIB_CONFIGURE_OPTIONS=None
  # pysam: (sysconfig) CC=gcc
  # pysam: (sysconfig) CFLAGS=-Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch x86_64 -g
  # pysam: (sysconfig) LDFLAGS=-arch x86_64 -g
  checking for gcc... gcc
...

                                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
    pysam/libchtslib.c:318:82: note: expanded from macro '__Pyx_PyCode_New'
              PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
              ~~~~~~~~~~                                                             ^~~~
    /Library/Frameworks/Python.framework/Versions/3.8/include/python3.8/code.h:122:12: note: 'PyCode_New' declared here
    PyAPI_FUNC(PyCodeObject *) PyCode_New(
               ^
    pysam/libchtslib.c:14673:255: error: too many arguments to function call, expected 15, have 16
      __pyx_codeobj__7 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__34, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_call, 304, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__7)) __PYX_ERR(0, 304, __pyx_L1_error)
                                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
    pysam/libchtslib.c:318:82: note: expanded from macro '__Pyx_PyCode_New'
              PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
              ~~~~~~~~~~                                                             ^~~~
    /Library/Frameworks/Python.framework/Versions/3.8/include/python3.8/code.h:122:12: note: 'PyCode_New' declared here
    PyAPI_FUNC(PyCodeObject *) PyCode_New(
               ^
    pysam/libchtslib.c:14685:255: error: too many arguments to function call, expected 15, have 16
      __pyx_codeobj__8 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__35, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_bool, 306, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__8)) __PYX_ERR(0, 306, __pyx_L1_error)
                                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
    pysam/libchtslib.c:318:82: note: expanded from macro '__Pyx_PyCode_New'
              PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
              ~~~~~~~~~~                                                             ^~~~
    /Library/Frameworks/Python.framework/Versions/3.8/include/python3.8/code.h:122:12: note: 'PyCode_New' declared here
    PyAPI_FUNC(PyCodeObject *) PyCode_New(
               ^
    pysam/libchtslib.c:14697:258: error: too many arguments to function call, expected 15, have 16
      __pyx_codeobj__9 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__36, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_nonzero, 308, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__9)) __PYX_ERR(0, 308, __pyx_L1_error)
                                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
    pysam/libchtslib.c:318:82: note: expanded from macro '__Pyx_PyCode_New'
              PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
              ~~~~~~~~~~                                                             ^~~~
    /Library/Frameworks/Python.framework/Versions/3.8/include/python3.8/code.h:122:12: note: 'PyCode_New' declared here
    PyAPI_FUNC(PyCodeObject *) PyCode_New(
               ^
    pysam/libchtslib.c:14709:254: error: too many arguments to function call, expected 15, have 16
      __pyx_codeobj__10 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__37, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_eq, 310, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__10)) __PYX_ERR(0, 310, __pyx_L1_error)
                                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
    pysam/libchtslib.c:318:82: note: expanded from macro '__Pyx_PyCode_New'
              PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
              ~~~~~~~~~~                                                             ^~~~
    /Library/Frameworks/Python.framework/Versions/3.8/include/python3.8/code.h:122:12: note: 'PyCode_New' declared here
    PyAPI_FUNC(PyCodeObject *) PyCode_New(
               ^
    pysam/libchtslib.c:14721:254: error: too many arguments to function call, expected 15, have 16
      __pyx_codeobj__11 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__38, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libchtslib_pyx, __pyx_n_s_ne, 312, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__11)) __PYX_ERR(0, 312, __pyx_L1_error)
                                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
    pysam/libchtslib.c:318:82: note: expanded from macro '__Pyx_PyCode_New'
              PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
              ~~~~~~~~~~                                                             ^~~~
    /Library/Frameworks/Python.framework/Versions/3.8/include/python3.8/code.h:122:12: note: 'PyCode_New' declared here
    PyAPI_FUNC(PyCodeObject *) PyCode_New(
               ^
    pysam/libchtslib.c:18225:9: error: too many arguments to function call, expected 15, have 16
            __pyx_empty_bytes  /*PyObject *lnotab*/
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    pysam/libchtslib.c:318:82: note: expanded from macro '__Pyx_PyCode_New'
              PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
              ~~~~~~~~~~                                                             ^~~~
    /Library/Frameworks/Python.framework/Versions/3.8/include/python3.8/code.h:122:12: note: 'PyCode_New' declared here
    PyAPI_FUNC(PyCodeObject *) PyCode_New(
               ^
    7 errors generated.
    error: command 'gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1:

Upvotes: 0

Views: 2686

Answers (1)

MSL
MSL

Reputation: 81

It's an issue in pysam which seems to be not yet fully compatible with Python 3.8. There is already a github issue for this problem, might be worth following it to see if a solution turns up: https://github.com/pysam-developers/pysam/issues/860

For now, falling back to Python 3.7 could be the easiest solution if you don't depend on 3.8 features (worked for me).

Upvotes: 2

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