pip install via wheel fails

[aakashsur]

So the package does get install by falling back onto the setup.py, but leaves this warning -

DEPRECATION: pairtools was installed using the legacy 'setup.py install' method, because a wheel could not be built for it. A possible replacement is to fix the wheel build issue reported above. You can find discussion regarding this at https://github.com/pypa/pip/issues/8368.

During the attempt to install with the wheel, there's a bunch of red ;

Building wheels for collected packages: pairtools Building wheel for pairtools (setup.py) ... error ERROR: Command errored out with exit status 1: command: /mmfs1/home/asur/.virtual/python-3/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/setup.py'"'"'; file='"'"'/tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/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 /tmp/pip-wheel-irs5wu9v cwd: /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/ Complete output (194 lines): running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-3.9 creating build/lib.linux-x86_64-3.9/pairtools copying pairtools/init.py -> build/lib.linux-x86_64-3.9/pairtools copying pairtools/main.py -> build/lib.linux-x86_64-3.9/pairtools copying pairtools/_fileio.py -> build/lib.linux-x86_64-3.9/pairtools copying pairtools/_headerops.py -> build/lib.linux-x86_64-3.9/pairtools copying pairtools/_pairsam_format.py -> build/lib.linux-x86_64-3.9/pairtools copying pairtools/pairtools_dedup.py -> build/lib.linux-x86_64-3.9/pairtools copying pairtools/pairtools_filterbycov.py -> build/lib.linux-x86_64-3.9/pairtools copying pairtools/pairtools_flip.py -> build/lib.linux-x86_64-3.9/pairtools copying pairtools/pairtools_markasdup.py -> build/lib.linux-x86_64-3.9/pairtools copying pairtools/pairtools_merge.py -> build/lib.linux-x86_64-3.9/pairtools copying pairtools/pairtools_parse.py -> build/lib.linux-x86_64-3.9/pairtools copying pairtools/pairtools_phase.py -> build/lib.linux-x86_64-3.9/pairtools copying pairtools/pairtools_restrict.py -> build/lib.linux-x86_64-3.9/pairtools copying pairtools/pairtools_sample.py -> build/lib.linux-x86_64-3.9/pairtools copying pairtools/pairtools_select.py -> build/lib.linux-x86_64-3.9/pairtools copying pairtools/pairtools_sort.py -> build/lib.linux-x86_64-3.9/pairtools copying pairtools/pairtools_split.py -> build/lib.linux-x86_64-3.9/pairtools copying pairtools/pairtools_stats.py -> build/lib.linux-x86_64-3.9/pairtools running build_ext building 'pairtools._dedup' extension creating build/temp.linux-x86_64-3.9 creating build/temp.linux-x86_64-3.9/tmp creating build/temp.linux-x86_64-3.9/tmp/pip-install-b0k8_llw creating build/temp.linux-x86_64-3.9/tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614 creating build/temp.linux-x86_64-3.9/tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -I/mmfs1/home/asur/.libraries/libffi/include -I/mmfs1/home/asur/.libraries/ncurses/include -I/mmfs1/home/asur/.libraries/ncurses/include/ncurses -I/mmfs1/home/asur/.libraries/zlib/include -I/mmfs1/home/asur/.libraries/xz/include -I/mmfs1/home/asur/.libraries/libffi/include -I/mmfs1/home/asur/.libraries/ncurses/include -I/mmfs1/home/asur/.libraries/ncurses/include/ncurses -I/mmfs1/home/asur/.libraries/zlib/include -I/mmfs1/home/asur/.libraries/xz/include -I/mmfs1/home/asur/.libraries/libffi/include -fPIC -I/mmfs1/home/asur/.virtual/python-3/include -I/mmfs1/home/asur/.python-3/include/python3.9 -I/mmfs1/home/asur/.virtual/python-3/lib/python3.9/site-packages/numpy/core/include -I/mmfs1/home/asur/.virtual/python-3/lib/python3.9/site-packages/numpy/core/include -c /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c -o build/temp.linux-x86_64-3.9/tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.o In file included from /mmfs1/home/asur/.virtual/python-3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, from /mmfs1/home/asur/.virtual/python-3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /mmfs1/home/asur/.virtual/python-3/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, from /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:614: /mmfs1/home/asur/.virtual/python-3/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17	#warning "Using deprecated NumPy API, disable it with " \	^~~ /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c: In function ‘Pyx_InitCachedConstants’: /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:24122:284: error: macro "Pyx_PyCode_New" requires 16 arguments, but only 15 given 24122	__pyx_codeobj29 = (PyObject*)Pyx_PyCode_New(8, 0, 14, 0, CO_OPTIMIZED	CO_NEWLOCALS, pyx_empty_bytes, pyx_empty_tuple, pyx_empty_tuple, pyx_tuple28, pyx_empty_tuple, pyx_empty_tuple, pyx_kp_s_pairtoolsdedup_pyx, pyx_n_s_mark_duplicates, 22, pyx_empty_bytes); if (unlikely(!__pyx_codeobj29)) __PYX_ERR(0, 22, __pyx_L1_error)	^ /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:330: note: macro "__Pyx_PyCode_New" defined here 330	#define __Pyx_PyCode_New(a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\

/tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:24122:34: error: ‘__Pyx_PyCode_New’ undeclared (first use in this function); did you mean ‘PyCode_New’? 24122	__pyx_codeobj29 = (PyObject*)Pyx_PyCode_New(8, 0, 14, 0, CO_OPTIMIZED	CO_NEWLOCALS, pyx_empty_bytes, pyx_empty_tuple, pyx_empty_tuple, pyx_tuple28, pyx_empty_tuple, pyx_empty_tuple, pyx_kp_s_pairtoolsdedup_pyx, pyx_n_s_mark_duplicates, 22, pyx_empty_bytes); if (unlikely(!__pyx_codeobj29)) __PYX_ERR(0, 22, __pyx_L1_error)	^~~~	PyCode_New /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:24122:34: note: each undeclared identifier is reported only once for each function it appears in /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:24132:289: error: macro "__Pyx_PyCode_New" requires 16 arguments, but only 15 given 24132	__pyx_codeobj31 = (PyObject*)Pyx_PyCode_New(3, 0, 5, 0, CO_OPTIMIZED	CO_NEWLOCALS, pyx_empty_bytes, pyx_empty_tuple, pyx_empty_tuple, pyx_tuple30, pyx_empty_tuple, pyx_empty_tuple, pyx_kp_s_stringsource, pyx_n_s_pyx_unpickle_OnlineDuplicateDe, 1, pyx_empty_bytes); if (unlikely(!pyx_codeobj31)) __PYX_ERR(1, 1, __pyx_L1_error)	^ /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:330: note: macro "__Pyx_PyCode_New" defined here 330	#define __Pyx_PyCode_New(a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\

/tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:24197:276: error: macro "__Pyx_PyCode_New" requires 16 arguments, but only 15 given 24197	__pyx_codeobj38 = (PyObject*)Pyx_PyCode_New(3, 0, 5, 0, CO_OPTIMIZED	CO_NEWLOCALS, pyx_empty_bytes, pyx_empty_tuple, pyx_empty_tuple, pyx_tuple37, pyx_empty_tuple, pyx_empty_tuple, pyx_kp_s_stringsource, pyx_n_s_pyx_unpickle_Enum, 1, pyx_empty_bytes); if (unlikely(!pyx_codeobj38)) __PYX_ERR(1, 1, __pyx_L1_error)	^ /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:330: note: macro "__Pyx_PyCode_New" defined here 330	#define __Pyx_PyCode_New(a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\

/tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c: In function ‘__Pyx_ParseOptionalKeywords’: /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:24933:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 24933	(PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :	^ In file included from /mmfs1/home/asur/.python-3/include/python3.9/unicodeobject.h:1026, from /mmfs1/home/asur/.python-3/include/python3.9/Python.h:97, from /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:17: /mmfs1/home/asur/.python-3/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446	static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {	^~~~~~ /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:24933:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 24933	(PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :	^ In file included from /mmfs1/home/asur/.python-3/include/python3.9/unicodeobject.h:1026, from /mmfs1/home/asur/.python-3/include/python3.9/Python.h:97, from /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:17: /mmfs1/home/asur/.python-3/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580	Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(	^~~~~~~ /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:24933:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 24933	(PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :	^ In file included from /mmfs1/home/asur/.python-3/include/python3.9/unicodeobject.h:1026, from /mmfs1/home/asur/.python-3/include/python3.9/Python.h:97, from /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:17: /mmfs1/home/asur/.python-3/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446	static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {	^~~~~~ /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:24933:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 24933	(PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :	^ In file included from /mmfs1/home/asur/.python-3/include/python3.9/unicodeobject.h:1026, from /mmfs1/home/asur/.python-3/include/python3.9/Python.h:97, from /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:17: /mmfs1/home/asur/.python-3/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446	static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {	^~~~~~ /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:24933:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 24933	(PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :	^ In file included from /mmfs1/home/asur/.python-3/include/python3.9/unicodeobject.h:1026, from /mmfs1/home/asur/.python-3/include/python3.9/Python.h:97, from /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:17: /mmfs1/home/asur/.python-3/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580	Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(	^~~~~~~ /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:24933:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 24933	(PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :	^ In file included from /mmfs1/home/asur/.python-3/include/python3.9/unicodeobject.h:1026, from /mmfs1/home/asur/.python-3/include/python3.9/Python.h:97, from /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:17: /mmfs1/home/asur/.python-3/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446	static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {	^~~~~~ /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:24949:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 24949	(PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :	^ In file included from /mmfs1/home/asur/.python-3/include/python3.9/unicodeobject.h:1026, from /mmfs1/home/asur/.python-3/include/python3.9/Python.h:97, from /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:17: /mmfs1/home/asur/.python-3/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446	static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {	^~~~~~ /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:24949:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 24949	(PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :	^ In file included from /mmfs1/home/asur/.python-3/include/python3.9/unicodeobject.h:1026, from /mmfs1/home/asur/.python-3/include/python3.9/Python.h:97, from /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:17: /mmfs1/home/asur/.python-3/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580	Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(	^~~~~~~ /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:24949:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 24949	(PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :	^ In file included from /mmfs1/home/asur/.python-3/include/python3.9/unicodeobject.h:1026, from /mmfs1/home/asur/.python-3/include/python3.9/Python.h:97, from /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:17: /mmfs1/home/asur/.python-3/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446	static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {	^~~~~~ /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:24949:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 24949	(PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :	^ In file included from /mmfs1/home/asur/.python-3/include/python3.9/unicodeobject.h:1026, from /mmfs1/home/asur/.python-3/include/python3.9/Python.h:97, from /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:17: /mmfs1/home/asur/.python-3/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446	static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {	^~~~~~ /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:24949:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 24949	(PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :	^ In file included from /mmfs1/home/asur/.python-3/include/python3.9/unicodeobject.h:1026, from /mmfs1/home/asur/.python-3/include/python3.9/Python.h:97, from /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:17: /mmfs1/home/asur/.python-3/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580	Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(	^~~~~~~ /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:24949:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 24949	(PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :	^ In file included from /mmfs1/home/asur/.python-3/include/python3.9/unicodeobject.h:1026, from /mmfs1/home/asur/.python-3/include/python3.9/Python.h:97, from /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:17: /mmfs1/home/asur/.python-3/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446	static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {	^~~~~~ /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c: In function ‘__Pyx_decode_c_string’: /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:26958:9: warning: ‘PyUnicode_FromUnicode’ is deprecated [-Wdeprecated-declarations] 26958	return PyUnicode_FromUnicode(NULL, 0);	^~ In file included from /mmfs1/home/asur/.python-3/include/python3.9/unicodeobject.h:1026, from /mmfs1/home/asur/.python-3/include/python3.9/Python.h:97, from /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:17: /mmfs1/home/asur/.python-3/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here 551	Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode(	^~~~~ /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c: In function ‘Pyx_CreateCodeObjectForTraceback’: /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:27650:5: error: macro "Pyx_PyCode_New" requires 16 arguments, but only 15 given 27650	);	^ /tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:330: note: macro "__Pyx_PyCode_New" defined here 330	#define __Pyx_PyCode_New(a, p, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\

/tmp/pip-install-b0k8_llw/pairtools_c87643fef5d34cf8810e86019fc6f614/pairtools/_dedup.c:27634:15: error: ‘Pyx_PyCode_New’ undeclared (first use in this function); did you mean ‘PyCode_New’? 27634 | py_code = Pyx_PyCode_New( | ^~~~ | PyCode_New error: command '/sw/gcc/10.2.0/bin/gcc' failed with exit code 1

ERROR: Failed building wheel for pairtools

[agalitsyna]

Feel free to re-open if it persists. We'll need your environment summary to reproduce the problem.