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2021-06-12 12:55
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Ubuntu安装Galaxy时自动安装bx-python安装失败

Ubuntu安装Galaxy时出现“error: command 'x86_64-linux-gnu-gcc' failed with exit status 1”,应该如何解决?

Running setup.py install for bx-python ... error
    ERROR: Command errored out with exit status 1:
     command: /home/lorenzo/Desktop/galaxy/.venv/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-y1r273q_/bx-python_bfeda7b26a5c4bcda67c0d47719ab321/setup.py'"'"'; __file__='"'"'/tmp/pip-install-y1r273q_/bx-python_bfeda7b26a5c4bcda67c0d47719ab321/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-ae_o2cef/install-record.txt --single-version-externally-managed --compile --install-headers /home/lorenzo/Desktop/galaxy/.venv/include/site/python3.8/bx-python
         cwd: /tmp/pip-install-y1r273q_/bx-python_bfeda7b26a5c4bcda67c0d47719ab321/
    Complete output (75 lines):
    running install
    running build
    running build_py
    running build_ext
    skipping 'lib/bx/bitset.c' Cython extension (up-to-date)
    skipping 'lib/bx/intervals/intersection.c' Cython extension (up-to-date)
    skipping 'lib/bx/align/_core.c' Cython extension (up-to-date)
    skipping 'lib/bx/seq/_nib.c' Cython extension (up-to-date)
    skipping 'lib/bx/seq/_twobit.c' Cython extension (up-to-date)
    skipping 'lib/bx/_seqmapping.c' Cython extension (up-to-date)
    skipping 'lib/bx/misc/bgzf.c' Cython extension (up-to-date)
    skipping 'lib/bx/intervals/cluster.c' Cython extension (up-to-date)
    skipping 'lib/bx/pwm/_position_weight_matrix.c' Cython extension (up-to-date)
    skipping 'lib/bx/motif/_pwm.c' Cython extension (up-to-date)
    skipping 'lib/bx/arrays/array_tree.c' Cython extension (up-to-date)
    skipping 'lib/bx/bbi/bpt_file.c' Cython extension (up-to-date)
    skipping 'lib/bx/bbi/cirtree_file.c' Cython extension (up-to-date)
    skipping 'lib/bx/bbi/bbi_file.c' Cython extension (up-to-date)
    skipping 'lib/bx/bbi/bigwig_file.c' Cython extension (up-to-date)
    skipping 'lib/bx/bbi/bigbed_file.c' Cython extension (up-to-date)
    skipping 'lib/bx/align/_epo.c' Cython extension (up-to-date)
    skipping 'lib/bx/arrays/bed.c' Cython extension (up-to-date)
    skipping 'lib/bx/arrays/wiggle.c' Cython extension (up-to-date)
    skipping 'lib/bx/align/sitemask/_cpg.c' Cython extension (up-to-date)
    skipping 'lib/bx/intseq/ngramcount.c' Cython extension (up-to-date)
    skipping 'lib/bx/misc/_seekbzip2.c' Cython extension (up-to-date)
    building 'bx.bitset' extension
    creating build/temp.linux-x86_64-3.8
    creating build/temp.linux-x86_64-3.8/lib
    creating build/temp.linux-x86_64-3.8/lib/bx
    creating build/temp.linux-x86_64-3.8/src
    creating build/temp.linux-x86_64-3.8/src/kent
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/kent -Isrc -I/usr/include/python3.8 -I/home/lorenzo/Desktop/galaxy/.venv/include/python3.8 -c lib/bx/bitset.c -o build/temp.linux-x86_64-3.8/lib/bx/bitset.o
    lib/bx/bitset.c: In function ‘__Pyx_CreateCodeObjectForTraceback’:
    lib/bx/bitset.c:7328:9: warning: passing argument 14 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion]
     7328 |         py_funcname,  /*PyObject *name,*/
          |         ^~~~~~~~~~~
          |         |
          |         PyObject * {aka struct _object *}
    lib/bx/bitset.c:318:69: note: in definition of macro ‘__Pyx_PyCode_New’
      318 |           PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
          |                                                                     ^~~~
    In file included from /usr/include/python3.8/compile.h:5,
                     from /usr/include/python3.8/Python.h:138,
                     from lib/bx/bitset.c:4:
    /usr/include/python3.8/code.h:122:28: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’}
      122 | PyAPI_FUNC(PyCodeObject *) PyCode_New(
          |                            ^~~~~~~~~~
    lib/bx/bitset.c:7329:9: warning: passing argument 15 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion]
     7329 |         py_line,
          |         ^~~~~~~
          |         |
          |         int
    lib/bx/bitset.c:318:75: note: in definition of macro ‘__Pyx_PyCode_New’
      318 |           PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
          |                                                                           ^~~~~
    In file included from /usr/include/python3.8/compile.h:5,
                     from /usr/include/python3.8/Python.h:138,
                     from lib/bx/bitset.c:4:
    /usr/include/python3.8/code.h:122:28: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’
      122 | PyAPI_FUNC(PyCodeObject *) PyCode_New(
          |                            ^~~~~~~~~~
    lib/bx/bitset.c:318:11: error: too many arguments to function ‘PyCode_New’
      318 |           PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
          |           ^~~~~~~~~~
    lib/bx/bitset.c:7315:15: note: in expansion of macro ‘__Pyx_PyCode_New’
     7315 |     py_code = __Pyx_PyCode_New(
          |               ^~~~~~~~~~~~~~~~
    In file included from /usr/include/python3.8/compile.h:5,
                     from /usr/include/python3.8/Python.h:138,
                     from lib/bx/bitset.c:4:
    /usr/include/python3.8/code.h:122:28: note: declared here
      122 | PyAPI_FUNC(PyCodeObject *) PyCode_New(
          |                            ^~~~~~~~~~
    error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /home/lorenzo/Desktop/galaxy/.venv/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-y1r273q_/bx-python_bfeda7b26a5c4bcda67c0d47719ab321/setup.py'"'"'; __file__='"'"'/tmp/pip-install-y1r273q_/bx-python_bfeda7b26a5c4bcda67c0d47719ab321/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-ae_o2cef/install-record.txt --single-version-externally-managed --compile --install-headers /home/lorenzo/Desktop/galaxy/.venv/include/site/python3.8/bx-python Check the logs for full command output.
 

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3条回答 默认 最新

  • CSDN专家-微编程 2021-06-12 13:32
    已采纳

    可以参考这篇文章,进行解决,如果对你有帮助记得采纳一下,谢谢~

    https://blog.csdn.net/weixin_42912498/article/details/108443386

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