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.
