lapa
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Published
20 hours ago •
mortazavilab
mortazavilab
Installation error
Hello,
I am encountering problems installing lapa. Here is the error I am getting
#0 1.082 Collecting lapa
#0 1.115 Downloading lapa-0.0.5-py3-none-any.whl (36 kB)
#0 1.132 Requirement already satisfied: setuptools in /opt/conda/lib/python3.10/site-packages (from lapa) (68.0.0)
#0 1.132 Requirement already satisfied: tqdm in /opt/conda/lib/python3.10/site-packages (from lapa) (4.65.0)
#0 1.360 Collecting numpy<=1.23 (from lapa)
#0 1.372 Downloading numpy-1.23.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.0 MB)
#0 1.565 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 17.0/17.0 MB 70.9 MB/s eta 0:00:00
#0 1.615 Collecting click (from lapa)
#0 1.623 Downloading click-8.1.6-py3-none-any.whl (97 kB)
#0 1.630 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 97.9/97.9 kB 17.3 MB/s eta 0:00:00
#0 1.781 Collecting pandas (from lapa)
#0 1.790 Downloading pandas-2.0.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.3 MB)
#0 1.889 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.3/12.3 MB 113.1 MB/s eta 0:00:00
#0 1.932 Collecting pybigwig (from lapa)
#0 1.945 Downloading pyBigWig-0.3.22-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (209 kB)
#0 1.954 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 209.7/209.7 kB 31.3 MB/s eta 0:00:00
#0 2.080 Collecting scipy (from lapa)
#0 2.092 Downloading scipy-1.11.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (36.3 MB)
#0 2.376 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 36.3/36.3 MB 63.5 MB/s eta 0:00:00
#0 2.444 Collecting bamread>=0.0.10 (from lapa)
#0 2.458 Downloading bamread-0.0.16-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (650 kB)
#0 2.470 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 650.3/650.3 kB 60.0 MB/s eta 0:00:00
#0 2.497 Collecting pyranges>=0.0.71 (from lapa)
#0 2.508 Downloading pyranges-0.0.129-py3-none-any.whl (1.5 MB)
#0 2.527 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.5/1.5 MB 87.0 MB/s eta 0:00:00
#0 2.552 Collecting sorted-nearest==0.0.33 (from lapa)
#0 2.565 Downloading sorted_nearest-0.0.33.tar.gz (1.2 MB)
#0 2.580 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 98.2 MB/s eta 0:00:00
#0 2.643 Installing build dependencies: started
#0 8.952 Installing build dependencies: finished with status 'done'
#0 8.954 Getting requirements to build wheel: started
#0 9.657 Getting requirements to build wheel: finished with status 'error'
#0 9.666 error: subprocess-exited-with-error
#0 9.666
#0 9.666 × Getting requirements to build wheel did not run successfully.
#0 9.666 │ exit code: 1
#0 9.666 ╰─> [173 lines of output]
#0 9.666
#0 9.666 Error compiling Cython file:
#0 9.666 ------------------------------------------------------------
#0 9.666 ...
#0 9.666 @cython.boundscheck(False)
#0 9.666 @cython.wraparound(False)
#0 9.666 @cython.initializedcheck(False)
#0 9.666 cpdef annotate_clusters64(const long [::1] starts, const long [::1] ends, int slack):
#0 9.666
#0 9.666 cpdef int min_start = starts[0]
#0 9.666 ^
#0 9.666 ------------------------------------------------------------
#0 9.666
#0 9.666 sorted_nearest/src/annotate_clusters.pyx:23:10: Variables cannot be declared with 'cpdef'. Use 'cdef' instead.
#0 9.666
#0 9.666 Error compiling Cython file:
#0 9.666 ------------------------------------------------------------
#0 9.666 ...
#0 9.666 @cython.wraparound(False)
#0 9.666 @cython.initializedcheck(False)
#0 9.666 cpdef annotate_clusters64(const long [::1] starts, const long [::1] ends, int slack):
#0 9.666
#0 9.666 cpdef int min_start = starts[0]
#0 9.666 cpdef int max_end = ends[0]
#0 9.666 ^
#0 9.666 ------------------------------------------------------------
#0 9.666
#0 9.666 sorted_nearest/src/annotate_clusters.pyx:24:10: Variables cannot be declared with 'cpdef'. Use 'cdef' instead.
#0 9.666
#0 9.666 Error compiling Cython file:
#0 9.666 ------------------------------------------------------------
#0 9.666 ...
#0 9.666 @cython.initializedcheck(False)
#0 9.666 cpdef annotate_clusters64(const long [::1] starts, const long [::1] ends, int slack):
#0 9.666
#0 9.666 cpdef int min_start = starts[0]
#0 9.666 cpdef int max_end = ends[0]
#0 9.666 cpdef int i = 0
#0 9.666 ^
#0 9.666 ------------------------------------------------------------
#0 9.666
#0 9.666 sorted_nearest/src/annotate_clusters.pyx:25:10: Variables cannot be declared with 'cpdef'. Use 'cdef' instead.
#0 9.666
#0 9.666 Error compiling Cython file:
#0 9.666 ------------------------------------------------------------
#0 9.666 ...
#0 9.666 cpdef annotate_clusters64(const long [::1] starts, const long [::1] ends, int slack):
#0 9.666
#0 9.666 cpdef int min_start = starts[0]
#0 9.666 cpdef int max_end = ends[0]
#0 9.666 cpdef int i = 0
#0 9.666 cpdef int n_clusters = 1
#0 9.666 ^
#0 9.666 ------------------------------------------------------------
#0 9.666
#0 9.666 sorted_nearest/src/annotate_clusters.pyx:26:10: Variables cannot be declared with 'cpdef'. Use 'cdef' instead.
#0 9.666
#0 9.666 Error compiling Cython file:
#0 9.666 ------------------------------------------------------------
#0 9.666 ...
#0 9.666
#0 9.666 cpdef int min_start = starts[0]
#0 9.666 cpdef int max_end = ends[0]
#0 9.666 cpdef int i = 0
#0 9.666 cpdef int n_clusters = 1
#0 9.666 cpdef int length = len(starts)
#0 9.666 ^
#0 9.666 ------------------------------------------------------------
#0 9.666
#0 9.666 sorted_nearest/src/annotate_clusters.pyx:27:10: Variables cannot be declared with 'cpdef'. Use 'cdef' instead.
#0 9.666
#0 9.666 Error compiling Cython file:
#0 9.666 ------------------------------------------------------------
#0 9.666 ...
#0 9.666 @cython.boundscheck(False)
#0 9.666 @cython.wraparound(False)
#0 9.666 @cython.initializedcheck(False)
#0 9.666 cpdef annotate_clusters32(const int32_t [::1] starts, const int32_t [::1] ends, int slack):
#0 9.666
#0 9.666 cpdef int min_start = starts[0]
#0 9.666 ^
#0 9.666 ------------------------------------------------------------
#0 9.666
#0 9.666 sorted_nearest/src/annotate_clusters.pyx:55:10: Variables cannot be declared with 'cpdef'. Use 'cdef' instead.
#0 9.666
#0 9.666 Error compiling Cython file:
#0 9.666 ------------------------------------------------------------
#0 9.666 ...
#0 9.666 @cython.wraparound(False)
#0 9.666 @cython.initializedcheck(False)
#0 9.666 cpdef annotate_clusters32(const int32_t [::1] starts, const int32_t [::1] ends, int slack):
#0 9.666
#0 9.666 cpdef int min_start = starts[0]
#0 9.666 cpdef int max_end = ends[0]
#0 9.666 ^
#0 9.666 ------------------------------------------------------------
#0 9.666
#0 9.666 sorted_nearest/src/annotate_clusters.pyx:56:10: Variables cannot be declared with 'cpdef'. Use 'cdef' instead.
#0 9.666
#0 9.666 Error compiling Cython file:
#0 9.666 ------------------------------------------------------------
#0 9.666 ...
#0 9.666 @cython.initializedcheck(False)
#0 9.666 cpdef annotate_clusters32(const int32_t [::1] starts, const int32_t [::1] ends, int slack):
#0 9.666
#0 9.666 cpdef int min_start = starts[0]
#0 9.666 cpdef int max_end = ends[0]
#0 9.666 cpdef int i = 0
#0 9.666 ^
#0 9.666 ------------------------------------------------------------
#0 9.666
#0 9.666 sorted_nearest/src/annotate_clusters.pyx:57:10: Variables cannot be declared with 'cpdef'. Use 'cdef' instead.
#0 9.666
#0 9.666 Error compiling Cython file:
#0 9.666 ------------------------------------------------------------
#0 9.666 ...
#0 9.666 cpdef annotate_clusters32(const int32_t [::1] starts, const int32_t [::1] ends, int slack):
#0 9.666
#0 9.666 cpdef int min_start = starts[0]
#0 9.666 cpdef int max_end = ends[0]
#0 9.666 cpdef int i = 0
#0 9.666 cpdef int n_clusters = 1
#0 9.666 ^
#0 9.666 ------------------------------------------------------------
#0 9.666
#0 9.666 sorted_nearest/src/annotate_clusters.pyx:58:10: Variables cannot be declared with 'cpdef'. Use 'cdef' instead.
#0 9.666
#0 9.666 Error compiling Cython file:
#0 9.666 ------------------------------------------------------------
#0 9.666 ...
#0 9.666
#0 9.666 cpdef int min_start = starts[0]
#0 9.666 cpdef int max_end = ends[0]
#0 9.666 cpdef int i = 0
#0 9.666 cpdef int n_clusters = 1
#0 9.666 cpdef int length = len(starts)
#0 9.666 ^
#0 9.666 ------------------------------------------------------------
#0 9.666
#0 9.666 sorted_nearest/src/annotate_clusters.pyx:59:10: Variables cannot be declared with 'cpdef'. Use 'cdef' instead.
#0 9.666 Compiling sorted_nearest/src/sorted_nearest.pyx because it changed.
#0 9.666 Compiling sorted_nearest/src/max_disjoint_intervals.pyx because it changed.
#0 9.666 Compiling sorted_nearest/src/k_nearest.pyx because it changed.
#0 9.666 Compiling sorted_nearest/src/k_nearest_ties.pyx because it changed.
#0 9.666 Compiling sorted_nearest/src/clusters.pyx because it changed.
#0 9.666 Compiling sorted_nearest/src/annotate_clusters.pyx because it changed.
#0 9.666 Compiling sorted_nearest/src/cluster_by.pyx because it changed.
#0 9.666 Compiling sorted_nearest/src/merge_by.pyx because it changed.
#0 9.666 Compiling sorted_nearest/src/introns.pyx because it changed.
#0 9.666 Compiling sorted_nearest/src/windows.pyx because it changed.
#0 9.666 Compiling sorted_nearest/src/tiles.pyx because it changed.
#0 9.666 [ 1/11] Cythonizing sorted_nearest/src/annotate_clusters.pyx
#0 9.666 Traceback (most recent call last):
#0 9.666 File "/opt/conda/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
#0 9.666 main()
#0 9.666 File "/opt/conda/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
#0 9.666 json_out['return_val'] = hook(**hook_input['kwargs'])
#0 9.666 File "/opt/conda/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
#0 9.666 return hook(config_settings)
#0 9.666 File "/tmp/pip-build-env-zg_oj5sl/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel
#0 9.666 return self._get_build_requires(config_settings, requirements=['wheel'])
#0 9.666 File "/tmp/pip-build-env-zg_oj5sl/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires
#0 9.666 self.run_setup()
#0 9.666 File "/tmp/pip-build-env-zg_oj5sl/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 487, in run_setup
#0 9.666 super(_BuildMetaLegacyBackend,
#0 9.666 File "/tmp/pip-build-env-zg_oj5sl/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 338, in run_setup
#0 9.666 exec(code, locals())
#0 9.666 File "<string>", line 79, in <module>
#0 9.666 File "/tmp/pip-build-env-zg_oj5sl/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize
#0 9.666 cythonize_one(*args)
#0 9.666 File "/tmp/pip-build-env-zg_oj5sl/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one
#0 9.666 raise CompileError(None, pyx_file)
#0 9.666 Cython.Compiler.Errors.CompileError: sorted_nearest/src/annotate_clusters.pyx
#0 9.666 [end of output]
#0 9.666
#0 9.666 note: This error originates from a subprocess, and is likely not a problem with pip.
#0 9.667 error: subprocess-exited-with-error
#0 9.667
#0 9.667 × Getting requirements to build wheel did not run successfully.
#0 9.667 │ exit code: 1
#0 9.667 ╰─> See above for output.
#0 9.667
#0 9.667 note: This error originates from a subprocess, and is likely not a problem with pip.
------
Dockerfile:11
--------------------
9 | RUN apt-get clean all
10 |
11 | >>> RUN pip3 install lapa
--------------------
ERROR: failed to solve: process "/bin/sh -c pip3 install lapa" did not complete successfully: exit code: 1
Thank you.
