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mortazavilab / lapa

Alternative polyadenylation detection from diverse data sources such as 3'-seq, long-read and short-reads.
https://www.biorxiv.org/content/10.1101/2022.11.08.515683v1
25 stars 13 forks source link

Installation error #22

Open sagnikbanerjee15 opened 1 year ago

sagnikbanerjee15 commented 1 year ago

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.

sagnikbanerjee15 commented 1 year ago

Is there a docker image I can use?

sagnikbanerjee15 commented 1 year ago

Hello,

Thanks for the update. But I am getting a different error now.

=> ERROR [7/7] RUN cd /lapa && python3 setup.py install                                                                                                                                                                                                                             11.1s
------                                                                                                                                                                                                                                                                                     
 > [7/7] RUN cd /lapa && python3 setup.py install:                                                                                                                                                                                                                                         
#0 0.446 /opt/conda/lib/python3.10/site-packages/setuptools/__init__.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.                                                                                                                                
#0 0.446 !!                                                                                                                                                                                                                                                                                
#0 0.446                                                                                                                                                                                                                                                                                   
#0 0.446         ********************************************************************************                                                                                                                                                                                          
#0 0.446         Requirements should be satisfied by a PEP 517 installer.
#0 0.446         If you are using pip, you can try `pip install --use-pep517`.
#0 0.446         ********************************************************************************
#0 0.446 
#0 0.446 !!
#0 0.446   dist.fetch_build_eggs(dist.setup_requires)
#0 0.872 running install
#0 0.872 /opt/conda/lib/python3.10/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
#0 0.872 !!
#0 0.872 
#0 0.872         ********************************************************************************
#0 0.872         Please avoid running ``setup.py`` directly.
#0 0.872         Instead, use pypa/build, pypa/installer or other
#0 0.872         standards-based tools.
#0 0.872 
#0 0.872         See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
#0 0.872         ********************************************************************************
#0 0.872 
#0 0.872 !!
#0 0.872   self.initialize_options()
#0 0.919 /opt/conda/lib/python3.10/site-packages/setuptools/_distutils/cmd.py:66: EasyInstallDeprecationWarning: easy_install command is deprecated.
#0 0.919 !!
#0 0.919 
#0 0.919         ********************************************************************************
#0 0.919         Please avoid running ``setup.py`` and ``easy_install``.
#0 0.919         Instead, use pypa/build, pypa/installer or other
#0 0.919         standards-based tools.
#0 0.919 
#0 0.919         See https://github.com/pypa/setuptools/issues/917 for details.
#0 0.919         ********************************************************************************
#0 0.919 
#0 0.919 !!
#0 0.919   self.initialize_options()
#0 0.938 running bdist_egg
#0 0.943 running egg_info
#0 0.943 creating lapa.egg-info
#0 0.944 writing lapa.egg-info/PKG-INFO
#0 0.945 writing dependency_links to lapa.egg-info/dependency_links.txt
#0 0.945 writing entry points to lapa.egg-info/entry_points.txt
#0 0.945 writing requirements to lapa.egg-info/requires.txt
#0 0.945 writing top-level names to lapa.egg-info/top_level.txt
#0 0.945 writing manifest file 'lapa.egg-info/SOURCES.txt'
#0 0.952 reading manifest file 'lapa.egg-info/SOURCES.txt'
#0 0.952 writing manifest file 'lapa.egg-info/SOURCES.txt'
#0 0.952 installing library code to build/bdist.linux-x86_64/egg
#0 0.953 running install_lib
#0 0.953 running build_py
#0 0.953 creating build
#0 0.953 creating build/lib
#0 0.953 creating build/lib/lapa
#0 0.953 copying lapa/genomic_regions.py -> build/lib/lapa
#0 0.953 copying lapa/lapa.py -> build/lib/lapa
#0 0.953 copying lapa/cluster.py -> build/lib/lapa
#0 0.953 copying lapa/__init__.py -> build/lib/lapa
#0 0.953 copying lapa/result.py -> build/lib/lapa
#0 0.953 copying lapa/replication.py -> build/lib/lapa
#0 0.953 copying lapa/correction.py -> build/lib/lapa
#0 0.953 copying lapa/count.py -> build/lib/lapa
#0 0.953 copying lapa/main.py -> build/lib/lapa
#0 0.954 copying lapa/link.py -> build/lib/lapa
#0 0.954 creating build/lib/lapa/utils
#0 0.954 copying lapa/utils/common.py -> build/lib/lapa/utils
#0 0.954 copying lapa/utils/__init__.py -> build/lib/lapa/utils
#0 0.954 copying lapa/utils/io.py -> build/lib/lapa/utils
#0 0.954 copying lapa/utils/gtf.py -> build/lib/lapa/utils
#0 0.955 creating build/bdist.linux-x86_64
#0 0.955 creating build/bdist.linux-x86_64/egg
#0 0.955 creating build/bdist.linux-x86_64/egg/lapa
#0 0.955 copying build/lib/lapa/genomic_regions.py -> build/bdist.linux-x86_64/egg/lapa
#0 0.955 copying build/lib/lapa/lapa.py -> build/bdist.linux-x86_64/egg/lapa
#0 0.955 copying build/lib/lapa/cluster.py -> build/bdist.linux-x86_64/egg/lapa
#0 0.955 copying build/lib/lapa/__init__.py -> build/bdist.linux-x86_64/egg/lapa
#0 0.955 copying build/lib/lapa/result.py -> build/bdist.linux-x86_64/egg/lapa
#0 0.955 copying build/lib/lapa/replication.py -> build/bdist.linux-x86_64/egg/lapa
#0 0.955 copying build/lib/lapa/correction.py -> build/bdist.linux-x86_64/egg/lapa
#0 0.955 copying build/lib/lapa/count.py -> build/bdist.linux-x86_64/egg/lapa
#0 0.956 copying build/lib/lapa/main.py -> build/bdist.linux-x86_64/egg/lapa
#0 0.956 copying build/lib/lapa/link.py -> build/bdist.linux-x86_64/egg/lapa
#0 0.956 creating build/bdist.linux-x86_64/egg/lapa/utils
#0 0.956 copying build/lib/lapa/utils/common.py -> build/bdist.linux-x86_64/egg/lapa/utils
#0 0.956 copying build/lib/lapa/utils/__init__.py -> build/bdist.linux-x86_64/egg/lapa/utils
#0 0.956 copying build/lib/lapa/utils/io.py -> build/bdist.linux-x86_64/egg/lapa/utils
#0 0.956 copying build/lib/lapa/utils/gtf.py -> build/bdist.linux-x86_64/egg/lapa/utils
#0 0.956 byte-compiling build/bdist.linux-x86_64/egg/lapa/genomic_regions.py to genomic_regions.cpython-310.pyc
#0 0.958 byte-compiling build/bdist.linux-x86_64/egg/lapa/lapa.py to lapa.cpython-310.pyc
#0 0.960 byte-compiling build/bdist.linux-x86_64/egg/lapa/cluster.py to cluster.cpython-310.pyc
#0 0.961 byte-compiling build/bdist.linux-x86_64/egg/lapa/__init__.py to __init__.cpython-310.pyc
#0 0.961 byte-compiling build/bdist.linux-x86_64/egg/lapa/result.py to result.cpython-310.pyc
#0 0.963 byte-compiling build/bdist.linux-x86_64/egg/lapa/replication.py to replication.cpython-310.pyc
#0 0.963 byte-compiling build/bdist.linux-x86_64/egg/lapa/correction.py to correction.cpython-310.pyc
#0 0.965 byte-compiling build/bdist.linux-x86_64/egg/lapa/count.py to count.cpython-310.pyc
#0 0.967 byte-compiling build/bdist.linux-x86_64/egg/lapa/main.py to main.cpython-310.pyc
#0 0.968 byte-compiling build/bdist.linux-x86_64/egg/lapa/link.py to link.cpython-310.pyc
#0 0.969 byte-compiling build/bdist.linux-x86_64/egg/lapa/utils/common.py to common.cpython-310.pyc
#0 0.969 byte-compiling build/bdist.linux-x86_64/egg/lapa/utils/__init__.py to __init__.cpython-310.pyc
#0 0.969 byte-compiling build/bdist.linux-x86_64/egg/lapa/utils/io.py to io.cpython-310.pyc
#0 0.970 byte-compiling build/bdist.linux-x86_64/egg/lapa/utils/gtf.py to gtf.cpython-310.pyc
#0 0.971 creating build/bdist.linux-x86_64/egg/EGG-INFO
#0 0.971 copying lapa.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
#0 0.971 copying lapa.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
#0 0.971 copying lapa.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
#0 0.971 copying lapa.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
#0 0.971 zip_safe flag not set; analyzing archive contents...
#0 0.971 copying lapa.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
#0 0.971 copying lapa.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
#0 0.975 creating dist
#0 0.975 creating 'dist/lapa-0.0.5-py3.10.egg' and adding 'build/bdist.linux-x86_64/egg' to it
#0 0.983 removing 'build/bdist.linux-x86_64/egg' (and everything under it)
#0 0.984 Processing lapa-0.0.5-py3.10.egg
#0 0.985 Copying lapa-0.0.5-py3.10.egg to /opt/conda/lib/python3.10/site-packages
#0 0.986 Adding lapa 0.0.5 to easy-install.pth file
#0 0.987 Installing lapa script to /opt/conda/bin
#0 0.987 Installing lapa_correct_talon script to /opt/conda/bin
#0 0.987 Installing lapa_correct_talon_gtf script to /opt/conda/bin
#0 0.987 Installing lapa_link_tss_to_tes script to /opt/conda/bin
#0 0.987 Installing lapa_tss script to /opt/conda/bin
#0 0.987 
#0 0.987 Installed /opt/conda/lib/python3.10/site-packages/lapa-0.0.5-py3.10.egg
#0 0.988 Processing dependencies for lapa==0.0.5
#0 0.988 Searching for betabinomial
#0 0.988 Reading https://pypi.org/simple/betabinomial/
#0 1.027 Downloading https://files.pythonhosted.org/packages/02/a6/2df0ccb3eef47721ad0db2297a6851341b70ab8ec74654c4546681fa2c8d/betabinomial-0.0.2-py3-none-any.whl#sha256=a28e4d0b008c5b53ae67da672f4d32d32fe83f9e390d733f4a22c3ece2e49dd3
#0 1.060 Best match: betabinomial 0.0.2
#0 1.060 Processing betabinomial-0.0.2-py3-none-any.whl
#0 1.060 Installing betabinomial-0.0.2-py3-none-any.whl to /opt/conda/lib/python3.10/site-packages
#0 1.070 Adding betabinomial 0.0.2 to easy-install.pth file
#0 1.070 detected new path './lapa-0.0.5-py3.10.egg'
#0 1.070 
#0 1.070 Installed /opt/conda/lib/python3.10/site-packages/betabinomial-0.0.2-py3.10.egg
#0 1.070 Searching for matplotlib
#0 1.070 Reading https://pypi.org/simple/matplotlib/
#0 1.201 Downloading https://files.pythonhosted.org/packages/59/50/5f9999c9085f69e654cf8e9543d178c578457f06d6a0451904893d7984a6/matplotlib-3.8.0rc1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=730cefef0ef9a757ba69f014aa26866d8d7e1bee35cc76c27d17985947f68c65
#0 1.312 Best match: matplotlib 3.8.0rc1
#0 1.312 Processing matplotlib-3.8.0rc1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
#0 1.313 Installing matplotlib-3.8.0rc1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl to /opt/conda/lib/python3.10/site-packages
#0 1.514 Adding matplotlib 3.8.0rc1 to easy-install.pth file
#0 1.515 detected new path './betabinomial-0.0.2-py3.10.egg'
#0 1.515 
#0 1.515 Installed /opt/conda/lib/python3.10/site-packages/matplotlib-3.8.0rc1-py3.10-linux-x86_64.egg
#0 1.518 Searching for kipoiseq>=0.3.0
#0 1.518 Reading https://pypi.org/simple/kipoiseq/
#0 1.555 Downloading https://files.pythonhosted.org/packages/d0/96/4620449840d295f8f8264e00b4c7527a28fbaf9f8bb4ba1551712728fd16/kipoiseq-0.7.1-py3-none-any.whl#sha256=ec6d600d44b490a78541a4c2b681be578876f466c2f7052d424c67c8c6e07947
#0 1.584 Best match: kipoiseq 0.7.1
#0 1.584 Processing kipoiseq-0.7.1-py3-none-any.whl
#0 1.584 Installing kipoiseq-0.7.1-py3-none-any.whl to /opt/conda/lib/python3.10/site-packages
#0 1.598 Adding kipoiseq 0.7.1 to easy-install.pth file
#0 1.598 detected new path './matplotlib-3.8.0rc1-py3.10-linux-x86_64.egg'
#0 1.599 
#0 1.599 Installed /opt/conda/lib/python3.10/site-packages/kipoiseq-0.7.1-py3.10.egg
#0 1.600 Searching for sorted-nearest>=0.0.35
#0 1.600 Reading https://pypi.org/simple/sorted-nearest/
#0 1.635 Downloading https://files.pythonhosted.org/packages/84/62/9df5b5ca5ec19126c89bbe53c7ffc318474603908c57438d73b5ff29b973/sorted_nearest-0.0.39-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=5c97d2088baffb19dcb0bf0a3921bf0b6ecd40157e24c0eabd881215994ee917
#0 1.723 Best match: sorted-nearest 0.0.39
#0 1.723 Processing sorted_nearest-0.0.39-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
#0 1.723 Installing sorted_nearest-0.0.39-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl to /opt/conda/lib/python3.10/site-packages
#0 1.824 Adding sorted-nearest 0.0.39 to easy-install.pth file
#0 1.824 detected new path './kipoiseq-0.7.1-py3.10.egg'
#0 1.825 
#0 1.825 Installed /opt/conda/lib/python3.10/site-packages/sorted_nearest-0.0.39-py3.10-linux-x86_64.egg
#0 1.826 Searching for pyranges>=0.0.71
#0 1.826 Reading https://pypi.org/simple/pyranges/
#0 1.882 Downloading https://files.pythonhosted.org/packages/db/d3/5b73b3271eb6cc7a2a6a0bf1dbcb8c0578467f4919c0c5e044b5329df85e/pyranges-0.0.129-py3-none-any.whl#sha256=e9f003696be1bf9c0759a0b4e08964d942d22bba2cf1113b6b9febdb779a2842
#0 1.973 Best match: pyranges 0.0.129
#0 1.973 Processing pyranges-0.0.129-py3-none-any.whl
#0 1.973 Installing pyranges-0.0.129-py3-none-any.whl to /opt/conda/lib/python3.10/site-packages
#0 2.013 Adding pyranges 0.0.129 to easy-install.pth file
#0 2.013 detected new path './sorted_nearest-0.0.39-py3.10-linux-x86_64.egg'
#0 2.014 
#0 2.014 Installed /opt/conda/lib/python3.10/site-packages/pyranges-0.0.129-py3.10.egg
#0 2.015 Searching for bamread>=0.0.10
#0 2.015 Reading https://pypi.org/simple/bamread/
#0 2.051 Downloading https://files.pythonhosted.org/packages/0a/c5/168a19608e4950f0734f20f465a16e33958e9a860025cb7d20d5414accb5/bamread-0.0.16-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=4ed59c49bcc1594b75fd2ba96273db38e8ed10c566dd81d13c59fecdfca865bc
#0 2.102 Best match: bamread 0.0.16
#0 2.102 Processing bamread-0.0.16-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
#0 2.102 Installing bamread-0.0.16-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl to /opt/conda/lib/python3.10/site-packages
#0 2.122 Adding bamread 0.0.16 to easy-install.pth file
#0 2.123 detected new path './pyranges-0.0.129-py3.10.egg'
#0 2.123 
#0 2.123 Installed /opt/conda/lib/python3.10/site-packages/bamread-0.0.16-py3.10-linux-x86_64.egg
#0 2.124 Searching for scipy
#0 2.124 Reading https://pypi.org/simple/scipy/
#0 2.246 Downloading https://files.pythonhosted.org/packages/a8/cc/c36f3439f5d47c3b13833ce6687b43a040cc7638c502ac46b41e2d4f3d6f/scipy-1.11.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=d690e1ca993c8f7ede6d22e5637541217fc6a4d3f78b3672a6fe454dbb7eb9a7
#0 2.423 Best match: scipy 1.11.2
#0 2.423 Processing scipy-1.11.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
#0 2.424 Installing scipy-1.11.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl to /opt/conda/lib/python3.10/site-packages
#0 2.991 Adding scipy 1.11.2 to easy-install.pth file
#0 2.991 detected new path './bamread-0.0.16-py3.10-linux-x86_64.egg'
#0 2.992 
#0 2.992 Installed /opt/conda/lib/python3.10/site-packages/scipy-1.11.2-py3.10-linux-x86_64.egg
#0 2.998 Searching for pybigwig
#0 2.998 Reading https://pypi.org/simple/pybigwig/
#0 3.032 Downloading https://files.pythonhosted.org/packages/3b/9c/b86f24903d39531876b98cb9b2bf17a3d4fcff5fa8a17dab9971bbe920f9/pyBigWig-0.3.22-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=55031f67de6b117d49ba191738ea9707239bdacbd623a046e03917913257ac29
#0 3.075 Best match: pyBigWig 0.3.22
#0 3.075 Processing pyBigWig-0.3.22-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
#0 3.075 Installing pyBigWig-0.3.22-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl to /opt/conda/lib/python3.10/site-packages
#0 3.087 Adding pyBigWig 0.3.22 to easy-install.pth file
#0 3.088 detected new path './scipy-1.11.2-py3.10-linux-x86_64.egg'
#0 3.088 
#0 3.088 Installed /opt/conda/lib/python3.10/site-packages/pyBigWig-0.3.22-py3.10-linux-x86_64.egg
#0 3.089 Searching for pandas
#0 3.089 Reading https://pypi.org/simple/pandas/
#0 3.250 Downloading https://files.pythonhosted.org/packages/92/d4/a3b91ef3103e23b8e39b94e51f0984368646680f42cc74ee857aa63b05ff/pandas-2.1.0rc0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=9a13b734f8844fb8d99aa175151f9919152a2531ec9a798465455f6408bccbd8
#0 3.370 Best match: pandas 2.1.0rc0
#0 3.370 Processing pandas-2.1.0rc0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
#0 3.370 Installing pandas-2.1.0rc0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl to /opt/conda/lib/python3.10/site-packages
#0 3.697 Adding pandas 2.1.0rc0 to easy-install.pth file
#0 3.697 detected new path './pyBigWig-0.3.22-py3.10-linux-x86_64.egg'
#0 3.698 
#0 3.698 Installed /opt/conda/lib/python3.10/site-packages/pandas-2.1.0rc0-py3.10-linux-x86_64.egg
#0 3.704 Searching for click
#0 3.704 Reading https://pypi.org/simple/click/
#0 3.755 Downloading https://files.pythonhosted.org/packages/00/2e/d53fa4befbf2cfa713304affc7ca780ce4fc1fd8710527771b58311a3229/click-8.1.7-py3-none-any.whl#sha256=ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28
#0 3.795 Best match: click 8.1.7
#0 3.795 Processing click-8.1.7-py3-none-any.whl
#0 3.795 Installing click-8.1.7-py3-none-any.whl to /opt/conda/lib/python3.10/site-packages
#0 3.806 Adding click 8.1.7 to easy-install.pth file
#0 3.807 detected new path './pandas-2.1.0rc0-py3.10-linux-x86_64.egg'
#0 3.808 
#0 3.808 Installed /opt/conda/lib/python3.10/site-packages/click-8.1.7-py3.10.egg
#0 3.808 Searching for numpy<=1.23
#0 3.808 Reading https://pypi.org/simple/numpy/
#0 4.001 Downloading https://files.pythonhosted.org/packages/7a/88/8404fbe4f6472e4e54106a8faacae1279a244422bc88f5ee3e33ba2dd72b/numpy-1.23.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=d54b3b828d618a19779a84c3ad952e96e2c2311b16384e973e671aa5be1f6187
#0 4.121 Best match: numpy 1.23.0
#0 4.121 Processing numpy-1.23.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
#0 4.121 Installing numpy-1.23.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl to /opt/conda/lib/python3.10/site-packages
#0 4.483 Adding numpy 1.23.0 to easy-install.pth file
#0 4.484 detected new path './click-8.1.7-py3.10.egg'
#0 4.486 Installing f2py script to /opt/conda/bin
#0 4.486 Installing f2py3 script to /opt/conda/bin
#0 4.486 Installing f2py3.10 script to /opt/conda/bin
#0 4.486 
#0 4.486 Installed /opt/conda/lib/python3.10/site-packages/numpy-1.23.0-py3.10-linux-x86_64.egg
#0 4.490 Searching for setuptools
#0 4.490 Reading https://pypi.org/simple/setuptools/
#0 6.302 Downloading https://files.pythonhosted.org/packages/4f/ab/0bcfebdfc3bfa8554b2b2c97a555569c4c1ebc74ea288741ea8326c51906/setuptools-68.1.2-py3-none-any.whl#sha256=3d8083eed2d13afc9426f227b24fd1659489ec107c0e86cec2ffdde5c92e790b
#0 6.348 Best match: setuptools 68.1.2
#0 6.348 Processing setuptools-68.1.2-py3-none-any.whl
#0 6.348 Installing setuptools-68.1.2-py3-none-any.whl to /opt/conda/lib/python3.10/site-packages
#0 6.395 Adding setuptools 68.1.2 to easy-install.pth file
#0 6.395 detected new path './numpy-1.23.0-py3.10-linux-x86_64.egg'
#0 6.399 
#0 6.399 Installed /opt/conda/lib/python3.10/site-packages/setuptools-68.1.2-py3.10.egg
#0 6.402 Searching for statsmodels
#0 6.402 Reading https://pypi.org/simple/statsmodels/
#0 6.481 Downloading https://files.pythonhosted.org/packages/d5/22/62831c11096ef030e35424326716d47d65d5f7eb323966c9e4725324770d/statsmodels-0.14.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=9c64ebe9cf376cba0c31aed138e15ed179a1d128612dd241cdf299d159e5e882
#0 6.605 Best match: statsmodels 0.14.0
#0 6.605 Processing statsmodels-0.14.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
#0 6.605 Installing statsmodels-0.14.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl to /opt/conda/lib/python3.10/site-packages
#0 6.867 Adding statsmodels 0.14.0 to easy-install.pth file
#0 6.868 detected new path './setuptools-68.1.2-py3.10.egg'
#0 6.869 
#0 6.869 Installed /opt/conda/lib/python3.10/site-packages/statsmodels-0.14.0-py3.10-linux-x86_64.egg
#0 6.872 Searching for python-dateutil>=2.7
#0 6.872 Reading https://pypi.org/simple/python-dateutil/
#0 6.909 Downloading https://files.pythonhosted.org/packages/36/7a/87837f39d0296e723bb9b62bbb257d0355c7f6128853c78955f57342a56d/python_dateutil-2.8.2-py2.py3-none-any.whl#sha256=961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9
#0 6.952 Best match: python-dateutil 2.8.2
#0 6.952 Processing python_dateutil-2.8.2-py2.py3-none-any.whl
#0 6.952 Installing python_dateutil-2.8.2-py2.py3-none-any.whl to /opt/conda/lib/python3.10/site-packages
#0 6.965 Adding python-dateutil 2.8.2 to easy-install.pth file
#0 6.966 detected new path './statsmodels-0.14.0-py3.10-linux-x86_64.egg'
#0 6.967 
#0 6.967 Installed /opt/conda/lib/python3.10/site-packages/python_dateutil-2.8.2-py3.10.egg
#0 6.967 Searching for pyparsing>=2.3.1
#0 6.967 Reading https://pypi.org/simple/pyparsing/
#0 7.049 Downloading https://files.pythonhosted.org/packages/39/92/8486ede85fcc088f1b3dba4ce92dd29d126fd96b0008ea213167940a2475/pyparsing-3.1.1-py3-none-any.whl#sha256=32c7c0b711493c72ff18a981d24f28aaf9c1fb7ed5e9667c9e84e3db623bdbfb
#0 7.082 Best match: pyparsing 3.1.1
#0 7.082 Processing pyparsing-3.1.1-py3-none-any.whl
#0 7.082 Installing pyparsing-3.1.1-py3-none-any.whl to /opt/conda/lib/python3.10/site-packages
#0 7.093 Adding pyparsing 3.1.1 to easy-install.pth file
#0 7.094 detected new path './python_dateutil-2.8.2-py3.10.egg'
#0 7.095 
#0 7.095 Installed /opt/conda/lib/python3.10/site-packages/pyparsing-3.1.1-py3.10.egg
#0 7.096 Searching for pillow>=6.2.0
#0 7.096 Reading https://pypi.org/simple/pillow/
#0 7.305 Downloading https://files.pythonhosted.org/packages/7b/c9/08de9a629ce7cdeaea0ddca716e9efcd1844b2650f5b9dd8ec5609e40ffe/Pillow-10.0.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=520f2a520dc040512699f20fa1c363eed506e94248d71f85412b625026f6142c
#0 7.397 Best match: Pillow 10.0.0
#0 7.397 Processing Pillow-10.0.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
#0 7.398 Installing Pillow-10.0.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl to /opt/conda/lib/python3.10/site-packages
#0 7.464 Adding Pillow 10.0.0 to easy-install.pth file
#0 7.465 detected new path './pyparsing-3.1.1-py3.10.egg'
#0 7.466 
#0 7.466 Installed /opt/conda/lib/python3.10/site-packages/Pillow-10.0.0-py3.10-linux-x86_64.egg
#0 7.468 Searching for kiwisolver>=1.0.1
#0 7.468 Reading https://pypi.org/simple/kiwisolver/
#0 7.539 Downloading https://files.pythonhosted.org/packages/6f/40/4ab1fdb57fced80ce5903f04ae1aed7c1d5939dda4fd0c0aa526c12fe28a/kiwisolver-1.4.5-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl#sha256=ec20916e7b4cbfb1f12380e46486ec4bcbaa91a9c448b97023fde0d5bbf9e4ff
#0 7.609 Best match: kiwisolver 1.4.5
#0 7.609 Processing kiwisolver-1.4.5-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl
#0 7.610 Installing kiwisolver-1.4.5-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl to /opt/conda/lib/python3.10/site-packages
#0 7.645 Adding kiwisolver 1.4.5 to easy-install.pth file
#0 7.646 detected new path './Pillow-10.0.0-py3.10-linux-x86_64.egg'
#0 7.647 
#0 7.647 Installed /opt/conda/lib/python3.10/site-packages/kiwisolver-1.4.5-py3.10-linux-x86_64.egg
#0 7.648 Searching for fonttools>=4.22.0
#0 7.648 Reading https://pypi.org/simple/fonttools/
#0 7.859 Downloading https://files.pythonhosted.org/packages/b9/97/8fb94ba61f1a098671639f60cda3d7e3e2bf3a5ccc4fca00fcb909f0882e/fonttools-4.42.1-py3-none-any.whl#sha256=9398f244e28e0596e2ee6024f808b06060109e33ed38dcc9bded452fd9bbb853
#0 7.902 Best match: fonttools 4.42.1
#0 7.903 Processing fonttools-4.42.1-py3-none-any.whl
#0 7.903 Installing fonttools-4.42.1-py3-none-any.whl to /opt/conda/lib/python3.10/site-packages
#0 7.960 Adding fonttools 4.42.1 to easy-install.pth file
#0 7.961 detected new path './kiwisolver-1.4.5-py3.10-linux-x86_64.egg'
#0 7.963 Installing fonttools script to /opt/conda/bin
#0 7.963 Installing pyftmerge script to /opt/conda/bin
#0 7.963 Installing pyftsubset script to /opt/conda/bin
#0 7.963 Installing ttx script to /opt/conda/bin
#0 7.963 
#0 7.963 Installed /opt/conda/lib/python3.10/site-packages/fonttools-4.42.1-py3.10.egg
#0 7.965 Searching for cycler>=0.10
#0 7.965 Reading https://pypi.org/simple/cycler/
#0 8.001 Downloading https://files.pythonhosted.org/packages/5c/f9/695d6bedebd747e5eb0fe8fad57b72fdf25411273a39791cde838d5a8f51/cycler-0.11.0-py3-none-any.whl#sha256=3a27e95f763a428a739d2add979fa7494c912a32c17c4c38c4d5f082cad165a3
#0 8.026 Best match: cycler 0.11.0
#0 8.026 Processing cycler-0.11.0-py3-none-any.whl
#0 8.026 Installing cycler-0.11.0-py3-none-any.whl to /opt/conda/lib/python3.10/site-packages
#0 8.035 Adding cycler 0.11.0 to easy-install.pth file
#0 8.036 detected new path './fonttools-4.42.1-py3.10.egg'
#0 8.037 
#0 8.037 Installed /opt/conda/lib/python3.10/site-packages/cycler-0.11.0-py3.10.egg
#0 8.037 Searching for contourpy>=1.0.1
#0 8.037 Reading https://pypi.org/simple/contourpy/
#0 8.136 Downloading https://files.pythonhosted.org/packages/aa/55/02c6d24804592b862b38a85c9b3283edc245081390a520ccd11697b6b24f/contourpy-1.1.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=90c81f22b4f572f8a2110b0b741bb64e5a6427e0a198b2cdc1fbaf85f352a3aa
#0 8.184 Best match: contourpy 1.1.0
#0 8.184 Processing contourpy-1.1.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
#0 8.184 Installing contourpy-1.1.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl to /opt/conda/lib/python3.10/site-packages
#0 8.201 Adding contourpy 1.1.0 to easy-install.pth file
#0 8.202 detected new path './cycler-0.11.0-py3.10.egg'
#0 8.203 
#0 8.203 Installed /opt/conda/lib/python3.10/site-packages/contourpy-1.1.0-py3.10-linux-x86_64.egg
#0 8.204 Searching for kipoi-conda>=0.1.0
#0 8.204 Reading https://pypi.org/simple/kipoi-conda/
#0 8.236 Downloading https://files.pythonhosted.org/packages/55/71/a5448107b5fd2eb22c5fa402985a0f7d0ff8725e7b7d44e6179255df4565/kipoi_conda-0.3.1-py3-none-any.whl#sha256=d780ce0711313d2b40501bd400fb7a39d90799d283c1bcb2f13e09e68d6f9ebd
#0 8.269 Best match: kipoi-conda 0.3.1
#0 8.269 Processing kipoi_conda-0.3.1-py3-none-any.whl
#0 8.269 Installing kipoi_conda-0.3.1-py3-none-any.whl to /opt/conda/lib/python3.10/site-packages
#0 8.280 Adding kipoi-conda 0.3.1 to easy-install.pth file
#0 8.281 detected new path './contourpy-1.1.0-py3.10-linux-x86_64.egg'
#0 8.282 
#0 8.282 Installed /opt/conda/lib/python3.10/site-packages/kipoi_conda-0.3.1-py3.10.egg
#0 8.283 Searching for kipoi-utils>=0.1.1
#0 8.283 Reading https://pypi.org/simple/kipoi-utils/
#0 8.323 Downloading https://files.pythonhosted.org/packages/80/06/d9ae96691b049713178ad95795a9fc3de2381e3b3768b7a1519f10aabb54/kipoi_utils-0.7.7-py3-none-any.whl#sha256=ebc72eaa24e23b576cbc186da4e10637989858883a3930baade74905d14e248b
#0 8.353 Best match: kipoi-utils 0.7.7
#0 8.353 Processing kipoi_utils-0.7.7-py3-none-any.whl
#0 8.353 Installing kipoi_utils-0.7.7-py3-none-any.whl to /opt/conda/lib/python3.10/site-packages
#0 8.366 Adding kipoi-utils 0.7.7 to easy-install.pth file
#0 8.367 detected new path './kipoi_conda-0.3.1-py3.10.egg'
#0 8.369 
#0 8.369 Installed /opt/conda/lib/python3.10/site-packages/kipoi_utils-0.7.7-py3.10.egg
#0 8.369 Searching for gffutils
#0 8.369 Reading https://pypi.org/simple/gffutils/
#0 8.399 Downloading https://files.pythonhosted.org/packages/b2/0a/eddd2f6667198100adb8fa6f983db66022e3c375c40d19795a3de05df986/gffutils-0.12-py3-none-any.whl#sha256=35aef6d02616ee658e846052a0d2eee8dd10a17aefc9829305fc5a28878d7702
#0 8.460 Best match: gffutils 0.12
#0 8.460 Processing gffutils-0.12-py3-none-any.whl
#0 8.460 Installing gffutils-0.12-py3-none-any.whl to /opt/conda/lib/python3.10/site-packages
#0 8.505 Adding gffutils 0.12 to easy-install.pth file
#0 8.506 detected new path './kipoi_utils-0.7.7-py3.10.egg'
#0 8.508 Installing gffutils-cli script to /opt/conda/bin
#0 8.509 
#0 8.509 Installed /opt/conda/lib/python3.10/site-packages/gffutils-0.12-py3.10.egg
#0 8.509 Searching for pyfaidx
#0 8.509 Reading https://pypi.org/simple/pyfaidx/
#0 8.569 Downloading https://files.pythonhosted.org/packages/eb/93/07273ec98d61de68a966d2ed7a3f4ee5a4501d1be7821c4c36855fc8548f/pyfaidx-0.7.2.1-py3-none-any.whl#sha256=eee13d35bb5f2aa65932a9ad9dd74fa695aefe6e0baafc5836cfa869a7695acc
#0 8.596 Best match: pyfaidx 0.7.2.1
#0 8.596 Processing pyfaidx-0.7.2.1-py3-none-any.whl
#0 8.596 Installing pyfaidx-0.7.2.1-py3-none-any.whl to /opt/conda/lib/python3.10/site-packages
#0 8.606 Adding pyfaidx 0.7.2.1 to easy-install.pth file
#0 8.607 detected new path './gffutils-0.12-py3.10.egg'
#0 8.609 Installing faidx script to /opt/conda/bin
#0 8.609 
#0 8.609 Installed /opt/conda/lib/python3.10/site-packages/pyfaidx-0.7.2.1-py3.10.egg
#0 8.609 Searching for kipoi>=0.5.5
#0 8.609 Reading https://pypi.org/simple/kipoi/
#0 8.663 Downloading https://files.pythonhosted.org/packages/ae/39/0cc82e5d2f6a42d0a23c73cb5801a06cfb541f818873faa8e4670663e01b/kipoi-0.8.6-py3-none-any.whl#sha256=1eca80e4e07383b69b36eec187cef249b0b7b049843b00ebe42e863e422da5cf
#0 8.706 Best match: kipoi 0.8.6
#0 8.706 Processing kipoi-0.8.6-py3-none-any.whl
#0 8.706 Installing kipoi-0.8.6-py3-none-any.whl to /opt/conda/lib/python3.10/site-packages
#0 8.725 Adding kipoi 0.8.6 to easy-install.pth file
#0 8.726 detected new path './pyfaidx-0.7.2.1-py3.10.egg'
#0 8.728 Installing kipoi script to /opt/conda/bin
#0 8.728 
#0 8.728 Installed /opt/conda/lib/python3.10/site-packages/kipoi-0.8.6-py3.10.egg
#0 8.730 Searching for natsort
#0 8.730 Reading https://pypi.org/simple/natsort/
#0 8.790 Downloading https://files.pythonhosted.org/packages/ef/82/7a9d0550484a62c6da82858ee9419f3dd1ccc9aa1c26a1e43da3ecd20b0d/natsort-8.4.0-py3-none-any.whl#sha256=4732914fb471f56b5cce04d7bae6f164a592c7712e1c85f9ef585e197299521c
#0 8.817 Best match: natsort 8.4.0
#0 8.817 Processing natsort-8.4.0-py3-none-any.whl
#0 8.817 Installing natsort-8.4.0-py3-none-any.whl to /opt/conda/lib/python3.10/site-packages
#0 8.828 Adding natsort 8.4.0 to easy-install.pth file
#0 8.829 detected new path './kipoi-0.8.6-py3.10.egg'
#0 8.831 Installing natsort script to /opt/conda/bin
#0 8.831 
#0 8.831 Installed /opt/conda/lib/python3.10/site-packages/natsort-8.4.0-py3.10.egg
#0 8.832 Searching for tabulate
#0 8.832 Reading https://pypi.org/simple/tabulate/
#0 8.866 Downloading https://files.pythonhosted.org/packages/40/44/4a5f08c96eb108af5cb50b41f76142f0afa346dfa99d5296fe7202a11854/tabulate-0.9.0-py3-none-any.whl#sha256=024ca478df22e9340661486f85298cff5f6dcdba14f3813e8830015b9ed1948f
#0 8.900 Best match: tabulate 0.9.0
#0 8.900 Processing tabulate-0.9.0-py3-none-any.whl
#0 8.900 Installing tabulate-0.9.0-py3-none-any.whl to /opt/conda/lib/python3.10/site-packages
#0 8.911 Adding tabulate 0.9.0 to easy-install.pth file
#0 8.912 detected new path './natsort-8.4.0-py3.10.egg'
#0 8.914 Installing tabulate script to /opt/conda/bin
#0 8.914 
#0 8.914 Installed /opt/conda/lib/python3.10/site-packages/tabulate-0.9.0-py3.10.egg
#0 8.914 Searching for ncls>=0.0.63
#0 8.914 Reading https://pypi.org/simple/ncls/
#0 8.969 Downloading https://files.pythonhosted.org/packages/fc/19/30f84863a8f6a4b3ed4bf886a7261549c2189e938945711cfbd2cca386a3/ncls-0.0.68-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=f67cb6531e4044663d89d27ff7baf0cf69e253751663aac84798e282ce8cfdd2
#0 9.035 Best match: ncls 0.0.68
#0 9.035 Processing ncls-0.0.68-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
#0 9.035 Installing ncls-0.0.68-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl to /opt/conda/lib/python3.10/site-packages
#0 9.083 Adding ncls 0.0.68 to easy-install.pth file
#0 9.084 detected new path './tabulate-0.9.0-py3.10.egg'
#0 9.086 
#0 9.086 Installed /opt/conda/lib/python3.10/site-packages/ncls-0.0.68-py3.10-linux-x86_64.egg
#0 9.086 Searching for pysam
#0 9.086 Reading https://pypi.org/simple/pysam/
#0 9.141 Downloading https://files.pythonhosted.org/packages/89/ba/d9a85addaaceb6e64e07498aa2f49c34851c72e1c367e91b43b47a6cdd91/pysam-0.21.0-cp310-cp310-manylinux_2_24_x86_64.whl#sha256=37e0ed17c05f7cb3b141c2c78ad23b3592479e8adc47453ae5681c6ffd0d5e00
#0 9.305 Best match: pysam 0.21.0
#0 9.305 Processing pysam-0.21.0-cp310-cp310-manylinux_2_24_x86_64.whl
#0 9.305 Installing pysam-0.21.0-cp310-cp310-manylinux_2_24_x86_64.whl to /opt/conda/lib/python3.10/site-packages
#0 9.634 Adding pysam 0.21.0 to easy-install.pth file
#0 9.636 detected new path './ncls-0.0.68-py3.10-linux-x86_64.egg'
#0 9.638 
#0 9.638 Installed /opt/conda/lib/python3.10/site-packages/pysam-0.21.0-py3.10-linux-x86_64.egg
#0 9.641 Searching for tzdata>=2022.1
#0 9.641 Reading https://pypi.org/simple/tzdata/
#0 9.679 Downloading https://files.pythonhosted.org/packages/d5/fb/a79efcab32b8a1f1ddca7f35109a50e4a80d42ac1c9187ab46522b2407d7/tzdata-2023.3-py2.py3-none-any.whl#sha256=7e65763eef3120314099b6939b5546db7adce1e7d6f2e179e3df563c70511eda
#0 9.711 Best match: tzdata 2023.3
#0 9.711 Processing tzdata-2023.3-py2.py3-none-any.whl
#0 9.711 Installing tzdata-2023.3-py2.py3-none-any.whl to /opt/conda/lib/python3.10/site-packages
#0 9.764 Adding tzdata 2023.3 to easy-install.pth file
#0 9.766 detected new path './pysam-0.21.0-py3.10-linux-x86_64.egg'
#0 9.767 
#0 9.767 Installed /opt/conda/lib/python3.10/site-packages/tzdata-2023.3-py3.10.egg
#0 9.768 Searching for pytz>=2020.1
#0 9.768 Reading https://pypi.org/simple/pytz/
#0 9.908 Downloading https://files.pythonhosted.org/packages/7f/99/ad6bd37e748257dd70d6f85d916cafe79c0b0f5e2e95b11f7fbc82bf3110/pytz-2023.3-py2.py3-none-any.whl#sha256=a151b3abb88eda1d4e34a9814df37de2a80e301e68ba0fd856fb9b46bfbbbffb
#0 9.958 Best match: pytz 2023.3
#0 9.958 Processing pytz-2023.3-py2.py3-none-any.whl
#0 9.958 Installing pytz-2023.3-py2.py3-none-any.whl to /opt/conda/lib/python3.10/site-packages
#0 10.01 Adding pytz 2023.3 to easy-install.pth file
#0 10.01 detected new path './tzdata-2023.3-py3.10.egg'
#0 10.02 
#0 10.02 Installed /opt/conda/lib/python3.10/site-packages/pytz-2023.3-py3.10.egg
#0 10.02 Searching for patsy>=0.5.2
#0 10.02 Reading https://pypi.org/simple/patsy/
#0 10.05 Downloading https://files.pythonhosted.org/packages/2a/e4/b3263b0e353f2be7b14f044d57874490c9cef1798a435f038683acea5c98/patsy-0.5.3-py2.py3-none-any.whl#sha256=7eb5349754ed6aa982af81f636479b1b8db9d5b1a6e957a6016ec0534b5c86b7
#0 10.09 Best match: patsy 0.5.3
#0 10.09 Processing patsy-0.5.3-py2.py3-none-any.whl
#0 10.09 Installing patsy-0.5.3-py2.py3-none-any.whl to /opt/conda/lib/python3.10/site-packages
#0 10.11 Adding patsy 0.5.3 to easy-install.pth file
#0 10.11 detected new path './pytz-2023.3-py3.10.egg'
#0 10.11 
#0 10.11 Installed /opt/conda/lib/python3.10/site-packages/patsy-0.5.3-py3.10.egg
#0 10.11 Searching for six>=1.5
#0 10.11 Reading https://pypi.org/simple/six/
#0 10.15 Downloading https://files.pythonhosted.org/packages/d9/5a/e7c31adbe875f2abbb91bd84cf2dc52d792b5a01506781dbcf25c91daf11/six-1.16.0-py2.py3-none-any.whl#sha256=8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254
#0 10.18 Best match: six 1.16.0
#0 10.18 Processing six-1.16.0-py2.py3-none-any.whl
#0 10.18 Installing six-1.16.0-py2.py3-none-any.whl to /opt/conda/lib/python3.10/site-packages
#0 10.19 Adding six 1.16.0 to easy-install.pth file
#0 10.19 detected new path './patsy-0.5.3-py3.10.egg'
#0 10.20 
#0 10.20 Installed /opt/conda/lib/python3.10/site-packages/six-1.16.0-py3.10.egg
#0 10.20 Searching for related
#0 10.20 Reading https://pypi.org/simple/related/
#0 10.23 Downloading https://files.pythonhosted.org/packages/f5/82/5b30d556a576172b2e771cfa31360884c8fb7edf2c34cee196b30f03e257/related-0.7.3-py2.py3-none-any.whl#sha256=d9b1f512b231f72911b7564370638b692fae81c54ef25fa4c04773db2ae58b75
#0 10.26 Best match: related 0.7.3
#0 10.26 Processing related-0.7.3-py2.py3-none-any.whl
#0 10.26 Installing related-0.7.3-py2.py3-none-any.whl to /opt/conda/lib/python3.10/site-packages
#0 10.27 Adding related 0.7.3 to easy-install.pth file
#0 10.27 detected new path './six-1.16.0-py3.10.egg'
#0 10.27 
#0 10.27 Installed /opt/conda/lib/python3.10/site-packages/related-0.7.3-py3.10.egg
#0 10.27 Searching for PyYAML>=5.1.0
#0 10.27 Reading https://pypi.org/simple/PyYAML/
#0 10.37 Downloading https://files.pythonhosted.org/packages/29/61/bf33c6c85c55bc45a29eee3195848ff2d518d84735eb0e2d8cb42e0d285e/PyYAML-6.0.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=ba336e390cd8e4d1739f42dfe9bb83a3cc2e80f567d8805e11b46f4a943f5515
#0 10.42 Best match: PyYAML 6.0.1
#0 10.42 Processing PyYAML-6.0.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
#0 10.42 Installing PyYAML-6.0.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl to /opt/conda/lib/python3.10/site-packages
#0 10.44 Adding PyYAML 6.0.1 to easy-install.pth file
#0 10.44 detected new path './related-0.7.3-py3.10.egg'
#0 10.45 
#0 10.45 Installed /opt/conda/lib/python3.10/site-packages/PyYAML-6.0.1-py3.10-linux-x86_64.egg
#0 10.45 Searching for attrs
#0 10.45 Reading https://pypi.org/simple/attrs/
#0 10.49 Downloading https://files.pythonhosted.org/packages/f0/eb/fcb708c7bf5056045e9e98f62b93bd7467eb718b0202e7698eb11d66416c/attrs-23.1.0-py3-none-any.whl#sha256=1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04
#0 10.52 Best match: attrs 23.1.0
#0 10.52 Processing attrs-23.1.0-py3-none-any.whl
#0 10.52 Installing attrs-23.1.0-py3-none-any.whl to /opt/conda/lib/python3.10/site-packages
#0 10.54 Adding attrs 23.1.0 to easy-install.pth file
#0 10.54 detected new path './PyYAML-6.0.1-py3.10-linux-x86_64.egg'
#0 10.54 
#0 10.54 Installed /opt/conda/lib/python3.10/site-packages/attrs-23.1.0-py3.10.egg
#0 10.54 Searching for simplejson
#0 10.54 Reading https://pypi.org/simple/simplejson/
#0 10.65 Downloading https://files.pythonhosted.org/packages/b8/00/9720ea26c0da200a39b89e25721970f50f4b80bb2ab6de0199324f93c4ca/simplejson-3.19.1-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=6e7c70f19405e5f99168077b785fe15fcb5f9b3c0b70b0b5c2757ce294922c8c
#0 10.69 Best match: simplejson 3.19.1
#0 10.69 Processing simplejson-3.19.1-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl
#0 10.69 Installing simplejson-3.19.1-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl to /opt/conda/lib/python3.10/site-packages
#0 10.70 Adding simplejson 3.19.1 to easy-install.pth file
#0 10.71 detected new path './attrs-23.1.0-py3.10.egg'
#0 10.71 
#0 10.71 Installed /opt/conda/lib/python3.10/site-packages/simplejson-3.19.1-py3.10-linux-x86_64.egg
#0 10.71 Searching for argcomplete>=1.9.4
#0 10.71 Reading https://pypi.org/simple/argcomplete/
#0 10.79 Downloading https://files.pythonhosted.org/packages/4f/ef/8b604222ba5e5190e25851aa3a5b754f2002361dc62a258a8e9f13e866f4/argcomplete-3.1.1-py3-none-any.whl#sha256=35fa893a88deea85ea7b20d241100e64516d6af6d7b0ae2bed1d263d26f70948
#0 10.82 Best match: argcomplete 3.1.1
#0 10.82 Processing argcomplete-3.1.1-py3-none-any.whl
#0 10.82 Installing argcomplete-3.1.1-py3-none-any.whl to /opt/conda/lib/python3.10/site-packages
#0 10.83 Adding argcomplete 3.1.1 to easy-install.pth file
#0 10.84 detected new path './simplejson-3.19.1-py3.10-linux-x86_64.egg'
#0 10.84 Installing activate-global-python-argcomplete script to /opt/conda/bin
#0 10.84 Installing python-argcomplete-check-easy-install-script script to /opt/conda/bin
#0 10.84 Installing register-python-argcomplete script to /opt/conda/bin
#0 10.84 
#0 10.84 Installed /opt/conda/lib/python3.10/site-packages/argcomplete-3.1.1-py3.10.egg
#0 10.84 Searching for argh>=0.26.2
#0 10.84 Reading https://pypi.org/simple/argh/
#0 10.88 Downloading https://files.pythonhosted.org/packages/b2/03/7cad222e3aed5ed668c3c93c35f7ee866bc1da5cdcac945275f45e8caf80/argh-0.28.1-py3-none-any.whl#sha256=10e7311f3ea54a78a366e5456900d8b81049f44d8d653b524eb90cf7d29a71ee
#0 10.92 Best match: argh 0.28.1
#0 10.92 Processing argh-0.28.1-py3-none-any.whl
#0 10.92 Installing argh-0.28.1-py3-none-any.whl to /opt/conda/lib/python3.10/site-packages
#0 10.93 Adding argh 0.28.1 to easy-install.pth file
#0 10.93 detected new path './argcomplete-3.1.1-py3.10.egg'
#0 10.93 
#0 10.93 Installed /opt/conda/lib/python3.10/site-packages/argh-0.28.1-py3.10.egg
#0 10.94 error: attrs 23.1.0 is installed but attrs<=21.4.0 is required by {'kipoi'}
------
Dockerfile:14
--------------------
  12 |     RUN pip3 install Cython 
  13 |     RUN git clone https://github.com/mortazavilab/lapa.git
  14 | >>> RUN cd /lapa && python3 setup.py install
--------------------
ERROR: failed to solve: process "/bin/sh -c cd /lapa && python3 setup.py install" did not complete successfully: exit code: 1

Here is my Dockerfile:

FROM condaforge/mambaforge LABEL maintainer="sagnik.banerjee@bms.com"

ENV TZ=America/New_York ENV DEBIAN_FRONTEND=noninteractive

RUN apt-get -y update RUN apt-get -y install git python3 python3-pip git RUN apt-get clean all

RUN pip3 install lapa

RUN pip3 install Cython RUN git clone https://github.com/mortazavilab/lapa.git RUN cd /lapa && python3 setup.py install

Thanks

fairliereese commented 1 year ago

Can you try to force pip install an attrs version that is compatible with the kipoi library?

Melirie commented 5 months ago

I had the same issue of "Variables cannot be declared with 'cpdef'..." and when I changed the version from sorted-nearest==0.0.33 to 0.0.39 it worked, so apparently it was fixed :)

omarelgarwany commented 4 months ago

I stopped getting the cpdef error when I did pip install git+https://github.com/mortazavilab/lapa