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lncLOOM / LncLOOMv1

LncLOOM is a graph-based framework that uses integer programming to identify combinations of short motifs that are deeply conserved in rapidly evolving sequences. This version is implemented in Python 2 and is supported on Linux/Unix-based systems.
Mozilla Public License 2.0
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Installation issue #2

Open fdegalez opened 3 years ago

fdegalez commented 3 years ago

Hello everyone, After reading the "Uncovering deeply conserved motif combinations in rapidly evolving noncoding sequences" paper, I wanted to install your software in order to apply your work on my various data. However, I can't get through the installation process:

1) I first tried with the first method: "python2 -m pip install --user -e ./LncLOOM_v1" however I get this error message: ERROR: Command errored out with exit status 1: python setup.py egg_info After several searches, it seems that it is related to a bad version of the setuptools package. However, even after reinstalling the package, nothing happens, the error message remains unchanged.

2) I then tried the second method you propose, notably with the "manual" installation of the different packages. It is also impossible to install packages like Pulp or pyBigWig.

Could you then advise me so that I can continue ? For information I use :

What are the different versions you are using? I saw that you are going to propose a python3 version, is it coming soon?

Thank you in advance and have a nice day. F. Degalez

lncLOOM commented 3 years ago

Hi fdegalez,

I'm sorry for the inconvenience. I think there may be some incompatibility between the versions of each package you are using. Can you please send me the error messages you get when you try to install Pulp and pyBigWig individually.

I am using: Python 2.7.17 pip 9.0.1 setuptools 39.0.1

The python3 version is almost ready, I plan to release it in the coming week.

Caroline

From: fdegalez notifications@github.com Sent: Monday, January 25, 2021 6:49 PM To: lncLOOM/lncLOOM lncLOOM@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [lncLOOM/lncLOOM] Installation issue (#2)

Hello everyone, After reading the "Uncovering deeply conserved motif combinations in rapidly evolving noncoding sequences" paper, I wanted to install your software in order to apply your work on my various data. However, I can't get through the installation process:

  1. I first tried with the first method: "python2 -m pip install --user -e ./LncLOOM_v1" however I get this error message: ERROR: Command errored out with exit status 1: python setup.py egg_info After several searches, it seems that it is related to a bad version of the setuptools package. However, even after reinstalling the package, nothing happens, the error message remains unchanged.

  2. I then tried the second method you propose, notably with the "manual" installation of the different packages. It is also impossible to install packages like Pulp or pyBigWig.

Could you then advise me so that I can continue ? For information I use :

What are the different versions you are using? I saw that you are going to propose a python3 version, is it coming soon?

Thank you in advance and have a nice day. F. Degalez

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fdegalez commented 3 years ago

Hello and thank you for your fast reply, indeed considering our differences of versions especially with pip I imagine that the error may come from that.

However, I provide you the error messages during the installation of Pulp and pyBigWig.

Pulp :

DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support pip 21.0 will remove support for this functionality. Collecting pulp Using cached PuLP-2.4.tar.gz (1.4 MB) Collecting amply>=0.1.2 Using cached amply-0.1.4.tar.gz (28 kB) Installing build dependencies ... done Getting requirements to build wheel ... done ERROR: Exception: Traceback (most recent call last): File "/usr/local/lib/python2.7/dist-packages/pip/_internal/cli/base_command.py", line 223, in _main status = self.run(options, args) File "/usr/local/lib/python2.7/dist-packages/pip/_internal/cli/req_command.py", line 180, in wrapper return func(self, options, args) File "/usr/local/lib/python2.7/dist-packages/pip/_internal/commands/install.py", line 321, in run reqs, check_supported_wheels=not options.target_dir File "/usr/local/lib/python2.7/dist-packages/pip/_internal/resolution/legacy/resolver.py", line 180, in resolve discovered_reqs.extend(self._resolve_one(requirement_set, req)) File "/usr/local/lib/python2.7/dist-packages/pip/_internal/resolution/legacy/resolver.py", line 385, in _resolve_one dist = self._get_dist_for(req_to_install) File "/usr/local/lib/python2.7/dist-packages/pip/_internal/resolution/legacy/resolver.py", line 337, in _get_dist_for dist = self.preparer.prepare_linked_requirement(req) File "/usr/local/lib/python2.7/dist-packages/pip/_internal/operations/prepare.py", line 480, in prepare_linked_requirement return self._prepare_linked_requirement(req, parallel_builds) File "/usr/local/lib/python2.7/dist-packages/pip/_internal/operations/prepare.py", line 524, in _prepare_linked_requirement req, self.req_tracker, self.finder, self.build_isolation, File "/usr/local/lib/python2.7/dist-packages/pip/_internal/operations/prepare.py", line 88, in _get_prepared_distribution abstract_dist.prepare_distribution_metadata(finder, build_isolation) File "/usr/local/lib/python2.7/dist-packages/pip/_internal/distributions/sdist.py", line 39, in prepare_distribution_metadata self._setup_isolation(finder) File "/usr/local/lib/python2.7/dist-packages/pip/_internal/distributions/sdist.py", line 97, in _setup_isolation reqs = backend.get_requires_for_build_wheel() File "/usr/local/lib/python2.7/dist-packages/pip/_vendor/pep517/wrappers.py", line 178, in get_requires_for_build_wheel 'config_settings': config_settings File "/usr/local/lib/python2.7/dist-packages/pip/_vendor/pep517/wrappers.py", line 284, in _call_hook raise BackendUnavailable(data.get('traceback', '')) BackendUnavailable

pyBigWig :

DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support pip 21.0 will remove support for this functionality. Collecting pyBigWig Using cached pyBigWig-0.3.17.tar.gz (64 kB) Building wheels for collected packages: pyBigWig Building wheel for pyBigWig (setup.py) ... error ERROR: Command errored out with exit status 1: command: /usr/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-VkaNvC/pybigwig/setup.py'"'"'; file='"'"'/tmp/pip-install-VkaNvC/pybigwig/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-lOOSbT cwd: /tmp/pip-install-VkaNvC/pybigwig/ Complete output (73 lines): /usr/local/lib/python2.7/dist-packages/distribute-0.6.10-py2.7.egg/setuptools/command/install_scripts.py:3: UserWarning: Module backports was already imported from None, but /usr/lib/python2.7/dist-packages is being added to sys.path from pkg_resources import Distribution, PathMetadata, ensure_directory /usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'classifier' warnings.warn(msg) running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-2.7 creating build/lib.linux-x86_64-2.7/pyBigWigTest copying pyBigWigTest/test.py -> build/lib.linux-x86_64-2.7/pyBigWigTest copying pyBigWigTest/init.py -> build/lib.linux-x86_64-2.7/pyBigWigTest running egg_info writing requirements to pyBigWig.egg-info/requires.txt writing pyBigWig.egg-info/PKG-INFO writing top-level names to pyBigWig.egg-info/top_level.txt writing dependency_links to pyBigWig.egg-info/dependency_links.txt writing requirements to pyBigWig.egg-info/requires.txt writing pyBigWig.egg-info/PKG-INFO writing top-level names to pyBigWig.egg-info/top_level.txt writing dependency_links to pyBigWig.egg-info/dependency_links.txt reading manifest file 'pyBigWig.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'pyBigWig.egg-info/SOURCES.txt' copying pyBigWigTest/test.bigBed -> build/lib.linux-x86_64-2.7/pyBigWigTest copying pyBigWigTest/test.bw -> build/lib.linux-x86_64-2.7/pyBigWigTest running build_ext building 'pyBigWig' extension Warning: Can't read registry to find the necessary compiler setting Make sure that Python modules _winreg, win32api or win32con are installed. Traceback (most recent call last): File "", line 1, in File "/tmp/pip-install-VkaNvC/pybigwig/setup.py", line 90, in ext_modules = [module1]) File "/usr/lib/python2.7/distutils/core.py", line 151, in setup dist.run_commands() File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands self.run_command(cmd) File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "/usr/lib/python2.7/dist-packages/wheel/bdist_wheel.py", line 188, in run self.run_command('build') File "/usr/lib/python2.7/distutils/cmd.py", line 326, in run_command self.distribution.run_command(command) File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "/usr/lib/python2.7/distutils/command/build.py", line 128, in run self.run_command(cmd_name) File "/usr/lib/python2.7/distutils/cmd.py", line 326, in run_command self.distribution.run_command(command) File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.10-py2.7.egg/setuptools/command/build_ext.py", line 46, in run _build_ext.run(self) File "/usr/lib/python2.7/distutils/command/build_ext.py", line 340, in run self.build_extensions() File "/usr/lib/python2.7/distutils/command/build_ext.py", line 449, in build_extensions self.build_extension(ext) File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.10-py2.7.egg/setuptools/command/build_ext.py", line 182, in build_extension _build_ext.build_extension(self,ext) File "/usr/lib/python2.7/distutils/command/build_ext.py", line 499, in build_extension depends=ext.depends) File "/usr/lib/python2.7/dist-packages/numpy/distutils/ccompiler.py", line 266, in CCompiler_compile jobs = get_num_build_jobs() File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 111, in get_num_build_jobs getattr(dist.get_command_obj('build_clib'), 'parallel', None)) File "/usr/lib/python2.7/distutils/dist.py", line 845, in get_command_obj klass = self.get_command_class(command) File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.10-py2.7.egg/setuptools/dist.py", line 361, in get_command_class self.cmdclass[command] = cmdclass = ep.load() File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.10-py2.7.egg/pkg_resources.py", line 1948, in load entry = import(self.module_name, globals(),globals(), ['name'])

ImportError: No module named build_clib

ERROR: Failed building wheel for pyBigWig Running setup.py clean for pyBigWig Failed to build pyBigWig Installing collected packages: pyBigWig Running setup.py install for pyBigWig ... error ERROR: Command errored out with exit status 1: command: /usr/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-VkaNvC/pybigwig/setup.py'"'"'; file='"'"'/tmp/pip-install-VkaNvC/pybigwig/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-Cp_RwN/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python2.7/pyBigWig cwd: /tmp/pip-install-VkaNvC/pybigwig/ Complete output (75 lines): /usr/local/lib/python2.7/dist-packages/distribute-0.6.10-py2.7.egg/setuptools/command/install_scripts.py:3: UserWarning: Module backports was already imported from None, but /usr/lib/python2.7/dist-packages is being added to sys.path from pkg_resources import Distribution, PathMetadata, ensure_directory /usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'classifier' warnings.warn(msg) running install running build running build_py creating build creating build/lib.linux-x86_64-2.7 creating build/lib.linux-x86_64-2.7/pyBigWigTest copying pyBigWigTest/test.py -> build/lib.linux-x86_64-2.7/pyBigWigTest copying pyBigWigTest/init.py -> build/lib.linux-x86_64-2.7/pyBigWigTest running egg_info writing requirements to pyBigWig.egg-info/requires.txt writing pyBigWig.egg-info/PKG-INFO writing top-level names to pyBigWig.egg-info/top_level.txt writing dependency_links to pyBigWig.egg-info/dependency_links.txt writing requirements to pyBigWig.egg-info/requires.txt writing pyBigWig.egg-info/PKG-INFO writing top-level names to pyBigWig.egg-info/top_level.txt writing dependency_links to pyBigWig.egg-info/dependency_links.txt reading manifest file 'pyBigWig.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'pyBigWig.egg-info/SOURCES.txt' copying pyBigWigTest/test.bigBed -> build/lib.linux-x86_64-2.7/pyBigWigTest copying pyBigWigTest/test.bw -> build/lib.linux-x86_64-2.7/pyBigWigTest running build_ext building 'pyBigWig' extension Warning: Can't read registry to find the necessary compiler setting Make sure that Python modules _winreg, win32api or win32con are installed. Traceback (most recent call last): File "", line 1, in File "/tmp/pip-install-VkaNvC/pybigwig/setup.py", line 90, in ext_modules = [module1]) File "/usr/lib/python2.7/distutils/core.py", line 151, in setup dist.run_commands() File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands self.run_command(cmd) File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.10-py2.7.egg/setuptools/command/install.py", line 53, in run return _install.run(self) File "/usr/lib/python2.7/distutils/command/install.py", line 601, in run self.run_command('build') File "/usr/lib/python2.7/distutils/cmd.py", line 326, in run_command self.distribution.run_command(command) File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "/usr/lib/python2.7/distutils/command/build.py", line 128, in run self.run_command(cmd_name) File "/usr/lib/python2.7/distutils/cmd.py", line 326, in run_command self.distribution.run_command(command) File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.10-py2.7.egg/setuptools/command/build_ext.py", line 46, in run _build_ext.run(self) File "/usr/lib/python2.7/distutils/command/build_ext.py", line 340, in run self.build_extensions() File "/usr/lib/python2.7/distutils/command/build_ext.py", line 449, in build_extensions self.build_extension(ext) File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.10-py2.7.egg/setuptools/command/build_ext.py", line 182, in build_extension _build_ext.build_extension(self,ext) File "/usr/lib/python2.7/distutils/command/build_ext.py", line 499, in build_extension depends=ext.depends) File "/usr/lib/python2.7/dist-packages/numpy/distutils/ccompiler.py", line 266, in CCompiler_compile jobs = get_num_build_jobs() File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 111, in get_num_build_jobs getattr(dist.get_command_obj('build_clib'), 'parallel', None)) File "/usr/lib/python2.7/distutils/dist.py", line 845, in get_command_obj klass = self.get_command_class(command) File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.10-py2.7.egg/setuptools/dist.py", line 361, in get_command_class self.cmdclass[command] = cmdclass = ep.load() File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.10-py2.7.egg/pkg_resources.py", line 1948, in load entry = import(self.module_name, globals(),globals(), ['name']) ImportError: No module named build_clib

ERROR: Command errored out with exit status 1: /usr/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-VkaNvC/pybigwig/setup.py'"'"'; file='"'"'/tmp/pip-install-VkaNvC/pybigwig/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-Cp_RwN/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python2.7/pyBigWig Check the logs for full command output.

From what I understand and from what I see it seems that the problem comes from the " wheels " management in pip. After several researches on the forums, I confess that I didn't find the solution, the notion of "wheels" being quite abstract to me. But here too I consider a problem coming from our different versions of pip.

If you don't have the solution, I can wait without problem for the python3 release which will potentially solve some problems.

Thanks again for your answer.

F. DEGALEZ