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PoonLab / OpenRDP

An open-source re-implementation of the RDP4 recombination detection program
GNU General Public License v3.0
45 stars 9 forks source link

Installing Failure #86

Closed guoqiangu closed 2 months ago

guoqiangu commented 2 months ago

Hi PoonLab, I have met some problems when installing OpenRDP. I am trying to install OpenRDP following the command line : sudo python3 setup.py install But it showed as beloved: warning: no files found matching 'AUTHORS' no previously-included directories found matching 'docs/_build' no previously-included directories found matching 'docs_api/_build' warning: no previously-included files found matching 'h5py/config.pxi' warning: no previously-included files found matching 'h5py/defs.pxd' warning: no previously-included files found matching 'h5py/defs.pyx' warning: no previously-included files found matching 'h5py/_hdf5.pxd' warning: no previously-included files matching '.DS_Store' found under directory '' warning: no previously-included files found matching 'ci' warning: no previously-included files found matching 'other' warning: no previously-included files found matching '.github' warning: no previously-included files matching '' found under directory 'ci' warning: no previously-included files matching '' found under directory 'other' warning: no previously-included files matching '' found under directory '.github' warning: no previously-included files found matching '.yml' warning: no previously-included files found matching '.yaml' warning: no previously-included files matching 'pycache' found under directory '' warning: no previously-included files matching '.py[co]' found under directory '' warning: no previously-included files found matching '.coveragerc' warning: no previously-included files found matching '.coverage_dir' warning: no previously-included files matching '' found under directory '.coverage_dir' warning: no previously-included files found matching '.mailmap' warning: no previously-included files found matching 'github_deploy_key_h5py_h5py.enc' warning: no previously-included files found matching 'rever.xsh' no previously-included directories found matching 'news' Traceback (most recent call last): File "/usr/lib/python3.6/site-packages/setuptools/sandbox.py", line 154, in save_modules yield saved File "/usr/lib/python3.6/site-packages/setuptools/sandbox.py", line 195, in setup_context yield File "/usr/lib/python3.6/site-packages/setuptools/sandbox.py", line 250, in run_setup _execfile(setup_script, ns) File "/usr/lib/python3.6/site-packages/setuptools/sandbox.py", line 45, in _execfile exec(code, globals, locals) File "/tmp/easy_install-h5_bpmin/h5py-3.11.0/setup.py", line 75, in File "/usr/lib/python3.6/site-packages/setuptools/init.py", line 129, in setup return distutils.core.setup(**attrs) File "/usr/lib64/python3.6/distutils/core.py", line 148, in setup dist.run_commands() File "/usr/lib64/python3.6/distutils/dist.py", line 955, in run_commands self.run_command(cmd) File "/usr/lib64/python3.6/distutils/dist.py", line 974, in run_command cmd_obj.run() File "/usr/lib/python3.6/site-packages/setuptools/command/bdist_egg.py", line 172, in run cmd = self.call_command('install_lib', warn_dir=0) File "/usr/lib/python3.6/site-packages/setuptools/command/bdist_egg.py", line 158, in call_command self.run_command(cmdname) File "/usr/lib64/python3.6/distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/usr/lib64/python3.6/distutils/dist.py", line 974, in run_command cmd_obj.run() File "/usr/lib/python3.6/site-packages/setuptools/command/install_lib.py", line 11, in run self.build() File "/usr/lib64/python3.6/distutils/command/install_lib.py", line 107, in build self.run_command('build_ext') File "/usr/lib64/python3.6/distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/usr/lib64/python3.6/distutils/dist.py", line 974, in run_command cmd_obj.run() File "/tmp/easy_install-h5_bpmin/h5py-3.11.0/setup_build.py", line 128, in run ModuleNotFoundError: No module named 'Cython'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "setup.py", line 28, in zip_safe=False File "/usr/lib/python3.6/site-packages/setuptools/init.py", line 129, in setup return distutils.core.setup(attrs) File "/usr/lib64/python3.6/distutils/core.py", line 148, in setup dist.run_commands() File "/usr/lib64/python3.6/distutils/dist.py", line 955, in run_commands self.run_command(cmd) File "/usr/lib64/python3.6/distutils/dist.py", line 974, in run_command cmd_obj.run() File "/usr/lib/python3.6/site-packages/setuptools/command/install.py", line 67, in run self.do_egg_install() File "/usr/lib/python3.6/site-packages/setuptools/command/install.py", line 117, in do_egg_install cmd.run() File "/usr/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 411, in run self.easy_install(spec, not self.no_deps) File "/usr/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 659, in easy_install return self.install_item(None, spec, tmpdir, deps, True) File "/usr/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 706, in install_item self.process_distribution(spec, dist, deps) File "/usr/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 751, in process_distribution [requirement], self.local_index, self.easy_install File "/usr/lib/python3.6/site-packages/pkg_resources/init.py", line 770, in resolve replace_conflicting=replace_conflicting File "/usr/lib/python3.6/site-packages/pkg_resources/init.py", line 1053, in best_match return self.obtain(req, installer) File "/usr/lib/python3.6/site-packages/pkg_resources/init.py", line 1065, in obtain return installer(requirement) File "/usr/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 678, in easy_install return self.install_item(spec, dist.location, tmpdir, deps) File "/usr/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 704, in install_item dists = self.install_eggs(spec, download, tmpdir) File "/usr/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 889, in install_eggs return self.build_and_install(setup_script, setup_base) File "/usr/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 1157, in build_and_install self.run_setup(setup_script, setup_base, args) File "/usr/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 1143, in run_setup run_setup(setup_script, args) File "/usr/lib/python3.6/site-packages/setuptools/sandbox.py", line 253, in run_setup raise File "/usr/lib64/python3.6/contextlib.py", line 99, in exit self.gen.throw(type, value, traceback) File "/usr/lib/python3.6/site-packages/setuptools/sandbox.py", line 195, in setup_context yield File "/usr/lib64/python3.6/contextlib.py", line 99, in exit self.gen.throw(type, value, traceback) File "/usr/lib/python3.6/site-packages/setuptools/sandbox.py", line 166, in save_modules saved_exc.resume() File "/usr/lib/python3.6/site-packages/setuptools/sandbox.py", line 141, in resume six.reraise(type, exc, self._tb) File "/usr/lib/python3.6/site-packages/setuptools/_vendor/six.py", line 685, in reraise raise value.with_traceback(tb) File "/usr/lib/python3.6/site-packages/setuptools/sandbox.py", line 154, in save_modules yield saved File "/usr/lib/python3.6/site-packages/setuptools/sandbox.py", line 195, in setup_context yield File "/usr/lib/python3.6/site-packages/setuptools/sandbox.py", line 250, in run_setup _execfile(setup_script, ns) File "/usr/lib/python3.6/site-packages/setuptools/sandbox.py", line 45, in _execfile exec(code, globals, locals) File "/tmp/easy_install-h5_bpmin/h5py-3.11.0/setup.py", line 75, in File "/usr/lib/python3.6/site-packages/setuptools/init.py", line 129, in setup return distutils.core.setup(attrs) File "/usr/lib64/python3.6/distutils/core.py", line 148, in setup dist.run_commands() File "/usr/lib64/python3.6/distutils/dist.py", line 955, in run_commands self.run_command(cmd) File "/usr/lib64/python3.6/distutils/dist.py", line 974, in run_command cmd_obj.run() File "/usr/lib/python3.6/site-packages/setuptools/command/bdist_egg.py", line 172, in run cmd = self.call_command('install_lib', warn_dir=0) File "/usr/lib/python3.6/site-packages/setuptools/command/bdist_egg.py", line 158, in call_command self.run_command(cmdname) File "/usr/lib64/python3.6/distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/usr/lib64/python3.6/distutils/dist.py", line 974, in run_command cmd_obj.run() File "/usr/lib/python3.6/site-packages/setuptools/command/install_lib.py", line 11, in run self.build() File "/usr/lib64/python3.6/distutils/command/install_lib.py", line 107, in build self.run_command('build_ext') File "/usr/lib64/python3.6/distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/usr/lib64/python3.6/distutils/dist.py", line 974, in run_command cmd_obj.run() File "/tmp/easy_install-h5_bpmin/h5py-3.11.0/setup_build.py", line 128, in run ModuleNotFoundError: No module named 'Cython'

Could you help me to fix it ? Looking forward to your reply ! Many Thanks

ArtPoon commented 2 months ago

Hi @guoqiangu thanks for reporting this issue. Can you please provide some details about your operating system and version of Python (looks like 3.6?), and we will try to reproduce the issue.

GopiGugan commented 2 months ago

I was able to reproduce this issue. The latest version of the h5py package requires Cython to be installed. I've updated the setup.py script to install version 3.8.0.

@guoqiangu can you please pull the latest update to the setup.py script and run sudo python3 setup.py install again

guoqiangu commented 2 months ago

I was able to reproduce this issue. The latest version of the h5py package requires Cython to be installed. I've updated the setup.py script to install version 3.8.0.

@guoqiangu can you please pull the latest update to the setup.py script and run sudo python3 setup.py install again

Hi, GopiGugan,

Thanks a lot! I will have a try and see .

guoqiangu commented 2 months ago

I was able to reproduce this issue. The latest version of the h5py package requires Cython to be installed. I've updated the setup.py script to install version 3.8.0.

@guoqiangu can you please pull the latest update to the setup.py script and run sudo python3 setup.py install again

hi,I have pull the latest update to the setup.py script and run sudo python3 setup.py install again but still not working

GopiGugan commented 2 months ago

hi,I have pull the latest update to the setup.py script and run sudo python3 setup.py install again but still not working

Can you please share the error message you are getting?

h5py requires Python >= 3.7 (https://pypi.org/project/h5py/3.8.0/). It looks like you are using Python 3.6, so this may be the reason you're still running into issues. I will update setup.py to reflect this.

guoqiangu commented 2 months ago

hi,I have pull the latest update to the setup.py script and run sudo python3 setup.py install again but still not working

Can you please share the error message you are getting?

h5py requires Python >= 3.7 (https://pypi.org/project/h5py/3.8.0/). It looks like you are using Python 3.6, so this may be the reason you're still running into issues. I will update setup.py to reflect this.

hi, here is the full message when I install:

/usr/lib64/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'python_requires' warnings.warn(msg) running install running bdist_egg running egg_info writing requirements to OpenRDP.egg-info/requires.txt writing OpenRDP.egg-info/PKG-INFO writing top-level names to OpenRDP.egg-info/top_level.txt writing dependency_links to OpenRDP.egg-info/dependency_links.txt reading manifest file 'OpenRDP.egg-info/SOURCES.txt' writing manifest file 'OpenRDP.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/openrdp copying build/lib/openrdp/init.py -> build/bdist.linux-x86_64/egg/openrdp copying build/lib/openrdp/bootscan.py -> build/bdist.linux-x86_64/egg/openrdp copying build/lib/openrdp/chimaera.py -> build/bdist.linux-x86_64/egg/openrdp copying build/lib/openrdp/common.py -> build/bdist.linux-x86_64/egg/openrdp copying build/lib/openrdp/geneconv.py -> build/bdist.linux-x86_64/egg/openrdp copying build/lib/openrdp/maxchi.py -> build/bdist.linux-x86_64/egg/openrdp copying build/lib/openrdp/preprocessing.py -> build/bdist.linux-x86_64/egg/openrdp copying build/lib/openrdp/rdp.py -> build/bdist.linux-x86_64/egg/openrdp copying build/lib/openrdp/siscan.py -> build/bdist.linux-x86_64/egg/openrdp copying build/lib/openrdp/threeseq.py -> build/bdist.linux-x86_64/egg/openrdp copying build/lib/openrdp/default.ini -> build/bdist.linux-x86_64/egg/openrdp creating build/bdist.linux-x86_64/egg/openrdp/bin creating build/bdist.linux-x86_64/egg/openrdp/bin/3Seq copying build/lib/openrdp/bin/3Seq/3seq.Unix -> build/bdist.linux-x86_64/egg/openrdp/bin/3Seq copying build/lib/openrdp/bin/3Seq/3seq.macOS -> build/bdist.linux-x86_64/egg/openrdp/bin/3Seq copying build/lib/openrdp/bin/3Seq/LICENSE.md -> build/bdist.linux-x86_64/egg/openrdp/bin/3Seq copying build/lib/openrdp/bin/3Seq/myPvalueTable -> build/bdist.linux-x86_64/egg/openrdp/bin/3Seq copying build/lib/openrdp/bin/3Seq/windows_3seq.exe -> build/bdist.linux-x86_64/egg/openrdp/bin/3Seq creating build/bdist.linux-x86_64/egg/openrdp/bin/GENECONV copying build/lib/openrdp/bin/GENECONV/LICENSE.md -> build/bdist.linux-x86_64/egg/openrdp/bin/GENECONV copying build/lib/openrdp/bin/GENECONV/geneconv.Unix -> build/bdist.linux-x86_64/egg/openrdp/bin/GENECONV copying build/lib/openrdp/bin/GENECONV/geneconv.macOS -> build/bdist.linux-x86_64/egg/openrdp/bin/GENECONV copying build/lib/openrdp/bin/GENECONV/windows_geneconv.exe -> build/bdist.linux-x86_64/egg/openrdp/bin/GENECONV byte-compiling build/bdist.linux-x86_64/egg/openrdp/init.py to init.pyc File "build/bdist.linux-x86_64/egg/openrdp/init.py", line 47 outfile.write(f'Geneconv,{e[2][0]},{e[2][1]},{e[0]},{e[1][0]},{e[1][1]},{e[3]}\n') ^ SyntaxError: invalid syntax

byte-compiling build/bdist.linux-x86_64/egg/openrdp/bootscan.py to bootscan.pyc File "build/bdist.linux-x86_64/egg/openrdp/bootscan.py", line 178 print(f"Scanning triplet {i + 1} / {self.total_triplet_combinations}") ^ SyntaxError: invalid syntax

byte-compiling build/bdist.linux-x86_64/egg/openrdp/chimaera.py to chimaera.pyc File "build/bdist.linux-x86_64/egg/openrdp/chimaera.py", line 217 if (rec_name, parents, *aln_pos) not in self.raw_results and p_values[peak] != 1.0 and p_values[peak] != 0.0: ^ SyntaxError: invalid syntax

byte-compiling build/bdist.linux-x86_64/egg/openrdp/common.py to common.pyc File "build/bdist.linux-x86_64/egg/openrdp/common.py", line 24 print(f"Error: Input {handle.name} does not appear to be in a FASTA format.") ^ SyntaxError: invalid syntax

byte-compiling build/bdist.linux-x86_64/egg/openrdp/geneconv.py to geneconv.pyc byte-compiling build/bdist.linux-x86_64/egg/openrdp/maxchi.py to maxchi.pyc File "build/bdist.linux-x86_64/egg/openrdp/maxchi.py", line 201 if (rec_name, parents, *aln_pos) not in self.raw_results and p_values[peak] != 1.0 and p_values[ ^ SyntaxError: invalid syntax

byte-compiling build/bdist.linux-x86_64/egg/openrdp/preprocessing.py to preprocessing.pyc byte-compiling build/bdist.linux-x86_64/egg/openrdp/rdp.py to rdp.pyc File "build/bdist.linux-x86_64/egg/openrdp/rdp.py", line 182 self.raw_results.append((rec_name, parents, *coord, corr_p_value)) ^ SyntaxError: invalid syntax

byte-compiling build/bdist.linux-x86_64/egg/openrdp/siscan.py to siscan.pyc File "build/bdist.linux-x86_64/egg/openrdp/siscan.py", line 219 if (rec_name, parents, *aln_pos, abs(sum_pat_zscore[peak])) not in self.raw_results: ^ SyntaxError: invalid syntax

byte-compiling build/bdist.linux-x86_64/egg/openrdp/threeseq.py to threeseq.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts running install_scripts running build_scripts creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/openrdp -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/openrdp to 755 copying OpenRDP.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying OpenRDP.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying OpenRDP.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying OpenRDP.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO copying OpenRDP.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying OpenRDP.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO creating 'dist/OpenRDP-0.1.0-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing OpenRDP-0.1.0-py2.7.egg removing '/usr/lib/python2.7/site-packages/OpenRDP-0.1.0-py2.7.egg' (and everything under it) creating /usr/lib/python2.7/site-packages/OpenRDP-0.1.0-py2.7.egg Extracting OpenRDP-0.1.0-py2.7.egg to /usr/lib/python2.7/site-packages File "/usr/lib/python2.7/site-packages/OpenRDP-0.1.0-py2.7.egg/openrdp/init.py", line 47 outfile.write(f'Geneconv,{e[2][0]},{e[2][1]},{e[0]},{e[1][0]},{e[1][1]},{e[3]}\n') ^ SyntaxError: invalid syntax

File "/usr/lib/python2.7/site-packages/OpenRDP-0.1.0-py2.7.egg/openrdp/bootscan.py", line 178 print(f"Scanning triplet {i + 1} / {self.total_triplet_combinations}") ^ SyntaxError: invalid syntax

File "/usr/lib/python2.7/site-packages/OpenRDP-0.1.0-py2.7.egg/openrdp/chimaera.py", line 217 if (rec_name, parents, *aln_pos) not in self.raw_results and p_values[peak] != 1.0 and p_values[peak] != 0.0: ^ SyntaxError: invalid syntax

File "/usr/lib/python2.7/site-packages/OpenRDP-0.1.0-py2.7.egg/openrdp/common.py", line 24 print(f"Error: Input {handle.name} does not appear to be in a FASTA format.") ^ SyntaxError: invalid syntax

File "/usr/lib/python2.7/site-packages/OpenRDP-0.1.0-py2.7.egg/openrdp/maxchi.py", line 201 if (rec_name, parents, *aln_pos) not in self.raw_results and p_values[peak] != 1.0 and p_values[ ^ SyntaxError: invalid syntax

File "/usr/lib/python2.7/site-packages/OpenRDP-0.1.0-py2.7.egg/openrdp/rdp.py", line 182 self.raw_results.append((rec_name, parents, *coord, corr_p_value)) ^ SyntaxError: invalid syntax

File "/usr/lib/python2.7/site-packages/OpenRDP-0.1.0-py2.7.egg/openrdp/siscan.py", line 219 if (rec_name, parents, *aln_pos, abs(sum_pat_zscore[peak])) not in self.raw_results: ^ SyntaxError: invalid syntax

OpenRDP 0.1.0 is already the active version in easy-install.pth Installing openrdp script to /usr/bin

Installed /usr/lib/python2.7/site-packages/OpenRDP-0.1.0-py2.7.egg Processing dependencies for OpenRDP==0.1.0 Searching for h5py==3.8.0 Reading https://pypi.python.org/simple/h5py/ Couldn't find index page for 'h5py' (maybe misspelled?) Scanning index of all packages (this may take a while) Reading https://pypi.python.org/simple/ No local packages or download links found for h5py==3.8.0 error: Could not find suitable distribution for Requirement.parse('h5py==3.8.0')

guoqiangu commented 2 months ago

hi,I have pull the latest update to the setup.py script and run sudo python3 setup.py install again but still not working

Can you please share the error message you are getting?

h5py requires Python >= 3.7 (https://pypi.org/project/h5py/3.8.0/). It looks like you are using Python 3.6, so this may be the reason you're still running into issues. I will update setup.py to reflect this.

I am using Conda, and my python version is 3.12

ArtPoon commented 2 months ago

Looks like the installation script is calling Python 2.7 though. Are you sure your conda environment is active?

ArtPoon commented 2 months ago

superuser may be defaulting to system Python (which may be 2.7) instead of your local (user-level) binaries

guoqiangu commented 2 months ago

superuser may be defaulting to system Python (which may be 2.7) instead of your local (user-level) binaries

So should I install as a local user?

guoqiangu commented 2 months ago

superuser may be defaulting to system Python (which may be 2.7) instead of your local (user-level) binaries

I try to install a local user and it look like this python setup.py install --user running install /home/GGQ_Virome/anaconda3/envs/openrdp/lib/python3.12/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !!

    ********************************************************************************
    Please avoid running ``setup.py`` directly.
    Instead, use pypa/build, pypa/installer or other
    standards-based tools.

    See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
    ********************************************************************************

!! self.initialize_options() error: [Errno 17] File exists: '/home/GGQ_Virome/anaconda3/envs/openrdp/bin/python3.12' (openrdp) [GGQ_Virome@localhost OpenRDP]$ python3 setup.py install --user running install /home/GGQ_Virome/anaconda3/envs/openrdp/lib/python3.12/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !!

    ********************************************************************************
    Please avoid running ``setup.py`` directly.
    Instead, use pypa/build, pypa/installer or other
    standards-based tools.

    See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
    ********************************************************************************

!! self.initialize_options() error: [Errno 17] File exists: '/home/GGQ_Virome/anaconda3/envs/openrdp/bin/python3.12'

GopiGugan commented 2 months ago

!! self.initialize_options() error: [Errno 17] File exists: '/home/GGQ_Virome/anaconda3/envs/openrdp/bin/python3.12'

I'm getting a similar error using Python 3.12 in a conda environment. However, I was able to successfully run python3 setup.py install --user in a conda environment with Python 3.11

guoqiangu commented 2 months ago

ok，I will try Python 3.11. and see

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!! self.initialize_options() error: [Errno 17] File exists: '/home/GGQ_Virome/anaconda3/envs/openrdp/bin/python3.12'

I'm getting a similar error using Python 3.12 in a conda environment. However, I was able to successfully run python3 setup.py install --user in a conda environment with Python 3.11

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guoqiangu commented 2 months ago

!! self.initialize_options() error: [Errno 17] File exists: '/home/GGQ_Virome/anaconda3/envs/openrdp/bin/python3.12'

I'm getting a similar error using Python 3.12 in a conda environment. However, I was able to successfully run python3 setup.py install --user in a conda environment with Python 3.11

I try but still，I even try python 3.8

GopiGugan commented 2 months ago

I try but still，I even try python 3.8

Can you please share the error message?

guoqiangu commented 2 months ago

I try but still，I even try python 3.8

Can you please share the error message?

running install /home/GGQ_Virome/anaconda3/envs/openrdp/lib/python3.8/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !!

    ********************************************************************************
    Please avoid running ``setup.py`` directly.
    Instead, use pypa/build, pypa/installer or other
    standards-based tools.

    See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
    ********************************************************************************

!! self.initialize_options() /home/GGQ_Virome/anaconda3/envs/openrdp/lib/python3.8/site-packages/setuptools/_distutils/cmd.py:66: EasyInstallDeprecationWarning: easy_install command is deprecated. !!

    ********************************************************************************
    Please avoid running ``setup.py`` and ``easy_install``.
    Instead, use pypa/build, pypa/installer or other
    standards-based tools.

    See https://github.com/pypa/setuptools/issues/917 for details.
    ********************************************************************************

!! self.initialize_options() running bdist_egg running egg_info error: Cannot update time stamp of directory 'OpenRDP.egg-info'

ArtPoon commented 2 months ago

Looks like a write permission issue - probably egg-info directory was generated by superuser. You'd need to rm that directory with sudo and then try again.

guoqiangu commented 2 months ago

Looks like a write permission issue - probably egg-info directory was generated by superuser. You'd need to rm that directory with sudo and then try again.

sure，but how can I fine this directory？

ArtPoon commented 2 months ago

Before we dig into that issue, can you make sure you are using the current version of OpenRDP (git pull origin master) and then run sudo python3 setup.py install?

guoqiangu commented 2 months ago

Before we dig into that issue, can you make sure you are using the current version of OpenRDP (git pull origin master) and then run sudo python3 setup.py install?

hi, I redownload followed git clone https://github.com/PoonLab/OpenRDP and install as python3 setup.py install --user. And it seem installed well. but after that I try to run openrdp but it showed this :

Traceback (most recent call last): File "/usr/local/bin/openrdp", line 4, in import('pkg_resources').run_script('OpenRDP==0.1.0', 'openrdp') File "/usr/lib/python3.6/site-packages/pkg_resources/init.py", line 3095, in @_call_aside File "/usr/lib/python3.6/site-packages/pkg_resources/init.py", line 3079, in _call_aside f(*args, **kwargs) File "/usr/lib/python3.6/site-packages/pkg_resources/init.py", line 3108, in _initialize_master_working_set working_set = WorkingSet._build_master() File "/usr/lib/python3.6/site-packages/pkg_resources/init.py", line 570, in _build_master ws.require(requires) File "/usr/lib/python3.6/site-packages/pkg_resources/init.py", line 888, in require needed = self.resolve(parse_requirements(requirements)) File "/usr/lib/python3.6/site-packages/pkg_resources/init.py", line 774, in resolve raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'OpenRDP==0.1.0' distribution was not found and is required by the application

guoqiangu commented 2 months ago

Before we dig into that issue, can you make sure you are using the current version of OpenRDP (git pull origin master) and then run sudo python3 setup.py install?

hi, I redownload followed git clone https://github.com/PoonLab/OpenRDP and install as python3 setup.py install --user. And it seem installed well. but after that I try to run openrdp but it showed this :

Traceback (most recent call last): File "/usr/local/bin/openrdp", line 4, in import('pkg_resources').run_script('OpenRDP==0.1.0', 'openrdp') File "/usr/lib/python3.6/site-packages/pkg_resources/init.py", line 3095, in @_call_aside File "/usr/lib/python3.6/site-packages/pkg_resources/init.py", line 3079, in _call_aside f(*args, kwargs) File "/usr/lib/python3.6/site-packages/pkg_resources/init.py", line 3108, in _initialize_master_working_set working_set = WorkingSet._build_master() File "/usr/lib/python3.6/site-packages/pkg_resources/init.py", line 570, in _build_master ws.require(requires) File "/usr/lib/python3.6/site-packages/pkg_resources/init.py", line 888, in require needed = self.resolve(parse_requirements(requirements)) File "/usr/lib/python3.6/site-packages/pkg_resources/init**.py", line 774, in resolve raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'OpenRDP==0.1.0' distribution was not found and is required by the application

Hi, I have fixed the problem when I install the dependencies as you showed. I guess it is because the different version of h5py

ArtPoon commented 2 months ago

Ok thanks for reporting that in. Is it okay to close this issue?

guoqiangu commented 2 months ago

Ok thanks for reporting that in. Is it okay to close this issue?

Sure. Thanks for your help