Installing Failure #86

guoqiangu · 2024-04-13T09:04:17Z

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 · 2024-04-16T13:46:48Z

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 · 2024-04-16T21:01:41Z

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 · 2024-04-17T03:42:25Z

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 · 2024-04-17T03:57:02Z

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 · 2024-04-17T16:20:33Z

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 · 2024-04-17T16:30:43Z

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 · 2024-04-17T16:38:32Z

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 · 2024-04-17T16:41:08Z

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

ArtPoon · 2024-04-17T16:41:36Z

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

guoqiangu · 2024-04-17T16:45:31Z

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 · 2024-04-17T16:49:53Z

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 · 2024-04-17T17:36:42Z

!! 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 · 2024-04-17T17:38:52Z

ok，I will try Python 3.11. and see 获取Outlook for Android<https://aka.ms/AAb9ysg>

…

________________________________ From: Gopi Gugan ***@***.***> Sent: Thursday, April 18, 2024 1:37:04 AM To: PoonLab/OpenRDP ***@***.***> Cc: GU Guoqian ***@***.***>; Mention ***@***.***> Subject: [Ext] Re: [PoonLab/OpenRDP] Installing Failure (Issue #86) CAUTION: External email. Do not reply, click on links or open attachments unless you recognize the sender and know the content is safe. !! 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 ― Reply to this email directly, view it on GitHub<#86 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A6VJR5YRY7UUM2W3E3SWJVTY52XMBAVCNFSM6AAAAABGFJW7PSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANRRHA2DSMRUGE>. You are receiving this because you were mentioned.Message ID: ***@***.***>

guoqiangu · 2024-04-17T17:48:17Z

!! 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 · 2024-04-17T17:51:15Z

I try but still，I even try python 3.8

Can you please share the error message?

guoqiangu · 2024-04-17T17:53:49Z

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 · 2024-04-17T17:56:17Z

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 · 2024-04-17T18:14:42Z

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 · 2024-04-17T19:32:10Z

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 · 2024-04-18T04:48:08Z

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 · 2024-04-18T05:04:23Z

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 · 2024-04-18T13:09:20Z

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

guoqiangu · 2024-04-19T02:35:54Z

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

Sure. Thanks for your help

guoqiangu closed this as completed Apr 13, 2024

guoqiangu closed this as not planned Won't fix, can't repro, duplicate, stale Apr 13, 2024

guoqiangu reopened this Apr 13, 2024

guoqiangu changed the title ~~nstalling~~ Installing Failure Apr 13, 2024

GopiGugan added a commit that referenced this issue Apr 16, 2024

Install previous version of h5py #86

bb02000

ArtPoon closed this as completed Apr 19, 2024

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Installing Failure #86

Installing Failure #86

guoqiangu commented Apr 13, 2024 •

edited

Loading

ArtPoon commented Apr 16, 2024

GopiGugan commented Apr 16, 2024

guoqiangu commented Apr 17, 2024

guoqiangu commented Apr 17, 2024

GopiGugan commented Apr 17, 2024

guoqiangu commented Apr 17, 2024

guoqiangu commented Apr 17, 2024

ArtPoon commented Apr 17, 2024

ArtPoon commented Apr 17, 2024

guoqiangu commented Apr 17, 2024

guoqiangu commented Apr 17, 2024

GopiGugan commented Apr 17, 2024

guoqiangu commented Apr 17, 2024 via email

guoqiangu commented Apr 17, 2024

GopiGugan commented Apr 17, 2024

guoqiangu commented Apr 17, 2024

ArtPoon commented Apr 17, 2024

guoqiangu commented Apr 17, 2024

ArtPoon commented Apr 17, 2024 •

edited

Loading

guoqiangu commented Apr 18, 2024

guoqiangu commented Apr 18, 2024

ArtPoon commented Apr 18, 2024

guoqiangu commented Apr 19, 2024

Installing Failure #86

Installing Failure #86

Comments

guoqiangu commented Apr 13, 2024 • edited Loading

ArtPoon commented Apr 16, 2024

GopiGugan commented Apr 16, 2024

guoqiangu commented Apr 17, 2024

guoqiangu commented Apr 17, 2024

GopiGugan commented Apr 17, 2024

guoqiangu commented Apr 17, 2024

guoqiangu commented Apr 17, 2024

ArtPoon commented Apr 17, 2024

ArtPoon commented Apr 17, 2024

guoqiangu commented Apr 17, 2024

guoqiangu commented Apr 17, 2024

GopiGugan commented Apr 17, 2024

guoqiangu commented Apr 17, 2024 via email

guoqiangu commented Apr 17, 2024

GopiGugan commented Apr 17, 2024

guoqiangu commented Apr 17, 2024

ArtPoon commented Apr 17, 2024

guoqiangu commented Apr 17, 2024

ArtPoon commented Apr 17, 2024 • edited Loading

guoqiangu commented Apr 18, 2024

guoqiangu commented Apr 18, 2024

ArtPoon commented Apr 18, 2024

guoqiangu commented Apr 19, 2024

guoqiangu commented Apr 13, 2024 •

edited

Loading

ArtPoon commented Apr 17, 2024 •

edited

Loading