I am trying to install pathos library from git, but getting the following error:
>pip install https://github.com/uqfoundation/pathos
Exception:
Traceback (most recent call last):
File "C:\Python27\lib\site-packages\pip\basecommand.py", line 122, in main
status = self.run(options, args)
File "C:\Python27\lib\site-packages\pip\commands\install.py", line 278, in run
requirement_set.prepare_files(finder, force_root_egg_info=self.bundle, bundl
e=self.bundle)
File "C:\Python27\lib\site-packages\pip\req.py", line 1197, in prepare_files
do_download,
File "C:\Python27\lib\site-packages\pip\req.py", line 1375, in unpack_url
self.session,
File "C:\Python27\lib\site-packages\pip\download.py", line 582, in unpack_http
_url
unpack_file(temp_location, location, content_type, link)
File "C:\Python27\lib\site-packages\pip\util.py", line 627, in unpack_file
and is_svn_page(file_contents(filename))):
File "C:\Python27\lib\site-packages\pip\util.py", line 210, in file_contents
return fp.read().decode('utf-8')
File "C:\Python27\lib\encodings\utf_8.py", line 16, in decode
return codecs.utf_8_decode(input, errors, True)
UnicodeDecodeError: 'utf8' codec can't decode byte 0x8b in position 1: invalid start byte
What is the problem here and how can I get around it?
Thanks
EDIT 1:
Tried the following:
pip install git+https://github.com/uqfoundation/pathos
...but still no luck:
>pip install git+https://github.com/uqfoundation/pathos
Downloading/unpacking git+https://github.com/uqfoundation/pathos
Cloning https://github.com/uqfoundation/pathos to c:\users\gronin\appdata\local\temp\pip-qstvgd-build
Cleaning up...
Cannot find command 'git'
EDIT 2:
Tried the following, recommended by cel:
pip install git+https://github.com/uqfoundation/pathos
...that definitely solved lookup problems (thanks, cel), still having installation issues:
Downloading/unpacking git+https://github.com/uqfoundation/pathos
Cloning https://github.com/uqfoundation/pathos to c:\users\gronin\appdata\loca
l\temp\pip-jldriz-build
Running setup.py (path:c:\users\gronin\appdata\local\temp\pip-jldriz-build\set
up.py) egg_info for package from git+https://github.com/uqfoundation/pathos
Downloading/unpacking pp>=1.6.4.4 (from pathos==0.2a1.dev)
Could not find any downloads that satisfy the requirement pp>=1.6.4.4 (from pathos==0.2a1.dev)
I have a long overdue pathos release that I need to push out (this month). I'll see what I can do to make it pip installable. There are two main issues: (1) the released versions of the packages are named in a non-standard way (e.g. 0.2.a1-dev), and (2) several dependencies are forked from other packages, and are only available on http://dev.danse.us/packages. The temporary workaround for (1) is either to install with the --pre flag for pip as well as using git+https, or to install them manually (easy_install actually works). The workaround for (2) is also as #cel has suggested… download the dependencies and install manually (or use easy_install).
This will be sorted out in the stable release. It's basically the blocker issue for getting the release out -- primarily due to (2) above.
Keep track of the status of this issue here: https://github.com/uqfoundation/pathos/issues/2
Related
As part of a script I am writing, I need to install the package autodock vina for the purpose of ligand and protein binding. Every time I attempt to "pip install vina", I recieve an error message " ValueError: Boost library location was not found!". Upon attempting to install boost manually, I have been unable to run the bootstrap file, as it does not make the b2 folder that online tutorials say it will make.
To resolve this issue, I installed conda, and made an active environment with every single prerequisite, including boost, installed. I have checked for the version of all of these prerequisites and confirmed their existence, as well as double and triple-checking that I am in the write active environment. Upon installation, I either get the same issue (using conda install vina) or when using "conda install -c bioconda autodock-vina", I get a message saying that the package does not exist (despite adding cforge and bioconda as active package handlers, and the existence of said package is clearly documented online). Does anyone have any suggestions? I've been attempting to install this piece of software for 3 days and I've completely exhausted the documentation, as well as all other similar question answers, with nothing working.
Full error message:
Collecting vina
Using cached vina-1.2.3.tar.gz (95 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... error
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [56 lines of output]
Version found 1.2.3 (from __init__.py)
running egg_info
creating vina.egg-info
writing vina.egg-info\PKG-INFO
writing dependency_links to vina.egg-info\dependency_links.txt
writing requirements to vina.egg-info\requires.txt
writing top-level names to vina.egg-info\top_level.txt
writing manifest file 'vina.egg-info\SOURCES.txt'
Boost library is not installed in this conda environment.
Traceback (most recent call last):
File "C:\Users\chris\AppData\Local\Programs\Python\Python310\lib\site-packages\pip\_vendor\pep517\in_process\_in_process.py", line 363, in <module>
main()
File "C:\Users\chris\AppData\Local\Programs\Python\Python310\lib\site-packages\pip\_vendor\pep517\in_process\_in_process.py", line 345, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "C:\Users\chris\AppData\Local\Programs\Python\Python310\lib\site-packages\pip\_vendor\pep517\in_process\_in_process.py", line 130, in get_requires_for_build_wheel
return hook(config_settings)
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\build_meta.py", line 177, in get_requires_for_build_wheel
return self._get_build_requires(
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\build_meta.py", line 159, in _get_build_requires
self.run_setup()
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\build_meta.py", line 174, in run_setup
exec(compile(code, __file__, 'exec'), locals())
File "setup.py", line 346, in <module>
setup(
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\__init__.py", line 87, in setup
return distutils.core.setup(**attrs)
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\_distutils\core.py", line 148, in setup
return run_commands(dist)
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\_distutils\core.py", line 163, in run_commands
dist.run_commands()
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\_distutils\dist.py", line 967, in run_commands
self.run_command(cmd)
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\dist.py", line 1214, in run_command
super().run_command(command)
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\_distutils\dist.py", line 986, in run_command
cmd_obj.run()
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\command\egg_info.py", line 308, in run
self.find_sources()
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\command\egg_info.py", line 315, in find_sources
mm.run()
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\command\egg_info.py", line 550, in run
self.add_defaults()
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\command\egg_info.py", line 587, in add_defaults
sdist.add_defaults(self)
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\_distutils\command\sdist.py", line 228, in add_defaults
self._add_defaults_ext()
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\_distutils\command\sdist.py", line 311, in _add_defaults_ext
build_ext = self.get_finalized_command('build_ext')
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\_distutils\cmd.py", line 299, in get_finalized_command
cmd_obj.ensure_finalized()
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\_distutils\cmd.py", line 107, in ensure_finalized
self.finalize_options()
File "setup.py", line 247, in finalize_options
raise ValueError(error_msg)
ValueError: Boost library location was not found!
Directories searched: conda env, /usr/local/include and /usr/include.
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.
I also get this error. I asked ResearchGate how to solve this problem and Cheng Shen adviced to use WSL/WSL2 to simulate a Linux environment and then run conda install -c bioconda vina (or another command like this)
What I did.
Install WSL and Ubuntu on Windows 2. Run code . in WSL terminal (for installing VS Code [recommended])
Install Anaconda/Miniconda following this guide
Type conda install -c bioconda vina in Ubuntu terminal (bioconda channel will download all required packages - boost, swig, etc.)
Vina should be successfully installed ( vina --version in WSL Terminal to check)
I found it much easier to install packages for docking via WSL and use VS Code to run scripts there. It's VERY easier than trying to solve this problem by configuring boost for Windows. If you have any questions you can ask me in ResearchGate.
I am getting No files/directories in /tmp/* errors while I try to install any package on my Ubuntu 18.04.2 LTS/ Python 3.6.8 / Python 2.7.15+ machine.
For instance,
pip install pyx
Collecting pyx
Using cached https://files.pythonhosted.org/packages/f7/25/59c136568c1b61ee087155c874fcd9f7196a943a6a5ee3429efeb30ea2a8/PyX-0.15.tar.gz
No files/directories in /tmp/pip-build-nRurCC/pyx/pip-egg-info (from PKG-INFO)
This happens for every package I am trying to install.
sudo is not helping.
Solution presented here, using --no-cache-dir option, is not helping.
Output of running the pip install command with vvv option gives the following output.
No files/directories in /tmp/pip-build-VU1cex/pyx/pip-egg-info (from PKG-INFO)
Exception information:
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/pip/basecommand.py", line 215, in main
status = self.run(options, args)
File "/usr/lib/python2.7/dist-packages/pip/commands/install.py", line 342, in run
requirement_set.prepare_files(finder)
File "/usr/lib/python2.7/dist-packages/pip/req/req_set.py", line 380, in prepare_files
ignore_dependencies=self.ignore_dependencies))
File "/usr/lib/python2.7/dist-packages/pip/req/req_set.py", line 634, in _prepare_file
abstract_dist.prep_for_dist()
File "/usr/lib/python2.7/dist-packages/pip/req/req_set.py", line 129, in prep_for_dist
self.req_to_install.run_egg_info()
File "/usr/lib/python2.7/dist-packages/pip/req/req_install.py", line 455, in run_egg_info
metadata_name = canonicalize_name(self.pkg_info()["Name"])
File "/usr/lib/python2.7/dist-packages/pip/req/req_install.py", line 533, in pkg_info
data = self.egg_info_data('PKG-INFO')
File "/usr/lib/python2.7/dist-packages/pip/req/req_install.py", line 471, in egg_info_data
filename = self.egg_info_path(filename)
File "/usr/lib/python2.7/dist-packages/pip/req/req_install.py", line 515, in egg_info_path
'No files/directories in %s (from %s)' % (base, filename)
InstallationError: No files/directories in /tmp/pip-build-VU1cex/pyx/pip-egg-info (from PKG-INFO)
I think it is an upstream issue I tried multiple things even installing using the latest commit pip install git+https://github.com/pyx-project/pyx.git#fc66c078727b02693b122ad346b9fa5472e06eb7, please try this version: pip install PyX==0.12 it should work.
If using pip 6.0 or newer, check if it works with the --no-cache-dir option.
You can also try to get a detailed output from pip using the -vvv argument
Source: https://stackoverflow.com/a/9510610/2542835
Apparently pip3 install x works for me. pip install x does not.
I'm trying to install cryptography to my system, but I get this error:
WARNING: Missing build requirements in pyproject.toml for cryptography from https://files.pythonhosted.org/packages/07/ca/bc827c5e55918ad223d59d299fff92f3563476c3b00d0a9157d9c0217449/cryptography-2.6.1.tar.gz#sha256=26c821cbeb683facb966045e2064303029d572a87ee69ca5a1bf54bf55f93ca6.
WARNING: The project does not specify a build backend, and pip cannot fall back to setuptools without 'setuptools>=40.8.0' and 'wheel'.
Getting requirements to build wheel ... done
ERROR: Exception:
Traceback (most recent call last):
File "/data/packages/usr/local/lib/python3.6/site-packages/pip/_internal/cli/base_command.py", line 178, in main
status = self.run(options, args)
File "/data/packages/usr/local/lib/python3.6/site-packages/pip/_internal/commands/install.py", line 352, in run
resolver.resolve(requirement_set)
File "/data/packages/usr/local/lib/python3.6/site-packages/pip/_internal/resolve.py", line 131, in resolve
self._resolve_one(requirement_set, req)
File "/data/packages/usr/local/lib/python3.6/site-packages/pip/_internal/resolve.py", line 294, in _resolve_one
abstract_dist = self._get_abstract_dist_for(req_to_install)
File "/data/packages/usr/local/lib/python3.6/site-packages/pip/_internal/resolve.py", line 242, in _get_abstract_dist_for
self.require_hashes
File "/data/packages/usr/local/lib/python3.6/site-packages/pip/_internal/operations/prepare.py", line 368, in prepare_linked_requirement
abstract_dist.prep_for_dist(finder, self.build_isolation)
File "/data/packages/usr/local/lib/python3.6/site-packages/pip/_internal/operations/prepare.py", line 175, in prep_for_dist
self.install_backend_dependencies(finder=finder)
File "/data/packages/usr/local/lib/python3.6/site-packages/pip/_internal/operations/prepare.py", line 123, in install_backend_dependencies
reqs = req.pep517_backend.get_requires_for_build_wheel()
File "/data/packages/usr/local/lib/python3.6/site-packages/pip/_vendor/pep517/wrappers.py", line 71, in get_requires_for_build_wheel
'config_settings': config_settings
File "/data/packages/usr/local/lib/python3.6/site-packages/pip/_vendor/pep517/wrappers.py", line 162, in _call_hook
raise BackendUnavailable
pip._vendor.pep517.wrappers.BackendUnavailable
This is my setup:
Alpine Linux 3.6.2
Python 3.6.3
pip 19.1
wheel 0.33.1
setuptools 41.0.1
Any idea what could be the problem, or how to solve it?
Thanks for the help in advance!
I did not find any uniform solution to this problem. You can try the following troubleshooting steps. one of them should work.
Upgrade the pip version.
Change the library/package version.
If you are installing from source, try a different .whl package or use tar.gz.
Use --no-use-pep517 with your pip install command (didn't work for me though, but I see it worked for some).
I got the same error with a different library and --no-use-pep517 did not help. However this did:
python -m pip install --upgrade pip
I'm running python 3.5.3 on Windows
I tried using
pip install --upgrade tensorflow
and here's what i get back
Using cached tensorflow-1.0.1-cp35-cp35m-win_amd64.whl
Requirement already up-to-date: wheel>=0.26 in
c:\users\max\miniconda3\lib\site-packages (from tensorflow)
Exception:
Traceback (most recent call last):
File "C:\Users\Max\Miniconda3\lib\site-packages\pip\basecommand.py", line
215, in main
status = self.run(options, args)
File "C:\Users\Max\Miniconda3\lib\site-packages\pip\commands\install.py", line 335, in run
wb.build(autobuilding=True)
File "C:\Users\Max\Miniconda3\lib\site-packages\pip\wheel.py", line 749, in build
self.requirement_set.prepare_files(self.finder)
File "C:\Users\Max\Miniconda3\lib\site-packages\pip\req\req_set.py", line 380, in prepare_files
ignore_dependencies=self.ignore_dependencies))
File "C:\Users\Max\Miniconda3\lib\site-packages\pip\req\req_set.py", line 666, in _prepare_file
check_dist_requires_python(dist)
File "C:\Users\Max\Miniconda3\lib\site-packages\pip\utils\packaging.py", line 48, in check_dist_requires_python
feed_parser.feed(metadata)
File "C:\Users\Max\Miniconda3\lib\email\feedparser.py", line 178, in feed
self._input.push(data)
File "C:\Users\Max\Miniconda3\lib\email\feedparser.py", line 104, in push
self._partial.write(data)
TypeError: string argument expected, got 'NoneType'
I've also tried
pip3 install --upgrade tensorflow
but I get back
'pip3' is not recognized as an internal or external command, operable program or batch file.
I'm not too sure what the error is, and googling hasn't gotten me any results
I also had the same issue. I'm using Anaconda, and I managed to install it with these commands:
conda create -n tensorflow
activate tensorflow
pip install --ignore-installed --upgrade https://storage.googleapis.com/tensorflow/windows/cpu/tensorflow-1.0.1-cp35-cp35m-win_amd64.whl
This worked for me, and probably this will work for miniconda too.
I am going to install numpy library as a *.whl file, as numpy-1.9.2rc1+mkl- cp27-none-win32, on my Windows 7 machine...
Here is my approaches to do that, are which pip and easy_install packages...
The odd thing is that both don't work in the case of either Python 3.4 or Python 2.7...
Here are the trace of the attempts in the command prompt:
pip:
"C:\Users\Matinking\Desktop\numpy- 1.9.2rc1+
mkl-cp27-none-win32.whl" f
Exception:
Traceback (most recent call last):
File "c:\python34\lib\site-packages\pip\basecommand.py", line 122, in main
status = self.run(options, args)
File "c:\python34\lib\site-packages\pip\commands\install.py", line 257, in r
InstallRequirement.from_line(name, None))
File "c:\python34\lib\site-packages\pip\req.py", line 172, in from_line
return cls(req, comes_from, url=url, prereleases=prereleases)
File "c:\python34\lib\site-packages\pip\req.py", line 70, in __init__
req = pkg_resources.Requirement.parse(req)
File "c:\python34\lib\site-packages\pip\_vendor\pkg_resources.py", line 2667
in parse
reqs = list(parse_requirements(s))
File "c:\python34\lib\site-packages\pip\_vendor\pkg_resources.py", line 2605
in parse_requirements
line, p, specs = scan_list(VERSION,LINE_END,line,p,(1,2),"version spec")
File "c:\python34\lib\site-packages\pip\_vendor\pkg_resources.py", line 2573
in scan_list
raise ValueError("Expected "+item_name+" in",line,"at",line[p:])
ValueError: ('Expected version spec in', ' C:\\Users\\Matinking\\Desktop\\numer
performance.pdf', 'at', ':\\Users\\Matinking\\Desktop\\numericperformance.pdf'
Storing debug log for failure in C:\Users\Matinking\pip\pip.log
and easy_install:
C:\Python34\Scripts>easy_install.exe "C:\Users\Matinking\Desktop\numpy- 1.9.2rc1+
mkl-cp27-none-win32.whl"
Processing numpy-1.9.2rc1+mkl-cp27-none-win32.whl
Writing C:\Users\MATINK~1\AppData\Local\Temp\easy_install- jr2ijafr\numpy\setup.c
fg
Running numpy\setup.py -q bdist_egg --dist-dir C:\Users\MATINK~1\AppData\Local\T
emp\easy_install-jr2ijafr\numpy\egg-dist-tmp-umy5kseg
This is the wrong setup.py file to run
No eggs found in C:\Users\MATINK~1\AppData\Local\Temp\easy_install-jr2ijafr\nump
y\egg-dist-tmp-umy5kseg (setup script problem?)
Any idea for the problem?!
You should upgrade your pip to version 6.0, the .whl file you're using isn't compatible with earlier versions.
To bump up your pip version on Windows :
python -m pip install -U pip
pip error -> why were you running an install on a pdf? That was never going to work.
easy_install error -> looks like you downloaded a python 2.7 binary and tried to install into a python 3.4 installation.
For scientific stack python, you are hard pressed to beat an Anaconda python distribution.