Error installing Python 3 with Homebrew - python

I'm having trouble when I want to install Python 3 using Homebrew.
This is my console:
$ brew install python3
Warning: You are using OS X 10.12.
We do not provide support for this pre-release version.
You may encounter build failures or other breakages.
Please create pull-requests instead of filing issues.
==> Installing dependencies for python3: readline, sqlite, gdbm, makedepend, openssl
==> Installing python3 dependency: readline
==> Downloading https://ftpmirror.gnu.org/readline/readline-6.3.tar.gz
Already downloaded: /Users/slorenzo/Library/Caches/Homebrew/readline-6.3.8.tar.gz
==> Downloading https://gist.githubusercontent.com/jacknagel/d886531fb6623b60b2af/raw/746fc543e56bc37
curl: (22) The requested URL returned error: 404 Not Found
Error: Failed to download resource "readline--patch"
Download failed: https://gist.githubusercontent.com/jacknagel/d886531fb6623b60b2af/raw/746fc543e56bc37a26ccf05d2946a45176b0894e/readline-6.3.8.diff
Does anyone know how I can solve this problem?
Thanks.

Try running:
If Homebrew was updated on Aug 10-11th 2016 and brew update always says Already up-to-date you need to run:
cd "$(brew --repo)" && git fetch && git reset --hard origin/master && brew update

You are using an old version of Homebrew. The patch file that's failing to download was removed from the recipe in September 2016, and the warning about macOS 10.12 being a "pre-release version" is clearly no longer correct.
Run brew update and try again.

Related

How to get Ansible on Fedora 30 to see modules

I installed Ansible 2.8.2 using dnf on Fedora 30. I have an Ansible plug-in that requires a library. Using pip3 install I installed the required library.
When I run ansible-playbook directly, I see a ModuleNotFoundError for that module.
But if I run python3 /usr/bin/ansible-playbook, the module is found.
How can I get Ansible as installed by dnf to see this library?
Edit: further info: as installed from dnf, the main Ansible script has a shebang for /usr/bin/python3 -s. If I remove the -s, this problem is solved.
What's the benefit that the repo maintainers were seeking in adding this -s flag?
Is there a case to be made for asking the repo maintainers to omit the flag?
How can I get pip3 to install the library I need into a directory that will be seen when the -s flag is in effect?
Edit: Here's the output of ansible --version, and thanks for asking.
ansible 2.8.2
config file = /home/jdashton/proj/ansible-ccharacter/ansible.cfg
configured module search path = ['/home/jdashton/.ansible/plugins/modules', '/usr/share/ansible/plugins/modules']
ansible python module location = /usr/lib/python3.7/site-packages/ansible
executable location = /usr/bin/ansible
python version = 3.7.4 (default, Jul 9 2019, 16:32:37) [GCC 9.1.1 20190503 (Red Hat 9.1.1-1)]
This is different from the suggested duplicate question because that question describes a "remote" task being run on localhost, in which case Ansible uses the default "remote" python interpreter. In this question, the library is being called from a local plugin, under Ansible's own python process. The -s flag in the shebang line at the top of the /usr/bin/ansible script is preventing Ansible from seeing some local libraries.
Edit: Following the suggestion from #zigarn I tried removing the library and reinstalling it as root. This resulted in the library being reinstalled into the same directory /usr/local/lib/... as before. Is there a way to get pip3 to install into the system library?
Here are the commands I attempted:
# pip3 uninstall tenacity
Uninstalling tenacity-5.0.4:
Would remove:
/usr/local/lib/python3.7/site-packages/tenacity-5.0.4.dist-info/*
/usr/local/lib/python3.7/site-packages/tenacity/*
Proceed (y/n)? y
Successfully uninstalled tenacity-5.0.4
# pip3 install tenacity
Collecting tenacity
Using cached https://files.pythonhosted.org/packages/6a/93/dfcf5b1b46ab29196274b78dcba69fab5e54b6dc303a7eed90a79194d277/tenacity-5.0.4-py2.py3-none-any.whl
Requirement already satisfied: six>=1.9.0 in /usr/lib/python3.7/site-packages (from tenacity) (1.12.0)
Installing collected packages: tenacity
Successfully installed tenacity-5.0.4
# pip show tenacity
Name: tenacity
Version: 5.0.4
Summary: Retry code until it succeeeds
Home-page: https://github.com/jd/tenacity
Author: Julien Danjou
Author-email: julien#danjou.info
License: Apache 2.0
Location: /usr/local/lib/python3.7/site-packages
Requires: six
Required-by:
Also, for clarity, here is the source for the Ansible installation:
# dnf list ansible
Last metadata expiration check: 0:09:48 ago on Mon 12 Aug 2019 11:12:58 AM EDT.
Installed Packages
ansible.noarch 2.8.2-1.fc30 #updates
According to the documentation -s option of python is "Don’t add the user site-packages directory to sys.path."
So I would guess that you did pip3 install as your user instead as root, so the library was installed at your user side instead of system wide.
Try to reinstall the library with pip3 as root and it should be ok.

Can't install pysam with pip in Python 3.6

Macbook
Mac OSX 10.12.6
Python 3.6.2
cython 0.28.5
pip 18.0
I'm trying to install pysam:
pip3 install pysam
It keeps hitting an error at:
creating build/temp.macosx-10.6-intel-3.6/htslib/cram
htslib/cram/cram_io.c:63:10: fatal error: 'os/lzma_stub.h' file not found
#include "os/lzma_stub.h"
^~~~~~~~~~~~~~~~
1 error generated.
error: command '/usr/bin/clang' failed with exit status 1
Seems like this issue, this, and this were version issues. But I've tried pip3 install pysam==0.13 and 0.14 and 0.15 with the same results.
Suggestions?
I really don't want to deal with installing conda...
My mistake! pip3 install pysam==0.13 actually DOES work. Just leaving this here for posterity.
Clearly, you are missing lzma, which is now part of xz library (https://tukaani.org/xz/). Install that and see if it works. In OSX, you can install it using homebrew: brew install xz.
Another option is to install htslib (http://www.htslib.org/download/), or samtools (can be found in the htslib url).

Why is pip install pyopenssl==0.13 failing?

I'm trying to install PyOpenSSL 0.13 on my Macbook Pro (OSX version 10.11, El-Capitan). But it keeps failing. These are the steps I took
Download and install Command Line Tools (OSX 10.11) for Xcode 7.3.1 from here
$ virtualenv my-new-virtualenv
$ source my-new-virtualenv/bin/activate
$ pip install pyopenssl==0.13
When I do step #4, I get the following error:
OpenSSL/crypto/x509.h:17:10: fatal error: 'openssl/ssl.h' file not found
#include <openssl/ssl.h>
^
1 error generated.
error: command 'cc' failed with exit status 1
----------------------------------------
Failed building wheel for pyopenssl
Here is the entire trace showing that error.
Why am I getting this error and how can I fix it??
It appears you are missing the OpenSSL development headers, as mentioned by #Klaus D. This most likely happened because due to upgrading to El Capitan, these development headers were broken. It can usually be fixed by reinstalling your command line tools.
If you have Homebrew, run this code:
brew install openssl
Also, just out of curiosity, is there a particular reason why you want to use version 0.13? When I did $ pip install pyopenssl==0.14 I got no errors. See the bit on pyOpenSSL's documentation:

Could not find a version that satisfies the requirement <package>

I'm installing several Python packages in Ubuntu 12.04 using the following requirements.txt file:
numpy>=1.8.2,<2.0.0
matplotlib>=1.3.1,<2.0.0
scipy>=0.14.0,<1.0.0
astroML>=0.2,<1.0
scikit-learn>=0.14.1,<1.0.0
rpy2>=2.4.3,<3.0.0
and these two commands:
$ pip install --download=/tmp -r requirements.txt
$ pip install --user --no-index --find-links=/tmp -r requirements.txt
(the first one downloads the packages and the second one installs them).
The process is frequently stopped with the error:
Could not find a version that satisfies the requirement <package> (from matplotlib<2.0.0,>=1.3.1->-r requirements.txt (line 2)) (from versions: )
No matching distribution found for <package> (from matplotlib<2.0.0,>=1.3.1->-r requirements.txt (line 2))
which I fix manually with:
pip install --user <package>
and then run the second pip install command again.
But that only works for that particular package. When I run the second pip install command again, the process is stopped now complaining about another required package and I need to repeat the process again, ie: install the new required package manually (with the command above) and then run the second pip install command.
So far I've had to manually install six, pytz, nose, and now it's complaining about needing mock.
Is there a way to tell pip to automatically install all needed dependencies so I don't have to do it manually one by one?
Add: This only happens in Ubuntu 12.04 BTW. In Ubuntu 14.04 the pip install commands applied on the requirements.txt file work without issues.
Although it doesn't really answers this specific question. Others got the same error message with this mistake.
For those who like me initial forgot the -r: Use pip install -r requirements.txt the -r is essential for the command.
The original answer:
https://stackoverflow.com/a/42876654/10093070
I had installed python3 but my python in /usr/bin/python was still the old 2.7 version
This worked (<pkg> was pyserial in my case):
python3 -m pip install <pkg>
This approach (having all dependencies in a directory and not downloading from an index) only works when the directory contains all packages. The directory should therefore contain all dependencies but also all packages that those dependencies depend on (e.g., six, pytz etc).
You should therefore manually include these in requirements.txt (so that the first step downloads them explicitly) or you should install all packages using PyPI and then pip freeze > requirements.txt to store the list of all packages needed.
Just a reminder to whom google this error and come here.
Let's say I get this error:
$ python3 example.py
Traceback (most recent call last):
File "example.py", line 7, in <module>
import aalib
ModuleNotFoundError: No module named 'aalib'
Since it mentions aalib, I was thought to try aalib:
$ python3.8 -m pip install aalib
ERROR: Could not find a version that satisfies the requirement aalib (from versions: none)
ERROR: No matching distribution found for aalib
But it actually wrong package name, ensure pip search(service disabled at the time of writing), or google, or search on pypi site to get the accurate package name:
Then install successfully:
$ python3.8 -m pip install python-aalib
Collecting python-aalib
Downloading python-aalib-0.3.2.tar.gz (14 kB)
...
As pip --help stated:
$ python3.8 -m pip --help
...
-v, --verbose Give more output. Option is additive, and can be used up to 3 times.
To have a systematic way to figure out the root causes instead of rely on luck, you can append -vvv option of pip command to see details, e.g.:
$ python3.8 -u -m pip install aalib -vvv
User install by explicit request
Created temporary directory: /tmp/pip-ephem-wheel-cache-b3ghm9eb
Created temporary directory: /tmp/pip-req-tracker-ygwnj94r
Initialized build tracking at /tmp/pip-req-tracker-ygwnj94r
Created build tracker: /tmp/pip-req-tracker-ygwnj94r
Entered build tracker: /tmp/pip-req-tracker-ygwnj94r
Created temporary directory: /tmp/pip-install-jfurrdbb
1 location(s) to search for versions of aalib:
* https://pypi.org/simple/aalib/
Fetching project page and analyzing links: https://pypi.org/simple/aalib/
Getting page https://pypi.org/simple/aalib/
Found index url https://pypi.org/simple
Getting credentials from keyring for https://pypi.org/simple
Getting credentials from keyring for pypi.org
Looking up "https://pypi.org/simple/aalib/" in the cache
Request header has "max_age" as 0, cache bypassed
Starting new HTTPS connection (1): pypi.org:443
https://pypi.org:443 "GET /simple/aalib/ HTTP/1.1" 404 13
[hole] Status code 404 not in (200, 203, 300, 301)
Could not fetch URL https://pypi.org/simple/aalib/: 404 Client Error: Not Found for url: https://pypi.org/simple/aalib/ - skipping
Given no hashes to check 0 links for project 'aalib': discarding no candidates
ERROR: Could not find a version that satisfies the requirement aalib (from versions: none)
Cleaning up...
Removed build tracker: '/tmp/pip-req-tracker-ygwnj94r'
ERROR: No matching distribution found for aalib
Exception information:
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 186, in _main
status = self.run(options, args)
File "/usr/lib/python3/dist-packages/pip/_internal/commands/install.py", line 357, in run
resolver.resolve(requirement_set)
File "/usr/lib/python3/dist-packages/pip/_internal/legacy_resolve.py", line 177, in resolve
discovered_reqs.extend(self._resolve_one(requirement_set, req))
File "/usr/lib/python3/dist-packages/pip/_internal/legacy_resolve.py", line 333, in _resolve_one
abstract_dist = self._get_abstract_dist_for(req_to_install)
File "/usr/lib/python3/dist-packages/pip/_internal/legacy_resolve.py", line 281, in _get_abstract_dist_for
req.populate_link(self.finder, upgrade_allowed, require_hashes)
File "/usr/lib/python3/dist-packages/pip/_internal/req/req_install.py", line 249, in populate_link
self.link = finder.find_requirement(self, upgrade)
File "/usr/lib/python3/dist-packages/pip/_internal/index/package_finder.py", line 926, in find_requirement
raise DistributionNotFound(
pip._internal.exceptions.DistributionNotFound: No matching distribution found for aalib
From above log, there is pretty obvious the URL https://pypi.org/simple/aalib/ 404 not found. Then you can guess the possible reasons which cause that 404, i.e. wrong package name. Another thing is I can modify relevant python files of pip modules to further debug with above log. To edit .whl file, you can use wheel command to unpack and pack.
After 2 hours of searching, I found a way to fix it with just one line of command. You need to know the version of the package (Just search up PACKAGE version).
Command:
python3 -m pip install --pre --upgrade PACKAGE==VERSION.VERSION.VERSION
Below command worked for me -
python -m pip install flask
Not always, but in some cases the package already exists. For example - getpass. It is not listed by "pip list" but it can be imported and used:
If I try to pip install getpass I get the following error:
"Could not find a version that satisfies the requirement getpass"
Try installing flask through the powershell using the following command.
pip install --isolated Flask
This will allow installation to avoide environment variables and user configuration.
If you facing this issue at the workplace. This might be the solution for you.
pip install -U <package_name> --user --proxy=<your proxy>
Pip install from pypi.org.
pip install -U -i https://pypi.org/simple package
One possible error, pip package requires python intepreter which you are not using.
I ran into the same problem, it occurred only when I ran commands from my Docker image (or Dockerfile). Finally many hours later I managed to solve it by updating my python intepreter. Pointed out that my pip-package required python>=3,7 but my Docker image was using python 3.6.
Tip: To check out if you have similar problem, just check pip package requirements and your python version. Private pip package intepreter requirements are wrote down inside setup.py or setup.cfg. Public pip packages are usuially hosted in pypi.org where you can just check intepreter requirements with your browser. To check your python intepreter version just write for example python --version or python3 --version in your console
General problem description
As other answers point out there can also be other requirements that you are not satisfying and that is why pip can not found suitable package version for you. All the requirements are wrote down in pip package documentation and can be easily readed from https://pypi.org/project/graphene-django/your-package
I got this error while installing awscli on Windows 10 in anaconda (python 3.7).
While troubleshooting, I went to the answer https://stackoverflow.com/a/49991357/6862405 and then to https://stackoverflow.com/a/54582701/6862405. Finally found that I need to install the libraries PyOpenSSL, cryptography, enum34, idna and ipaddress. After installing these (using simply pip install command), I was able to install awscli.
When I lost my internet connection, I had this error.
Since it's a pretty annoying problem that may stuck beginners for a long period of time, here I write a complete guild.
if you are running pip install PACKAGE or python -m pip install PACKAGE, and a no matching version found error reported, here's how to solve the problem.
search your package on browser, for example my package is pycypto, here I search pycypto pypi
find your package, open the link on pypi, click download file
open a python shell, import any of your installed package, for example, I have installed Pillow before.
>>> import PIL
>>> PIL.__path__
['/Applications/MAMP/htdocs/canvas/src/zzd/env/lib/python3.7/site-packages/PIL']
PACKAGE.__path__ function will gives you the side packages path where all packages should go into.
PLUS:
if you have no idea what packages you installed before, run pip list to get a list of installed packages.
after we obtain the path, open a shell, cd to the path
cd /Applications/MAMP/htdocs/canvas/src/zzd/env/lib/python3.7/site-packages/
open
unzip the downloaded file, drag it into site-packages.
cd into the downloaded directory, and run setup.py to install
cd pycrypto-2.6.1
python setup.py install
Then you should be able to import and use the package in python.
Same error in slightly different circumstances, on MacOs. Apparently setuptools versions past 45 can expose some issues and this command got me past it:
pip3 install setuptools==45
If the package is local, don't miss the relative path.
E.g.
pip install ./<pkg>
finally worked in my case, while
pip install <pkg>
yielded:
ERROR: Could not find a version that satisfies the requirement <pkg> (from versions: none)
ERROR: No matching distribution found for <pkg>
I had a problem installing pandas-1.4.3, and the problem was my python patch version. pandas-1.4.3 required python version 3.8.13 and did not work with 3.8.9:
python install -r requirements.txt # or pip install pandas==1.4.3
# -> Could not find a version that satisfies...
conda activate my_project # creates a virtual env for a new python version
conda install python=3.8.13 # installing the new python version
python --version # displays 3.8.13
pip install -r python/requirements.txt
# -> pandas installed as expected
Search in google if you find some other version of that package available
use that for example
I was getting errors using the glob so I used glob2 instead

Scrapy Installation Fails with error 'cannot open include: 'openssl/aes.h '

I am trying to install Scrapy with easy_install -U Scrapy but it ends up in a strange error "Can not open include file " while trying to install it. Does any one know what is going on? Here is my complete traceback:
C:\Users\Mubashar Kamran>easy_install -U Scrapy
Searching for Scrapy
Reading https://pypi.python.org/simple/Scrapy/
Best match: scrapy 0.24.4
Processing scrapy-0.24.4-py2.7.egg
scrapy 0.24.4 is already the active version in easy-install.pth
Installing scrapy-script.py script to C:\Python27\Scripts
Installing scrapy.exe script to C:\Python27\Scripts
Installing scrapy.exe.manifest script to C:\Python27\Scripts
Using c:\python27\lib\site-packages\scrapy-0.24.4-py2.7.egg
Processing dependencies for Scrapy
Searching for cryptography>=0.2.1
Reading https://pypi.python.org/simple/cryptography/
Best match: cryptography 0.5.4
Downloading https://pypi.python.org/packages/source/c/cryptography/cryptography-
0.5.4.tar.gz#md5=4fd1f10e9f99009a44667fabe7980aec
Processing cryptography-0.5.4.tar.gz
Writing c:\users\mubash~1\appdata\local\temp\easy_install-jjms3i\cryptography-0.
5.4\setup.cfg
Running cryptography-0.5.4\setup.py -q bdist_egg --dist-dir c:\users\mubash~1\ap
pdata\local\temp\easy_install-jjms3i\cryptography-0.5.4\egg-dist-tmp-ry6bwd
C:\Python27\lib\distutils\dist.py:267: UserWarning: Unknown distribution option:
'setup_requires'
warnings.warn(msg)
_Cryptography_cffi_684bb40axf342507b.c
Creating library c:\users\mubash~1\appdata\local\temp\easy_install-jjms3i\cry
ptography-0.5.4\cryptography\hazmat\primitives\__pycache__\Release\cryptography\
hazmat\primitives\__pycache__\_Cryptography_cffi_684bb40axf342507b.lib and objec
t c:\users\mubash~1\appdata\local\temp\easy_install-jjms3i\cryptography-0.5.4\cr
yptography\hazmat\primitives\__pycache__\Release\cryptography\hazmat\primitives\
__pycache__\_Cryptography_cffi_684bb40axf342507b.exp
_Cryptography_cffi_8f86901cxc1767c5a.c
Creating library c:\users\mubash~1\appdata\local\temp\easy_install-jjms3i\cry
ptography-0.5.4\cryptography\hazmat\primitives\__pycache__\Release\cryptography\
hazmat\primitives\__pycache__\_Cryptography_cffi_8f86901cxc1767c5a.lib and objec
t c:\users\mubash~1\appdata\local\temp\easy_install-jjms3i\cryptography-0.5.4\cr
yptography\hazmat\primitives\__pycache__\Release\cryptography\hazmat\primitives\
__pycache__\_Cryptography_cffi_8f86901cxc1767c5a.exp
_Cryptography_cffi_4ed9e37dx4000d087.c
cryptography\hazmat\bindings\__pycache__\_Cryptography_cffi_4ed9e37dx4000d087.c(
194) : fatal error C1083: Cannot open include file: 'openssl/aes.h': No such fil
e or directory
error: c:\users\mubash~1\appdata\local\temp\easy_install-jjms3i\cryptography-0.5
.4\cryptography\hazmat\primitives\__pycache__\_Cryptography_cffi_684bb40axf34250
7b.pyd: Access is denied
I got same error installing different python app. I was missing OpenSSL dev package, solved by:
sudo apt-get install libssl-dev
On OSX
brew install openssl and then possibly brew link openssl --force if you are informed that links were not created.
Install Scrapy using the following command
env CRYPTOGRAPHY_OSX_NO_LINK_FLAGS=1 LDFLAGS="$(brew --prefix openssl)/lib/libssl.a $(brew --prefix openssl)/lib/libcrypto.a" CFLAGS="-I$(brew --prefix openssl)/include" pip install scrapy
You can, if you wish, substitute openssl for libressl.
It is enough to install openssl
brew install openssl
and export
export LDFLAGS=-L/usr/local/opt/openssl/lib
export CPPFLAGS=-I/usr/local/opt/openssl/include
in ~/.bash_profile.
Try to avoid linking with --force parameter because it can lead to the conflicts with system libraries.
To All who end up in the errors while installing scrapy should follow http://community.spiceworks.com/how_to/38490-setting-up-scrapy-on-windows-7. This link describes the most accurate and easy way to install scrapy without coming across any errors on windows 7 and 8 .

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