I was trying to install XMM-NEWTON SAS to my device. But unfortunately, there is an error.
Checking whether Python is in PATH ... No.
Error: Please add python to your PATH !
I am using a bash shell and have installed python3.9. How can I rectify this problem?
The SAS installation script searches for "python" in the PATH, not for "python3" specifically. For a correct installation, you could try to create a soft link for the python3 binary as /usr/bin/python:
sudo ln -s /usr/bin/python3 /usr/bin/python
This needs to be done with root privileges (thus the 'sudo' in front).
In this way, SAS should find the correct Python version to complete installation.
Related
I am trying to get to grips with Python on my Mac running OS X 10.15.7 Catalina.
My goal is to be able to run a program requiring Python 3.9 and associated libraries, in its own virtual environment, using venv.
My quest has led me over many rocky paths and blind alleys - including via Anaconda and Brew.
I am running zsh - specifically oh-my-zsh ys version. If that's important. Most online forums and tutorials assume bash. I would prefer to do all in zsh to avoid having to edit both zsh and bash profiles.
Current Shell Outputs
$ python -V
Python 2.7.16
$ which python
/usr/bin/python
$ python3 -V
Python 3.8.2
$ which python3.8
python3.8 not found
$ which python3.9
python3.9 not found
$ python3 -m -V
/Library/Developer/CommandLineTools/usr/bin/python3: No module named -V
Pausing there ..
Py 2.7 is the OS X system Python and I don't want to do anything with it.
It is odd that python3 -m returns a reference to the CLI tools. See below. The only location for py3.8 is in the CL tools.
What pythons do I have (output below is edited so as to show only main directories and Files)?
$ locate python
/Applications/LibreOffice.app/Contents/Frameworks/LibreOfficePython.framework/Versions/3.7/bin/python3
/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/bin/python3.8
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python
/Library/Developer/CommandLineTools/usr/bin/python3.8
/Library/Frameworks/Python.framework/Versions/3.9/bin/python3
/Library/Frameworks/Python.framework/Versions/3.9/bin/python3-config
/Library/Frameworks/Python.framework/Versions/3.9/bin/python3.9
/Library/Frameworks/Python.framework/Versions/3.9/bin/python3.9-config
/Library/Frameworks/Python.framework/Versions/3.9/share/man/man1/python3.1
/Library/Frameworks/Python.framework/Versions/3.9/share/man/man1/python3.9.1
/Library/Frameworks/SAVI.framework/Versions/A/Frameworks/Python.framework/Versions/3.6/lib/python3.6
/usr/bin/python
/usr/bin/python-config
/usr/bin/python2
/usr/bin/python2.7
/usr/bin/python2.7-config
/usr/bin/python3
/usr/bin/pythonw
/usr/bin/pythonw2.7
/usr/lib/libpython.dylib
/usr/lib/libpython2.7.dylib
/usr/lib/python2.7
/usr/local/bin/python3
/usr/local/bin/python3-config
/usr/local/bin/python3.9
/usr/local/bin/python3.9-config
/usr/share/file/magic/python
/usr/share/man/man1/python.1
/usr/share/man/man1/python2.7.1
/usr/share/man/man1/pythonw.1
/usr/share/man/man1/pythonw2.7.1
/usr/share/vim/vim81/autoload/python3complete.vim
/usr/share/vim/vim81/autoload/pythoncomplete.vim
/usr/share/vim/vim81/ftplugin/python.vim
/usr/share/vim/vim81/indent/python.vim
/usr/share/vim/vim81/syntax/python.vim
/usr/share/zsh/5.7.1/functions/_bpython
/usr/share/zsh/5.7.1/functions/_python
/usr/share/zsh/5.7.1/functions/_python_modules
WHAT ABOUT PIP?
$ pip3
WARNING: pip is being invoked by an old script wrapper. This will fail in a future version of pip.
Please see https://github.com/pypa/pip/issues/5599 for advice on fixing the underlying issue.
To avoid this problem you can invoke Python with '-m pip' instead of running pip directly.
$ pip3 install --upgrade pip
WARNING: pip is being invoked by an old script wrapper. This will fail in a future version of pip.
Please see https://github.com/pypa/pip/issues/5599 for advice on fixing the underlying issue.
To avoid this problem you can invoke Python with '-m pip' instead of running pip directly.
Defaulting to user installation because normal site-packages is not writeable
Requirement already satisfied: pip in ./Library/Python/3.8/lib/python/site-packages (20.3.3)
Note two points
Although the wrapper warning comes up, PIP 20.3.3 is latest version which I have upgraded. Probably the reason for the warning is in the next lines, which suggest that PIP3 is being invoked from the CL Tools.
2; The ‘normal site-packages is not writeable’ error is supposed to be cured by specifying the Path. I have tried already to specify the correct path - see below - but this has not cured the problem and is another major reason for asking the question at the end of this post.
$ python -m pip
/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python: No module named pip
$ python3 -m pip
Usage:
/Library/Developer/CommandLineTools/usr/bin/python3 -m pip <command> [options]
$ which pip3
/usr/bin/pip3
$ locate pip3
/Applications/LibreOffice.app/Contents/Frameworks/LibreOfficePython.framework/Versions/3.7/bin/pip3
/Applications/LibreOffice.app/Contents/Frameworks/LibreOfficePython.framework/Versions/3.7/bin/pip3.7
/Library/Developer/CommandLineTools/usr/bin/pip3
/Library/Developer/CommandLineTools/usr/bin/pip3.8
/Library/Frameworks/Python.framework/Versions/3.9/bin/pip3
/Library/Frameworks/Python.framework/Versions/3.9/bin/pip3.9
/usr/bin/pip3
/usr/local/bin/pip3
/usr/local/bin/pip3.9
SYSTEM FILES
~/.zprofile contents - edited a few times to remove references to virfualenv and penv, both originally installed with brew and now removed. I have run brew uninstall and brew remove to try to clean everything up but may not have succeeded.
Start
# THIS FILE COMMENTED OUT RH 21DEC20
## Setting PATH for Python 3.9
## The original version is saved in .zprofile.pysave. **Note in this post only - cannot find this file**
PATH="/Library/Frameworks/Python.framework/Versions/3.9/bin:${PATH}"
export PATH **Note in this post only - this does not seem to have worked - see above Python3 -V**
# export WORKON_HOME=~/.virtualenvs
# mkdir -p $WORKON_HOME
# . ~/.pyenv/versions/3.9.0/bin/virtualenvwrapper.sh
# eval "$(pyenv init -)"
# # AND THESE LINES ADDED FOLLOWING STACKOVERFLOW Q 33216679 **Note in this post only - commented out as shell threw errors .’cannot find virtualenvwrapper.sh**
# export WORKON_HOME=$HOME/.Envs
# # export VIRTUALENVWRAPPER_PYTHON=$/usr/bin/python3
# export VIRTUALENVWRAPPER_PYTHON=$/usr/local/bin/python3
#source $HOME/.local/bin/virtualenvwrapper.sh
END
Finally a word about Brew. Many tutorials advised the use of Brew to install Python, pyenv, and libraries etc. I did that and successfully created a test environment, but could not the utilise it. I have then removed as much as possible in order to get back to a ‘clean’ state to work with.
Current brew status is
$ brew doctor
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry or file an issue; just ignore this. Thanks!
Warning: Unbrewed dylibs were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected dylibs:
/usr/local/lib/libdvdcss.2.dylib
/usr/local/lib/libfuse.0.dylib
/usr/local/lib/libulockmgr.0.dylib
Warning: Unbrewed header files were found in /usr/local/include.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected header files:
/usr/local/include/ulockmgr.h
Warning: Unbrewed .la files were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected .la files:
/usr/local/lib/libulockmgr.la
Warning: Unbrewed static libraries were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected static libraries:
/usr/local/lib/libfuse.a
/usr/local/lib/libulockmgr.a
SUMMARY
My first goal is to set Py3.9.x as default for new projects. I think also this would require/imply that pip and other commands run from v3.9 and not any other version or location. Must admit to being hazy about that.
Then I want to be able to create a virtual environment into which I can put the program I want to run and its associated libraries and packages. Doing this implies using terminal, but I need to know which directory I need to be in to run which commands.
At this point I have also been running into confusion with tutorials on how to create a virtual environment. From what I have read I think I should use venv over pyenv. What is not clear is whether I run the venv command (s) from root, or whether I have to create and cd to a different location, and if so what.
Any help in
1 Changing the default Python to 3.9
2 Creating a venv to use v3.9.
3 What commands to run where.
Will be greatly appreciated. Please keep it simple and don't assume any prior knowledge!
This is what I would do :
# For 1 Changing the default python to 3.9
cd /usr/local/bin
sudo ln -fs /Library/Frameworks/Python.framework/Versions/3.9/bin/python3.9 python3
sudo ln -fs python3 python
# And make sure /usr/local/bin is before (/usr/bin and /Library/Developer/CommandLineTools/usr/bin) in your $PATH
# For 2 Creating a venv to use v3.9
/usr/local/bin/python3.9 -m venv /tmp/python3.9-venv
I am having a problem about linuxbrew.
bash: /lustre7/home/lustre4/user1/applications/bin/cut: /lustre7/home/lustre4/user1/.linuxbrew/lib/ld.so: bad ELF interpreter: No such file or directory
I tried to uninstall linuxbrew using instructions at its website, but somehow it didn't work (because of sudo requirements).
there is linuxbrew directory but I can't remove when I type rm -r linuxbrew it says;
-bash: /lustre7/home/lustre4/user1/applications/bin/rm: /lustre7/home/lustre4/user1/.linuxbrew/lib/ld.so: bad ELF interpreter: No such file or directory
When I tried to install homebrew it says your CPU is not supported. (I tried this before and it worked, but now it is not working.)
I want to solve this problem but I couldn't find any solution. I am not able to run sudo and yum commands because I am not root. I am a user at a linux cluster.
OK. I finally was able to solve this issue.
I am wring in case someone else may have the same issue.
First, this was related to a bash problem. I recently installed a tool that put some variables to both bashrc and bash_profile and altered path of bin directory.
I wasn't able to use system commands such as rm, ls, cat etc. and I wasn't able to run system ruby. Paths of all commands and ruby were in my bin directory under my application directory.
What I did is;
I edited my bash_profile by cancelling the new path that caused conflict between bash_profile and bashrc. This enabled me run system commands.
I uninstalled linuxbrew as described in its website.
I removed linuxbrew from my home directory, and cancelled its path in bash_profile (comment out).
I installed homebrew again and put its path to my bashrc.
Now it is working.
I could uninstall linuxbrew using the procedure I described in here:
How to completely uninstall brew and re-install brew in ubuntu 19.04
-> In short, I just replaced install.sh by uninstall.sh and it worked...
$/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/uninstall.sh)"
I installed python 3.6 before and installed python 3.7.4 today. When I type python3 in command, it opens python 3.6, I want to change it to python 3.7.4.
which python3 shows /Library/Frameworks/Python.framework/Versions/3.6/bin/python3,
but the link in /usr/local/bin/ is :
python3 -> ../../../Library/Frameworks/Python.framework/Versions/3.7/bin/python3
so is the case of pip3. why? ?
How can I change which python3 to python 3.7.4? I don't want to use alias.
I use MacOS 10.14.2
Your OS uses the PATH environment variable to look for the commands you write into the shell, so if you type python3 it will go through the directories listed in this PATH and check if there's your programm. It takes the first matching program and executes it, so in your case the directory /Library/Frameworks/.../3.6/bin is before the directory usr/local/bin, which means that the python3 from /Library/Frameworks/.../3.6/bin will be used.
You need therefore to change this PATH variable:
export PATH="/Users/sky/Documents/software/Montage-master/bin:/usr/share/file/magic/mercurial:/Library/Frameworks/Python.framework/Versions/3.7/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/local/mysql/bin:/Library/Frameworks/Python.framework/Versions/3.6/bin"
You can put that into your ~/.bash_profile so that it is permanent, and you don't need to set it every time you open a new terminal window.
Note that this will not automatically update your path for the remainder of the session. To do this, you should run:
source ~/.bash_profile
Are you sure have python3.7 intalled?
you can view the folder
cd /usr/bin
Next you search the python's file:
find /usr/bin/ python3
if don´t exist filename python3.7 install
sudo apt install python3.7
sudo apt update
I need to install Torch on server,
but its installation guide requires the following line as the first step:
curl -s https://raw.githubusercontent.com/torch/ezinstall/master/install-deps | bash
curl is not installed on my server, and I'm not the root, so I don't have permission to install it.
I downloaded the script file in the URL, and chmod-ed it,
but can't execute it, again due to permission.
Is there a way to install torch without usage of curl?
bash install-deps
resulted in
xxxx is not in the sudoers file. This incident will be reported.
Torch dependencies needs to be installed - if you install it via this script, that'll require root privileges.
If you saved the script, you can start it (without chmod) with
bash install-deps
Iam getting some error while installing executable in /usr/local/bin thru makefile:
install -m 755 my_execble /usr/local/bin
install: cannot create regular file /usr/local/bin/my_execble: Permission denied
If use sudo before 'install' command ..
then it will work .. but is there other way of installing without using sudo?
The OP ask long time ago, but I will guess it can be useful for others.
Since your make install command try to install files in directory requiring root privileges (ex: /usr/local/bin) you can either:
Become root before launching your command (as you stated in your description: using sudo for example)
OR
Install it in another directory that do not require specific privilege. For this purpose you can use a specific parameter named 'DESTDIR' that is usually supported in makefile, so that your command looks like:
make DESTDIR=/home/myuser/my_dest_dir install
This is named Staged Installs.
You can either tweak the Makefile (or use a configure script) to have it install the program in your home directory... or become root.