I have been trying to run RStudio Quarto script in a fresh Ubuntu 20.04 installation but got into some trouble. Some Python packages that are required to run the simple hello.qmd were not there. I was getting these errors:
MoudleNotFoundError: No module named 'nbclient'
and a second error:
ModuleNotFoundError: No module named 'matplotlib_inline'
The first error was due to I had install the nbclient package. My default Python installation is python2.7. Quarto will not run well with Python 2.7; we should try with 3.7+. If your Linux doesn't come with it by default, this can easily be addressed by installing another Python version and configuring multiple Python versions with the help of the command:
sudo update-alternatives --config python
If no Python version shows up, then it means you have first to configure all your installed Python versions. This is very well explained at https://www.rosehosting.com/blog/how-to-install-and-switch-python-versions-on-ubuntu-20-04/
Once you have configured all your Python versions, every time that you run
sudo update-alternatives --config python, you will be prompted to enter the Python version you want as default. If you have a fresh Ubuntu 20.04, most likely that you have two: Python 2.7 and Python 3.8. Select 3.8 and you will fine. Quarto won't work with Python 2.7.
After you have python3 running and switched into, install nbclient with:
pip install nbclient.
The first error will now pass, but most likely you will get now
ModuleNotFoundError: No module named 'matplotlib_inline'. This is because you also need to install the package matplotlib-inline. This is not documented in the installation instructions of Quarto. But easy to fix. Run:
pip install matplotlib-inline
Now, go back to your VS Code, open the command palette and run Quarto: Render, or just type from the terminal:
quarto preview hello.qmd --no-browser --no-watch-inputs
You are done!
I'm trying to uninstall all django packages in my superuser environment to ensure that all my webapp dependencies are installed to my virtualenv.
sudo su
sudo pip freeze | grep -E '^django-' | xargs pip -q uninstall
But pip wants to confirm every package uninstall, and there doesn't seem to be a -y option for pip. Is there a better way to uninstall a batch of python modules? Is rm -rf .../site-packages/ a proper way to go? Is there an easy_install alternative?
Alternatively, would it be better to force pip to install all dependencies to the virtualenv rather than relying on the system python modules to meet those dependencies, e.g. pip --upgrade install, but forcing even equally old versions to be installed to override any system modules. I tried activating my virtualenv and then pip install --upgrade -r requirements.txt and that does seem to install the dependencies, even those existing in my system path, but I can't be sure if that's because my system modules were old. And man pip doesn't seem to guarantee this behavior (i.e. installing the same version of a package that already exists in the system site-packages).
starting with pip version 7.1.2 you can run pip uninstall -y <python package(s)>
pip uninstall -y package1 package2 package3
or from file
pip uninstall -y -r requirements.txt
Pip does NOT include a --yes option (as of pip version 1.3.1).
WORKAROUND: pipe yes to it!
$ sudo ls # enter pw so not prompted again
$ /usr/bin/yes | sudo pip uninstall pymongo
If you want to uninstall every package from requirements.txt,
pip uninstall -y -r requirements.txt
on www.saturncloud.io, Jupiter notebooks one can use like this:
!yes | pip uninstall tensorflow
!yes | pip uninstall gast
!yes | pip uninstall tensorflow-probability
Alternatively, would it be better to force pip to install all dependencies to the virtualenv rather than relying on the system python modules to meet those dependencies,
Yes. Don't mess too much with the inbuilt system installed packages. Many of the system packages, particularly in OS X (even the debian and the derived varieties) depend too much on them.
pip --upgrade install, but forcing even equally old versions to be installed to override any system modules.
It should not be a big deal if there are a few more packages installed within the venv that are already there in the system package, particularly if they are of different version. Thats the whole point of virtualenv.
I tried activating my virtualenv and then pip install --upgrade -r requirements.txt and that does seem to install the dependencies, even those existing in my system path, but I can't be sure if that's because my system modules were old. And man pip doesn't seem to guarantee this behavior (i.e. installing the same version of a package that already exists in the system site-packages).
No, it doesn't install the packages already there in the main installation unless you have used the --no-site-packages flag to create it, or the required and present versions are different..
Lakshman Prasad was right, pip --upgrade and/or virtualenv --no-site-packages is the way to go. Uninstalling the system-wide python modules is bad.
The --upgrade option to pip does install required modules in the virtual env, even if they already exist in the system environment, and even if the required version or latest available version is the same as the system version.
pip --upgrade install
And, using the --no-site-packages option when creating the virtual environment ensures that missing dependencies can't possibly be masked by the presence of missing modules in the system path. This helps expose problems during migration of a module from one package to another, e.g. pinax.apps.groups -> django-groups, especially when the problem is with load templatetags statements in django which search all available modules for templatetags directories and the tag definitions within.
pip install -U xxxx
can bypass confirm
I have successfully installed the Caffe on Ubuntu 18.* using
`sudo apt-get install caffe-cpu`
The which caffe returns /usr/bin/caffe
I am successfully able to run caffe command on terminal, but problem is running the test files, as they are link to build directories of caffe and the problem is if I manually get the github repository of caffe and make build, it keeps failing and some of the dependencies candidates dont't have an installation candidate on Ubuntu 18.
Also all the examples on net available are for the previous type of manually built caffe
Normally, it will use with the default python in /usr/bin/python3. You can check
/usr/bin/python3
>>> import caffe
With the python in /usr/bin/python3, it does not require to add any addtional PYTHONPATH
I am trying to install Tensorflow in R as explained here- https://github.com/rstudio/tensorflow. I want to use Keras for deep learning in R.
devtools::install_github("rstudio/tensorflow")
library(tensorflow)
install_tensorflow()
but there was an error
Error: Prerequisites for installing TensorFlow not available.
Execute the following at a terminal to install the prerequisites:
$ sudo /usr/local/bin/pip install --upgrade virtualenv
i followed the code given to put into terminal but this seems like another error
The directory '/Users/liangweiteo/Library/Caches/pip/http' or its
parent directory is not owned by the current user and the cache has
been disabled. Please check the permissions and owner of that
directory. If executing pip with sudo, you may want sudo's -H flag.
The directory '/Users/liangweiteo/Library/Caches/pip' or its parent
directory is not owned by the current user and caching wheels has been
disabled. check the permissions and owner of that directory. If
executing pip with sudo, you may want sudo's -H flag. Requirement
already up-to-date: virtualenv in
/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages
tried to look for help on this site
Error while installing Tensorflow in R
but somehow the error is still there
I am trying to install numpy on a remote host where I have no admin rights. I have sucessfully installed Python 2.7 and pip inside a virtualenv ,and can use pip to install trivial things like pip install Markdown. But if I pip install numpy or scipy, it errors on SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel. I do not have rights to sudo apt-get or apt-get, so can not do sudo apt-get install python27-devel or sudo apt-get install python-devel. I wanted to build from source so that I could use the option --user but the source is a .deb file and building it requires even more things I have to apt-get. I tried contacted the admin but I am advised to keep my own installations in my own local environment. What should I do?
The OS system is Ubuntu 14.04 LTS.
The reason for the admins answer is simple. Ubuntu also uses python for internal scripts. So the admin will not update or change the python installation if you need a more recent version of a package.
This is what I would try:
Compile source of python 2.7 yourself and install it in your preferred path in your home directory. This way you always have all needed headers. Put the interpreter into your PATH.
(Optional) Set PYTHONUSERHOME to your local python site packages
Install virtualenv package via pip
Setup virtualenv envirnoment for numpy etc...
(Optional) 4. Build Blas libraries e.g. OpenBlas in your home
Install cython in virtualenv ... and probably some more packages needed for numpy
Install numpy scipy in the virtualenv with the correct settings BLAS libraries settings
If you use your own python installation, the virtualenv is not really necessary. So you might want to omit that. You just need to make sure that your python interpreter is always first to be found.