I am using google colab for python programming.
however, the package UpSetPlot was not installed. I tried using the command:
!pip install UpSetPlot
but the following error appears:
Collecting UpSetPlot
Using cached https://files.pythonhosted.org/packages/a7/11/5cc8a0ebaf4f3a9a8e02cd3a9a13806eaebfc1d2ffb4a40031bdc83ad1be/UpSetPlot-0.5.0.tar.gz
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
There seems to be a problem in versions after 0.4.1 of upsetplot which may be related to the version of Python that is used in Colab.
Try this in a Colab cell.
!pip install upsetplot==0.4.1
Related
New to this. I'm trying to install manim in Google Colab following the instructions from the Manim Community site.
Ran:
!sudo apt update
!sudo apt install libcairo2-dev ffmpeg texlive texlive-latex-extra texlive-fonts-extra texlive-latex-recommended texlive-science tipa libpango1.0-dev
!pip install -U manim==0.3.0
!pip install IPython --upgrade
returned the following error;
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
google-colab 1.0.0 requires ipython~=7.9.0, but you have ipython 8.9.0 which is incompatible.
I wasn't aware that I had any version of Python installed
I do not know what to do as I have no experience in this area.
For a deep-learning project, I was trying to import the 'models' library. But it's not installed on my colab notebook. So, I tried pip install models to install the library but it shows error which is as on the screenshot. I've also read somewhere that the library is renamed as 'pymodels'. I've also tried it but still not working.
I would be thankful for any help you can provide.
When I ran the following commands in the Jupiter notebook, it gives me an error.
!apt-get install openslide-tools
!pip install openslide-python
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
It was working before but right now it gives me an error when I try to run it.
Seems you have to install the python libraries for openslide through apt-get. Try this
!apt-get install openslide-tools
!apt-get install python3-openslide
I'm trying to run this notebook on Google Cloud Datalab: https://github.com/GoogleCloudPlatform/training-data-analyst/blob/master/courses/machine_learning/feateng/feateng.ipynb
While it was perfectly working yesterday, today running the first block results in cffi.error.VerificationError (undefined symbol: SSLv2_client_method).
Can you advise on how I can fix this?
I've tried to do the same from a different GC profile and the problem remains.
I've also tried to fix 'pip install' as described here: pip install fails with "connection error: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:598)". Doing this in Datalab causes the same error; doing this in Cloud shell outside Datalab doesn't change anything.
This has been answered on github by #ekuuni:
https://github.com/GoogleCloudPlatform/training-data-analyst/issues/313
%%bash
source activate py2env
conda install -y pytz
conda update -y pyopenssl
pip uninstall -y google-cloud-dataflow
pip install --upgrade apache-beam[gcp]
I needed these 2 more lines for it to work.
pip install tensorflow_transform
pip install tensorflow==1.9.0
A good workaround is using virtual environments rather than Datalab so you don't have to deal with version updates:
https://cloud.google.com/dataflow/docs/quickstarts/quickstart-python
I have successfully installed the following on python 2.7
apache-beam==2.7.0
tensorflow==1.11.0
tensorflow-transform==0.8.0
I know google colaboratory doesn't yet support an R kernel. What about rmagic? Can I use rpy2?
I tried :
!pip install rpy2==2.8.6
And got :
Collecting rpy2==2.8.6
Using cached https://files.pythonhosted.org/packages/32/54/d102eec14f9cabd0df60682a38bd45c36169a1ec8fb8a690bf436cb6d758/rpy2-2.8.6.tar.gz
Complete output from command python setup.py egg_info:
Error: Tried to guess R's HOME but no command 'R' in the PATH.
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-install-3bSiiD/rpy2/
I'm guessing that it isn't working because R isn't installed on whatever cloud machine this notebook is running on, and that it probably isn't possible to install it. But I'm hoping I'm wrong and someone may know of a work around.
OK, I answered my own question. I thought for sure this would fail, but tried anyway:
!apt-get update
!apt-get install r-base
!pip install rpy2==2.8.6
And it worked!