How to install GLIBC_2.14 without admin right - glibc

I want to use gdc-client, however, after I download it and run it. the system reported as:
./gdc-client: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /tmp/_MEI5oSpPi/libz.so.1)
It is our University Server, I don't have any admin right. Do you know how to install GLIBC_2.14 without admin right?
[shg047#tscc-login2 software]$ lsb_release -a
LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
Distributor ID: CentOS
Description: CentOS release 6.6 (Final)
Release: 6.6
Codename: Final
[

gdc-client github issued this problem that glibc 2.12 is the latest that's available for CentOS 6.
If your system is CentOS release 6.6, I think you should download the gdc-client source code and compile it yourself. gdc-client is based on the py2.
git clone https://github.com/NCI-GDC/gdc-client
python setup.py install
You may meet the problem
The 'lxml==3.5.0b1' distribution was not found and is required by gdc-client
or
ImportError: /usr/lib64/libxml2.so.2: version `LIBXML2_2.9.0' not found (required by lxml/etree.so)
You need to install libxslt and libxml2 in your home path. And add xml2-config and xslt-config to your path. export PATH="/prog_path/libxslt-1.1.29/bin:/prog_path/libxml2-2.9.4/bin:$PATH"
Then
pip uninstall lxml
pip install lxml==3.5.0b1 --install-option="--auto-rpath"
Finnaly, compile gdc-client source code.
python setup.py install
It worked.

Related

Message "note: This error originates from a subprocess, and is likely not a problem with pip"

While downloading pip install allennlp==1.0.0 allennlp-models==1.0.0, I faced this problem:
[6 lines of output]
running bdist_wheel
running build
running build_py
running build_ext
building 'srsly.msgpack._unpacker' extension
error: Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for srsly
Failed to build thinc blis srsly
ERROR: Could not build wheels for srsly, which is required to install pyproject.toml-based projects
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error
× pip subprocess to install build dependencies 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 have downloaded:
pip install -vvv torch
pip install numpy
pip3 install --pre torch -f https://download.pytorch.org/whl/nightly/cpu/torch_nightly.html
and it still not working.
I am using Python 3.10.2 on Windows 11 Pro.
What should I do?
I had Python 3.10 and had the same error installing psutil from pip. I fixed the problem by installing an older version of pip using the command:
pip install pip==21.3.1
You have to install the Python 3.9.10 version from python.org and after installation, upgrade your pip and everything will be sorted.
It is the problem in Python 3.10.2... This method is working. I was suffering from the same problem in installing the turtle, so I did that and error was solved.
This particular error is caused by not having a C/C++ compiler installed. As said in the error message, either install MSVC or another compiler to compile it.
Please read your error messages; they are there for a reason.
If you're using a Python 3 image, this might help:
RUN apk update
RUN apk add make automake gcc g++ subversion python3-dev
Reference from Problems with pip install numpy - RuntimeError: Broken toolchain: cannot link a simple C program
https://visualstudio.microsoft.com/visual-cpp-build-tools/
Download and install or update
Microsoft Visual C++ 14.0 or greater is required.
You must be install build visual tools 15, 17, 19, or greater.
Download from Microsoft C++ Build Tools.
To solve this problem, you need to download Visual Studio from its main page.
If Visual Studio is already installed, then when you run the installer, you can modify it (by clicking the modify button):
During Visual Studio installation (or installation modification) choose Desktop Development with C++:
First: You installed the Mingw-w64 compiler with a full MSYS2 package, and this package included Python.
Second: you get the error because the plugin is not in the Python packages installed by MSYS2.
So: uninstall MSYS2 and install a minimalistic MinGW (MinGW - minimalistic GNU for Windows).
And finally Install a version of Python from the official Python page.
Now if you can install plugins.
I've found a similar question from GitHub, and credits goes to thaibee. Here I quote:
It's a problem with Microsoft products and is
very easy to solve.
If you can't install these plugins as well,
need to download it from other repositories like this one:
https://www.lfd.uci.edu/~gohlke/pythonlibs/ depends on the version of python and the system.
For example: for my Windows 11 (x64) and Python 3.10 I took this file: pyodbc‑4.0.32‑cp310‑cp310‑win_amd64.whl
It's very easy to install: pip install pyodbc‑4.0.32‑cp310‑cp310‑win_amd64.whl
After it, the system works well and didn't ask you about VC.
This solution I found in problem with the MySQL plugin for Django. I don't understand why - but they also use VC for the installation process.
I understand your problem, and I have faced it too. I tried multiple solutions, but it didn't work, so I simply uninstalled my Python and installed some older version of it. Example: I recently uninstalled Python 3.10.2 and installed 3.9.10.
It worked without any errors.
I had a similar problem while installing with pip3: building wheel for box2d-py (setup.py) ... error
The solution was just to install SWIG prior to box2d, so I added the following steps manually:
pip install swig
pip install gym[box2d]
For Mac, there is a possible workaround for this problem if you use Conda. The idea is to create an x86 environment on the Mac and do your pip install after that.
conda create -n <name>
conda activate <name>
conda config --env --set subdir osx-64
conda install python=3.8
Here I choose Python 3.8, but you can choose another version.
If you are on macOS (maybe Apple silicon) then first try to do this from your base location of the terminal:
eval "$(/opt/homebrew/bin/brew shellenv)"
Then, do brew update and brew upgrade.
Once you are done with that, type
brew install geos
Now again go to your virtual environment and activate it (if you are working in the virtualenv) and then type:
python3.10 -m pip3 install [module name]
I was facing the same problem when executing:
python -m pip install package-name
After many failed tentatives, what fixed the problem for me was executing:
py -m pip install package-name
When I type py in the terminal, it shows this information:
Python 3.9.8 (tags/v3.9.8:bb3fdcf, Nov 5 2021, 20:48:33) [MSC v.1929 64 bit (AMD64)] on win32
When I type python in the terminal, it shows this information:
Python 3.8.2 (default, Apr 9 2020, 13:17:39) [GCC 9.3.0 64 bit (AMD64)] on win32
I believe that this problem is related to the Python interpreter version.
I tried all recommendations that were written, but none worked. My Python was 3.11.
So I just installed Python 3.8.10 from here:
https://www.python.org/downloads/release/python-3810/
And ran
C:\Python38\python.exe -m pip install matplotlib
And it worked.
I faced a similar problem while installing pandas-datareader.
I was using Python 3.11.0, and after trying all possible solutions, I downloaded Python 9.10.0 and it worked fine.
We can install DVC with the below commands:
conda install -c conda-forge mamba # installs much faster than conda
mamba install -c conda-forge dvc
For more information please refer this: https://dvc.org/doc/install/

Installation problem with PyTorch's Geometric. "torch-scatter" produces an error with exit status 1

Could anyone if used PyTorch geometric before, help me resolve this issue. I'm having trouble installing torch-scatter from PyTorch Geometric to deal with some tabular data for question answering task based on TAPAS model. I presume there is a compile error at source. I tried checking other forums and found no solution for this yet.
Procedure followed to produce the error:
pip3 install torch==1.8.1+cpu torchvision==0.9.1+cpu torchaudio===0.8.1 -f https://download.pytorch.org/whl/torch_stable.html
pip3 install torch-scatter
Console output:
ERROR: Command errored out with exit status 1:
I also tried using the python -f flag and specifically tried to pull from the source at:
pip3 install torch-scatter -f https://pytorch-geometric.com/whl/torch-1.8.1+cpu.html
Following are my PyTorch and CUDA versions with the respective imports and console outputs:
python -c "import torch; print(torch.__version__)"
Output:
1.8.1+cpu
CUDA version:
python -c "import torch; print(torch.version.cuda)"
Output:
None
Python version:
Python 3.7.5
Thank you very much for your time and guidance.
Solution found:
The error is due to wrong/unsupported GCC versions (that's indeed more PyTorch related). I tried installing from binaries which couldn't find compatible version. After some research, I found that Pytorch geometric installation documentation suggests that only PyTorch versions 1.4.0, 1.5.0, 1.6.0, 1.7.0, and 1.8.0 are compatible, but does not explicitly mentions this.
Following solution worked:
Downgrading PyTorch to any of the above versions solved the issue. Make sure that you use the same version of PyTorch and torch-scatter while installation. In my case, 1.8.0
I had this problem too which is solved by install C++ build tools. You can install it from vs_buildtools.exe that is downloadable here
I also had some issues related to the torch_geometric, and I resolved those issues after some research. Following are the solutions that I have applied:
After installing torch, please install the following libs:
1. torch-scatter
2. torch-sparse
3. torch-cluster
Then install torch-geometric.
You can install the above packages using pip command (pip install ), If it does not work install through HTML link by selecting your specific version.
Command: pip install libname -f link
Example: pip install torch-scatter -f https://pytorch-geometric.com/whl/torch-1.12.0%2Bcpu.html
For my case, I have used the torch 1.12 and install the above packages from the above link.
Thanks

pip3 packages are being installed in ~/.local folder

I recently upgraded to ubuntu 20.04 LTS. As python3.8 was preinstalled, I installed pip using the command sudo apt install python3-pip , and I started installing python3 libraries. All the libraries I install are being installed into ~/.local/lib/Python3.8/site-packages folder. If I remember correctly, these packages should be installed into /usr/local/lib/python3.8/dist-packages.
madhan#madhan:~$ pip3 show tensorflow
Name: tensorflow
Version: 2.2.0
Summary: TensorFlow is an open source machine learning framework for everyone.
Home-page: https://www.tensorflow.org/
Author: Google Inc.
Author-email: packages#tensorflow.org
License: Apache 2.0
Location: /home/madhan/.local/lib/python3.8/site-packages
After the packages are installed, I get a warning saying ~/.local/bin is not included in $PATH variable.
Installing collected packages: appdirs, cachelib, pygments, cssselect, lxml, pyquery, howdoi
WARNING: The script pygmentize is installed in '/home/madhan/.local/bin' which is not on PATH.
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
WARNING: The script howdoi is installed in '/home/madhan/.local/bin' which is not on PATH.
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Successfully installed appdirs-1.4.4 cachelib-0.1 cssselect-1.1.0 howdoi-1.2.1 lxml-4.5.1 pygments-2.6.1 pyquery-1.4.1
even if ~/.local/bin is not included in $PATH variable, I am still able to import the packages.
madhan#madhan:~$ python3
Python 3.8.2 (default, Apr 27 2020, 15:53:34)
[GCC 9.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import tensorflow
>>>
Does anybody know why this is happening? How do I change the default folder to which pip3 packages are installed. Is it okay leave the packages in ~/.local folder or will it be a problem in the future?

Installing python-igraph for python 3.6 on Windows

I want to install the python-igraph package, but I am currently using python 3.6.1 and I don't find any installer for this new version of python. Do you know how can I install python-igraph for this version?
I have tried to install python-igraph for older versions from anaconda cloud but a version problem occurs.
!conda install -c vtraag python-igraph
Fetching package metadata .............
Solving package specifications: .
UnsatisfiableError: The following specifications were found to be in conflict:
- python 3.6*
- python-igraph -> python 3.5*
Use "conda info <package>" to see the dependencies for each package.`
I know that python-igraph exists for older python versions, but I don't want to overwrite the current python 3.6 version, so I think I need a new environment to install the older version and be able to use both.
I have already tried to create a new environment for python 3.5:
!conda create -n py35 python=3.5 ipykernel
But after 30min I didn't obtain any response...
I have also followed the same procedure to install a package for python 2.7 (from marufr contributor), but I get the same problem creating an environment for python 2.7.
Note: I am working from Jupyter notebook on Windows (win-64) and using Anaconda.
Update:
Solution found here:
https://medium.com/towards-data-science/environment-management-with-conda-python-2-3-b9961a8a5097
Since there is no python-igraph for python 3.6 yet, I have to use an older version.
First, from Anaconda Prompt, install the nb_conda_kernels package before creating the new environment:
conda install nb_conda_kernels
Then, create the environment where I will work with the older python version:
conda create -n py35 python=3.5 ipykernel
Finally, install the package through the wheel (found here: http://www.lfd.uci.edu/~gohlke/pythonlibs/#python-igraph)
pip install python_igraph‑0.7.1.post6‑cp35‑none‑win_amd64.whl (You have to this command in the same folder that you donwloaded the wheel!)
There is a Windows installer for igraph‘s Python interface on the Python Package Index. Download the one that is suitable for your Python version (currently there are binary packages for Python 2.6, Python 2.7 and Python 3.2, though it might change in the future). To test the installed package, launch your favourite Python IDE and type the following:
import igraph.test
igraph.test.run_tests()
The above commands run the bundled test cases to ensure that everything is fine with your igraph installation.
Now, you can download 'python_geohash‑0.8.5‑cp36‑cp36m‑win_amd64.whl'.
Use the following command to install:
pip install python_geohash‑0.8.5‑cp36‑cp36m‑win_amd64.whl
Then you can use python-igraph in your Python3.6

How to install rst2man on windows

I am trying to install the rst2man client for windows after recieveing this message:
'rest2man' not found, man page not installed.
This is a prerequisite to install https://github.com/bluss/git-remote-gcrypt which I will install later.
The only solution I have found was for Linux:
http://phaseportrait.blogspot.ca/2009/07/installing-docutils-for-mercurial.html
Thanks!
MSYS2 (http://www.msys2.org/), both mingw32 and mingw64, have the docutils package, which contains rst2man. Both python2 and python3 versions are available.

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