Cannot install pycoQC on Ubuntu 20.04.1 LTS

[michielmuliergithub]

1. Bug description

Installing pycoQC on my new Ubuntu 20.04.1 LTS system fails. I'll go through the steps I took and elaborate on the failure in the end.

First I install some software that pycoQC apparently needs:

$ sudo apt-get install libbz2-dev
$ sudo apt-get install liblzma-dev
$ sudo apt-get install libblas-dev
$ sudo apt-get install liblapack-dev

Next I install all the required python packages:

$ sudo pip3 install numpy
$ sudo pip3 install pandas
$ sudo pip3 install pysam
$ sudo pip3 install scipy

Finally, I issue the command to install pycoQC:

$ sudo pip3 install pycoQC

I get a lot of output, with the following error lines:

[..]
Building wheel for pandas (setup.py) ... error
[..]
Building wheel for numpy (setup.py) ... error
[..]
Building wheel for pysam (setup.py) ... error
[..]
Building wheel for scipy (PEP 517) ... error
[..]
Failed to build pandas numpy pysam scipy

2. What I've tried

Ubuntu 20.04.1 LTS natively has Python 3.8. I was worried that pycoQC might not yet be tested on such a recent Python version, leading to the failure. Therefore, I installed a Python 3.6.0 virtual environment to try the pycoQC installation again. Unfortunately, this didn't help.

3. Console output

When trying the second time (with Python 3.6.0) I logged all the console output to a file:

error_output.txt

Please check this error output. Hopefully it helps to fix the installation bug.

[a-slide]

Hi @michielmuliergithub, You should not need to install any dependencies if you use pip or conda. Can you just try pip install pycoQC==2.5.0.23 in a fresh python3.6 virtual environment ? What sort of virtual env manager do you use ?

[michielmuliergithub]

Hi @a-slide , Thank you very much. It worked!

I first installed Miniconda (see https://docs.conda.io). Then I issued the following commands:

$ conda create -n pycoQC python=3.6
$ conda activate pycoQC
$ conda install -c bioconda pycoqc
$ pycoQC --version
    pycoQC v2.2.3

Thank you very much! Kind regards, Michiel Mulier

[a-slide]

Great By default the bioconda version is installed, but it is quite outdated. To get the last stable version use my personal channel instead

conda install -c aleg pycoqc=2.5.0.23

[nbeckloff]

piperror.txt Hi @a-slide , I tried to install pycoQC 2.5.0.23 using both the conda and pip commands above but both produced errors. When using the conda command above I received this error: Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: - Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

and when trying the PIP installer I received errors in the txt (piperror.txt).

I'm running Ubuntu 20 on a WLS. piperror.txt

Thanks in advance, cheers, Nick

[a-slide]

Hi @nbeckloff, Have you tried to install the package in a virtual environment as recommended in the documentation?

conda create -n pycoQC python=3.6
conda activate pycoQC
conda install -c aleg pycoqc=2.5.0.23

[nbeckloff]

Hi @a-slide, Ultimately, I was able to get it installed, there was an errant dependency issue that I had to fix manually. Thanks for your help and great program!

cheers, Nick

[michielmuliergithub]

Thank you very much

It worked to install pycoQC

Michiel Mulier

Op zo 8 nov. 2020 om 16:26 schreef Adrien Leger notifications@github.com:

Hi @michielmuliergithub https://github.com/michielmuliergithub, You should not need to install any dependencies if you use pip or conda. Can you just try pip install pycoQC==2.5.0.23 in a fresh python3.6 virtual environment ? What sort of virtual env manager do you use ?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/a-slide/pycoQC/issues/123#issuecomment-723592796, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEJZDCMPPULTHOTEBIIJ6CDSO22EFANCNFSM4TOK4QZQ .