RuntimeWarning: pysam.libcalignedsegment.PileupColumn size changed, may indicate binary incompatibility. Expected 72 from C header, got 88 from PyObject

[Nilad]

Same issue than #105

I install pysamstats on Singularity container.
I tried multiples version of pysamstats, cython, pysam with pip and with conda without succes.

Here my last try, if you can help me on that point.

INSTALL

python3 -m pip install --no-cache-dir pysamstats
Collecting pysamstats
  Downloading pysamstats-1.1.2.tar.gz (251 kB)
     |################################| 251 kB 3.1 MB/s 
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
    Preparing wheel metadata ... done
Collecting pysam<0.16
  Downloading pysam-0.15.4-cp36-cp36m-manylinux2010_x86_64.whl (10.7 MB)
     |################################| 10.7 MB 4.9 MB/s 
Requirement already satisfied: numpy in /usr/lib/python3/dist-packages (from pysamstats) (1.13.3)
Building wheels for collected packages: pysamstats
  Building wheel for pysamstats (PEP 517) ... done
  Created wheel for pysamstats: filename=pysamstats-1.1.2-cp36-cp36m-linux_x86_64.whl size=943862 sha256=9a34d1ddfaf42590a2a5d7a6eec221a66e9f0daadf0b825d4e9639201bde054a
  Stored in directory: /tmp/pip-ephem-wheel-cache-yht4rllm/wheels/3b/dd/a8/4e343b4884ef154f6e5e695ce7aec996ab25ed54def89dd3a5
Successfully built pysamstats
Installing collected packages: pysam, pysamstats
Successfully installed pysam-0.15.4 pysamstats-1.1.2

RUN

Python 3.6.9 (default, Oct  8 2020, 12:12:24) 
[GCC 8.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pysam
>>> pysam.__version__
'0.15.4'
>>> import pysamstats
/usr/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: pysam.libcalignedsegment.PileupColumn size changed, may indicate binary incompatibility. Expected 72 from C header, got 88 from PyObject
  return f(*args, **kwds)
>>> pysamstats.__version__
'1.1.2'

[marade]

I added comments #105 as well. Clearly it's still an issue.

[stewalsh04]

Has this problem been resolved yet? I am having the same issue when trying to get pysamstats running in a container?

[fedarko]

For other people encountering this, installing pysam and pysamstats through bioconda (rather than pip) seems to get rid of the warning. Here is a small set of commands that demonstrates this in a fresh conda environment on an Ubuntu system:

> conda create -n psswarntest python=3.7
> conda activate psswarntest
> # Demonstrate that pip installation causes the warning to show up
> pip install "pysam < 0.16" pysamstats
> python3
>>> import pysam
>>> import pysamstats
_frozen_importlib:219: RuntimeWarning: pysam.libcalignedsegment.PileupColumn size changed, may indicate binary incompatibility. Expected 72 from C header, got 88 from PyObject
>>> quit()
> # Demonstrate how to get rid of the warning using bioconda
> pip uninstall pysam
> pip uninstall pysamstats
> conda install -c bioconda "pysam < 0.16" pysamstats
> python3
>>> import pysam
>>> import pysamstats
>>> # No warning!