ELF load command address/offset not properly aligned

[lainiwa]

I am trying to debianize a python package, containing a few non pure-python libraries. I was excluding them in the debian/rules:

override_dh_shlibdeps:
	dh_shlibdeps -X/x86/ -X/numpy/.libs -X/cv2/.libs -X/PIL/.libs

up until dpkg-buildpackage was able to create a .deb file.

However, after installation, calling the package's entry point results in an error:

Traceback (most recent call last):
  [ ... ]
    import cv2
  File "/opt/venvs/py3software/lib/python3.6/site-packages/cv2/__init__.py", line 3, in <module>
    from .cv2 import *
ImportError: /opt/venvs/py3software/lib/python3.6/site-packages/cv2/cv2.cpython-36m-x86_64-linux-gnu.so: ELF load command address/offset not properly aligned.

I have read through this numpy issue mentioning similar problem, but I am still very lost.

Am I doing it the wrong way?

[Jürgen Hermann]

The other problem (mentioned in docs) is stripping. Also, layout seems to have changes (no .libs).

For working code, see https://github.com/1and1/debianized-jupyterhub/blob/master/debian/rules#L47-L54

If that fixes your build, please close.

[lainiwa]

I tried this (copied override_dh_strip from the file you linked and changed the layout to have no .libs), but unfortunately this does not seem to change anything.

[Jürgen Hermann]

You have to list YOUR deps of course, in this case /cv2.

[lainiwa]

Yes, of course I listed it:

override_dh_shlibdeps:
	dh_shlibdeps -X/x86/ -X/numpy/ -X/cv2/ -X/PIL/

I mean, the package creation works just fine. The error fires when I try to execute a python script (an entrypoint) it provides.

I created a minimal python package, in case you might want to reproduce the error: https://github.com/lainiwa/py3software.

[Jürgen Hermann]

The problem is that you still strip certain libs, destroying them in the process.

[lainiwa]

I think @nailor wrongly referenced this thread, as the problem I am experiencing here is unlikely to be a consequence of what is discussed in that issue.
I am having virtualenv==15.1.0 and when .deb installed, it does not create self-referencing links:

root@93961807e1d7:/app# ls -l /opt/venvs/py3software/lib/python3.6/importlib/abc.py                                                                                                           
-rw-r--r-- 1 root root 10782 Oct 22 11:32 /opt/venvs/py3software/lib/python3.6/importlib/abc.py                                                                                               
root@93961807e1d7:/app# ls -l /usr/lib/python3.6/importlib/abc.py                                                                                                                             
-rw-r--r-- 1 root root 10782 Oct 22 11:32 /usr/lib/python3.6/importlib/abc.py

Should it be "#274 and #275" instead?

[lainiwa]

The problem is that your strip certain libs, destroying them in the process.

Am I right that it is a bug of some sort, and this behavior is not intended?

Otherwise, could you suggest some workaround/right way to install C-written libs? I saw debianized-jupyterhub and it looks like the only thing you do with those "problematic" dependencies is excluding them in override_dh_shlibdeps section of debian/rules.

I thought about listing those libs as apt-get'able dependencies. The problem is I can probably do this with opencv but not with dlib.

[silvanbrummen]

Hi lainiwa,

I'm currently experiencing the same issue when packaging python packages. Did you manage to solve this in the end?

Cheers,
Sil

[Jürgen Hermann]

The problem is recognizing the difference between ´shlibdeps´ and ´strip´.

[lainiwa]

Hi lainiwa,

I'm currently experiencing the same issue when packaging python packages. Did you manage to solve this in the end?

Cheers,
Sil

Unfortunately, no. I failed this.

[Sebastien Leger]

Hey, dh-virtualenv is an awesome tool. I believe you will find the answer to ELF question in the Loud ML repository: https://github.com/regel/loudml

See in file debian/rules how dh_strip is used.

If you get the ELF load error again then add extra --exclude in dh_strip as needed. Repeat this process until the ELF errors are gone and you will have a working package.

It worked for me with trial and error, but it worked. Having a CI test in place is probably a good idea to test it repeatedly and make sure it does not break.

If it helps, please give a star to the Loud ML repo!

[Joe Mullally]

Try this:

override_dh_strip:
	dh_strip --exclude=/site-packages/

override_dh_shlibdeps:
	dh_shlibdeps --exclude=/site-packages/

Not sure if its correct, but it seems to work OK for me. I sent in a PR to include in the docs.

[Jyrki Pulliainen]

Looks like there is a fix for the issue, closing the issue