clipper -h fails after clean install

[MattBrauer]

Matplotlib is building the font cache; this may take a moment.
Traceback (most recent call last):
  File "/opt/anaconda3/bin/clipper", line 5, in <module>
    from clipper.src.main import call_main
  File "/Users/mbrauer/maze/clipper/clipper/src/main.py", line 16, in <module>
    from clipper.src.call_peak import call_peaks
  File "/Users/mbrauer/maze/clipper/clipper/src/call_peak.py", line 28, in <module>
    from clipper.src.peaks import shuffle, find_sections
ImportError: dlopen(/Users/mbrauer/maze/clipper/clipper/src/peaks.so, 2): no suitable image found.  Did find:
	/Users/mbrauer/maze/clipper/clipper/src/peaks.so: unknown file type, first eight bytes: 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00
	/Users/mbrauer/maze/clipper/clipper/src/peaks.so: unknown file type, first eight bytes: 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00

macos 10.15.6
Python 3.7.6

[MattBrauer]

It looks like peaks.so is architecture-dependent compiled code, which makes the application non-portable.

Can you include a makefile and the build process in the install procedure?

[algaebrown]

@mlovci @gpratt I googled a bit and it seems .so files are executable files built from .c. Correct me if I am wrong. I wonder do you have the original code? Thanks!

[gpratt]

I build this some files from cython. Its fallen out of vogue now, but it was how I got some important speed increases. Gabriel Pratt

…

On Fri, Jan 22, 2021 at 6:27 PM Hsuan-lin Her ***@***.***> wrote: @mlovci <https://github.com/mlovci> @gpratt <https://github.com/gpratt> I googled a bit and it seems .so files are executable files built from .c. Correct me if I am wrong. I wonder do you have the original code? Thanks! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#86 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJVIW2PAJAMEVEB3Q2C3WDS3IXYDANCNFSM4R7FEPZA> .

[algaebrown]

Which Cython file is it from? Is it from peaksmodule.cc? And how can I make it platform compatible?

thank you so much!

[gpratt]

yup, As for how to make it platform compatible, I've got no idea. Honestly you may have to re-write that code, not entirely sure how to fix it these days. Gabriel Pratt

…

On Fri, Jan 22, 2021 at 6:36 PM Hsuan-lin Her ***@***.***> wrote: Which Cython file is it from? Is it from peaksmodule.cc? And how can I make it platform compatible? thank you so much! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#86 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJVIW4OOYZCPX4Z2T6Z23LS3IY33ANCNFSM4R7FEPZA> .

[bakerwm]

Which Cython file is it from? Is it from peaksmodule.cc? And how can I make it platform compatible?

thank you so much!

The file peaks.so might not work with python3.x; (I cannot run the latest version clipper v2.1.0, on Ubuntu 18.04, Python 3.8)

$ cd clipper/src
$ python2
Python 2.7.18 (default, Mar  8 2021, 13:02:45)
[GCC 9.3.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import peaks
>>> dir(peaks)
['__doc__', '__file__', '__name__', '__package__', 'find_sections', 'readsToWiggle_pysam', 'shuffle']

$ python3
Python 3.8.5 (default, Jan 27 2021, 15:41:15)
[GCC 9.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import peaks
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: dynamic module does not define module export function (PyInit_peaks)