search

statgen / swiss

Software to help identify overlap between association scan results and GWAS hit catalogs.
Other
13 stars 5 forks source link

UCS2 vs UCS4 #13

Open ariza-droid opened 4 years ago

ariza-droid commented 4 years ago

Problem description

Compiler problem. UCS2 vs UCS4

Program output

swiss --version Traceback (most recent call last): File "~/.local/bin/swiss", line 18, in from swiss.main import main File "~/.local/lib/python2.7/site-packages/swiss/main.py", line 40, in from LDClumper import File "~/.local/lib/python2.7/site-packages/swiss/LDClumper.py", line 20, in from AssocResults import File "~/.local/lib/python2.7/site-packages/swiss/AssocResults.py", line 23, in from bx.intervals.intersection import File "~/.local/lib/python2.7/site-packages/bx/intervals/init.py", line 7, in from bx.intervals.intersection import # noqa: F40 ImportError: ~/.local/lib/python2.7/site-packages/bx/intervals/intersection.so: undefined symbol: PyUnicodeUCS2_FromStringAndSize

python Python 2.7.18rc1 (default, Apr 7 2020, 12:05:55) [GCC 9.3.0] on linux2 Type "help", "copyright", "credits" or "license" for more information.

import sys print sys.maxunicode 1114111 quit() Which shows I am using UCS4

Would you kindly be able to suggest approaches to sort this out, please?

welchr commented 4 years ago

Seems similar to this: https://stackoverflow.com/questions/11878666/python-undefined-symbol-pyunicodeucs2-decodeutf8

Are you running multiple installations of python on the same system? Try which -a python and which -a python2 to see how many python interpreters are on your PATH.

You'll want to ensure you are installing/compiling the package and running it with the exact same python.

ariza-droid commented 4 years ago

May have rushed to conclusions. At the time, indeed, the system I was trying swiss on had both python3 (since it comes with Ubuntu 20) and python2 installed, with alternatives set and priority set to python2.

Regardless, I tried a fresh start on a new virtual machine (for sudo privileges), used snapshots to change several times the order in which I installed/compiled several of the software/dependencies/compilers, gcc etc. All of this to say it worked and I have no idea what was significantly different this time. I will not dwell any more on this, but get on to making the machine work for me, rather than the reverse. All not before thanking you for your prompt response and help with troubleshooting. Last but not least, thank you and your team for developing these tools, as well as making them available!

Best wishes, Anca Riza

On Tue, Jul 28, 2020 at 6:14 PM Ryan Welch notifications@github.com wrote:

Seems similar to this: https://stackoverflow.com/questions/11878666/python-undefined-symbol-pyunicodeucs2-decodeutf8

Are you running multiple installations of python on the same system? Try which -a python and which -a python2 to see how many python interpreters are on your PATH.

You'll want to ensure you are installing/compiling the package and running it with the exact same python.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/statgen/swiss/issues/13#issuecomment-665100665, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQNDSQ2G42WGMGQFINEML3LR53TNRANCNFSM4PKMLTIA .