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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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PennCNV error #54

Closed hui-1 closed 4 years ago

hui-1 commented 4 years ago

Hello, i first time use penncnv, I have some problems, no matter what version of perl installing, the detect_cnv.pl can't work. error information as following: PennCNV error: Can't load './kext/5.8.8/x86_64-linux/khmm.so' for module khmm: ./kext/5.8.8/x86_64-linux/khmm.so: undefined symbol: PL_thr_key at /home/my/perl5/perlbrew/perls/perl-5.8.8-PIC/lib/5.8.8/x86_64-linux/DynaLoader.pm line 230. at kext/khmm.pm line 11 Compilation failed in require at detect_cnv.pl line 10. PennCNV compilation error: Please download source code from http://www.openbioinformatics.org/penncnv/ and compile executable program. how can i do? thanks and hope for your reply! sincerely

nikmanadli commented 4 years ago

I had this issue before. If I can remember correctly, what I did were 1) I downloaded the source code again, 2) recompile them, and then 3) I sudo apt-get install libperl-dev. If I'm not mistaken my issue was that the perl version I had was the updated version, but detect_cnv.pl kind of need the previous versions to execute it. You can also use perlbrew to go back to previous versions I think. Hope this helps.

hui-1 commented 4 years ago

I had this issue before. If I can remember correctly, what I did were 1) I downloaded the source code again, 2) recompile them, and then 3) I sudo apt-get install libperl-dev. If I'm not mistaken my issue was that the perl version I had was the updated version, but detect_cnv.pl kind of need the previous versions to execute it. You can also use perlbrew to go back to previous versions I think. Hope this helps.

Thanks for your help. I have solved it.

kaichop commented 4 years ago

Thank you @nikmanadli !

nikmanadli commented 4 years ago

Thank you @nikmanadli ! @kaichop

Hi Dr Kai Wang, can you please help me in addressing an issue I raised last week? the link is here: https://github.com/WGLab/PennCNV/issues/55

Please I really need to solve it quick...thank you.