undefined symbol when I ran MutSig2CV on Linux.

[liux2250]

Hi,

I downloaded MutSig2CV and installed Matlab Runtime R2013a. When I tried to run MutSig2CV, I got the following error. ./MutSig2CV: symbol lookup error: ./MutSig2CV: undefined symbol: _Z14standaloneMainRKSt6vectorISsSaISsEEbb

I have already set the LD_LIBRARY_PATH before I ran it.

Did anyone encounter this error before? If so, could you give me some guidance about how to address this issue? Thanks in advance.

Best, Yang

[julianhess]

Hi Yang,

What operating system are you running?

[liux2250]

Hi, Thanks for your prompt response!

I ran it on our HPC server. The system is running Redhat Enterprise Linux. The Linux version is: Linux 3.10.0-1160.15.2.el7.x86_64 #1 SMP Thu Jan 21 16:15:07 EST 2021 x86_64 x86_64 x86_64 GNU/Linux

Best, Yang

[liux2250]

Hi,

I ran it on my computer with Ubuntu Linux and it works. I think MutSig2CV maybe need to be recompiled on Redhat Enterprise Linux.

Best, Yang

[julianhess]

It's possible that the precompiled C/C++ .mex files are binary incompatible with RHEL. If you have access to the MATLAB compiler on your HPC cluster, try recompiling those files with mex and then rebuilding the MutSig executable with mcc -m -I src -d bin -o MutSig2CV src/MutSig2CV.

The C/C++ files that need to be rebuilt are:

• https://github.com/getzlab/MutSig2CV/blob/master/src/count_overlaps_fast2.c
• https://github.com/getzlab/MutSig2CV/blob/master/src/hist2d_fast.c
• https://github.com/getzlab/MutSig2CV/blob/master/src/projection_1d_convolutions_fast.c
• https://github.com/getzlab/MutSig2CV/blob/master/src/str2doubleq.cpp

[liux2250]

Hi Julianhess,

This problem was solved by recompiling those files. Thank you for your response. I really appreciate.

Best

[julianhess]

Great, glad that worked!