./install.sh error: undefined reference

[JuliaLopezDelgado]

Hello. When running ./install.sh I get a very long message, ending with:
collect2: error: ld returned 1 exit status make: *** [CONSENT-correction] Error 1

When tracing through it, the message includes the following several times:
DBG.cpp:(.text+0x78d): undefined reference to str2num correctionDBG.cpp:(.text+0xc04): undefined reference to str2num

I downloaded the latest version of Consent, and have Python v. 3.8.2 and Gcc v.8.3.0
What could be causing this issue? Thanks in advance

[morispi]

Hello,

This is a weird error indeed. I haven't been able to reproduce it in any of my computers.
Just tested right now on a computer with no prior installation of any bioinformatics tool, which had G++ 5.4, and it worked well.

What is your g++ version?

Cheers,
Pierre

[JuliaLopezDelgado]

Hello,

Thanks for your reply.

The default version in is g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-36). But I switched it to version 8.3.0 by typing: module switch intel gnu/8.3.0.
Is there anything else I could do?

Cheers.

[morispi]

Hi,

If your g++ version is up to date, then maybe it has to do with CONSENT's submodules, I believe BMEAN in particular. Is the BMEAN folder inside of your CONSENT folder empty? If so, that should be the error.

Did you clone the CONSENT repo with git clone --recursive https://github.com/morispi/CONSENT? This should take care of the submodules so you don't have to do it manually.

If you didn't clone like so, can you try, and then attempt to build again?

Cheers,
Pierre

[morispi]

Oops, misclicked on close and comment. Reopened the issue, my bad.
Tell me if anything else goes wrong.

[JuliaLopezDelgado]

Hi,

The BMEAN folder wasn't empty and I had downloaded the repo using that code, but it still wasn't working. So I removed the entire folder and made sure to switch to the 8.3 g++ version before downloading the repo again, and the installation now seems to have worked.

When running CONSENT-correct, I am getting the following error though:
/home/bin/CONSENT/CONSENT-correct: line 183: minimap2: command not found
Could this mean there is still an error with the installation?

Thanks for your help.

[morispi]

This simply means that minimap2 is not in your PATH.

Try adding it by doing PATH=/path/to/CONSENT/minimap2/:$PATH and rerun. You can add that line to your ~/.bashrc if you do not wish to readd it to your PATH each time you runCONSENT.

This should take care of this last error :)

Tell me if you need anything else.

Cheers,
Pierre

[JuliaLopezDelgado]

Perfect, I added the path to minimap2 and the previous error hasn't showed up again. It seems to be working fine.

Thanks for your help!