Errors During make

[robin-sto]

Hello,

I am trying to run a make and am getting errors regarding regex (errors attached). Could you please review and let me know what could be the issue?

Thank you. preseq.txt

[andrewdavidsmith]

Your specific compiler version has a bug for the regex library. Try anything more recent among gcc compilers.

[robin-sto]

Thank you. I was able to compile using gcc 9.3.0. However, when I try to run it, I get an error with glibcxx:

preseq -h preseq: /lib64/libstdc++.so.6: version GLIBCXX_3.4.20' not found (required by preseq) preseq: /lib64/libstdc++.so.6: version GLIBCXX_3.4.26' not found (required by preseq) preseq: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by preseq)

[andrewdavidsmith]

That's due to a mismatch in the environment likely caused by an incomplete installation or configuration of the new compiler. Are you administering your system? If so, I can probably give pointers. If not, you'd have to take it up with your admin.

[robin-sto]

Yes, I am the admin. We have an HPC cluster and I configured preseq as an R module which calls the binary. We can normally configure binaries this way.

[andrewdavidsmith]

In that case I suggest fully removing all c compilers you are able to, and then reinstalling the one you are using (should be gcc 5.3 or later I think; I use 13 currently). This is the simplest If you can do it. Otherwise we will need to adjust paths.

[robin-sto]

thanks, I added module load gcc/9.3.0 in the R tcl file and it works fine now. You can close this.

[andrewdavidsmith]

Great! Thanks for the tip @stooz5