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Errors During make #69

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robin-sto opened this issue Nov 28, 2023 · 7 comments
Open

Errors During make #69

robin-sto opened this issue Nov 28, 2023 · 7 comments

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

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

@andrewdavidsmith
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Great! Thanks for the tip @stooz5

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