Installation issues

[AntonPetrov]

When I run cargo build I get the same error as described in https://github.com/ViennaRNA/ViennaRNA/issues/215. What is the suggested workaround? Is it okay to downgrade to ViennaRNA 2.5.x or is there another way?

[dincarnato]

Hi Anton,

we are awaiting for the ViennaRNA team to fix this. In the meantime, yes, either use Vienna 2.5.x, or manually amend the RNAlib to add the parameter -lgomp.

Please let me know if this fixes!

Cheers, Danny

[dincarnato]

@AntonPetrov,

one note: keep in mind that ViennaRNA is only used for evaluating the consensus folding of the aligned matches, but it is not necessary for the SHAPEwarp search itself.

[AntonPetrov]

@dincarnato Thank you for a quick response Danny!

we are awaiting for the ViennaRNA team to fix this.

I can raise this with ViennaRNA folks when I see them in Benasque.

In the meantime, yes, either use Vienna 2.5.x, or manually amend the RNAlib to add the parameter -lgomp.

I installed it using Vienna 2.5.1 but had to use the --without-python flag because it complained about circular imports in Python bindings (cannot import name '_RNA' from partially initialized module 'RNA').

SHAPEwarp compiled in the end but there seem to be many undocumented dependencies, like gfortran for example. I might send a pull request with a Dockerfile for SHAPEwarp, as it would provide a useful starting point for new users and would increase reproducibility.

[dincarnato]

Ok, althought SHAPEwarp does not use Python, so those issues are all ViennaRNA-related.

[RaumZeit]

Hi all,

so I just commented on a related issue here: https://github.com/fncnt/librna-sys/issues/3#issuecomment-2247919017

So, I'm just wondering whether adding

cargo:rustc-link-lib=gomp

to the build.rs file would already solve the problem.

Cheers, Ronny