Open AntonPetrov opened 1 month ago
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
@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.
@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.
Ok, althought SHAPEwarp does not use Python, so those issues are all ViennaRNA-related.
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
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?