Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Bug on Mac #4

Open
sebel76 opened this issue Apr 29, 2022 · 1 comment
Open

Bug on Mac #4

sebel76 opened this issue Apr 29, 2022 · 1 comment

Comments

@sebel76
Copy link

sebel76 commented Apr 29, 2022

Hello,

I try to perform my transcript assembly on Mac. I installed Ryuto using Conda. The installed environment contain:

% mamba list -n ryuto

packages in environment at /Users/sbelanger/mambaforge/envs/ryuto:

Name Version Build Channel

boost-cpp 1.70.0 hef959ae_3 conda-forge
bzip2 1.0.8 h0d85af4_4 conda-forge
c-ares 1.18.1 h0d85af4_0 conda-forge
ca-certificates 2021.10.8 h033912b_0 conda-forge
htslib 1.10.2 h422799e_1 bioconda
icu 67.1 hb1e8313_0 conda-forge
krb5 1.19.3 hb98e516_0 conda-forge
libcurl 7.83.0 h23f1065_0 conda-forge
libcxx 13.0.1 hc203e6f_0 conda-forge
libdeflate 1.6 h0b31af3_0 conda-forge
libedit 3.1.20191231 h0678c8f_2 conda-forge
libev 4.33 haf1e3a3_1 conda-forge
libnghttp2 1.47.0 hca56917_0 conda-forge
libssh2 1.10.0 hd3787cc_2 conda-forge
libzlib 1.2.11 h6c3fc93_1014 conda-forge
llvm-openmp 14.0.0 ha654fa7_0 conda-forge
lz4-c 1.9.3 he49afe7_1 conda-forge
ncurses 6.3 h96cf925_1 conda-forge
openssl 3.0.2 h6c3fc93_1 conda-forge
ryuto 1.6.2 h72337ff_0 bioconda
xz 5.2.5 haf1e3a3_1 conda-forge
zlib 1.2.11 h6c3fc93_1014 conda-forge
zstd 1.4.9 h582d3a0_0 conda-forge

When I run the program, I got the following error message:

OMP: Info #276: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
libc++abi: terminating with uncaught exception of type boost::wrapexceptboost::bad_any_cast: boost::bad_any_cast: failed conversion using boost::any_cast

I could not solve the issue myself, please, can you help?

Best,
Sébastien

@TGatter
Copy link
Collaborator

TGatter commented Apr 30, 2022

This error seems to be caused by a build incompatibility of the Conda system.
It appears that a feature used by Ryuto was deprecated in the newest version of OMP.
The Clang compiler on Mac Systems is usually fairly strict and aborts the compilation despite the fact it would work ok.

There is no trivial way around this using Conda. I can try and test if I can replicate this error on their testbuild-servers, but it is likely I can't.

I would recommend you try to compile the program yourself instead. Please follow the instruction on the main page of the tool.
I don't have a mac-computer myself to compile a standalone binary for it sadly. I'll try and ask around if I can find a machine.
If you are working on a new machine with the M1 chips I am unsure if this can compile well at all.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants