Illegal instruction with no arguments

[fgvieira]

Describe the bug I getting an error without any providing options:

$ sortmerna -h
Illegal instruction (core dumped)

To Reproduce

1. install with conda
2. run sortmerna -h

Expected behavior Help message

Desktop (please complete the following information):

• OS: RedHat
• Version: v4.3.7

Additional context

Installed with conda:

  Name              Version    Build               Channel    
────────────────────────────────────────────────────────────────
  _libgcc_mutex     0.1        conda_forge         conda-forge
  _openmp_mutex     4.5        2_gnu               conda-forge
  bzip2             1.0.8      h4bc722e_7          conda-forge
  ca-certificates   2025.1.31  hbcca054_0          conda-forge
  ld_impl_linux-64  2.43       h712a8e2_2          conda-forge
  libexpat          2.6.4      h5888daf_0          conda-forge
  libffi            3.4.2      h7f98852_5          conda-forge
  libgcc            14.2.0     h77fa898_1          conda-forge
  libgcc-ng         14.2.0     h69a702a_1          conda-forge
  libgomp           14.2.0     h77fa898_1          conda-forge
  liblzma           5.6.3      hb9d3cd8_1          conda-forge
  libnsl            2.0.1      hd590300_0          conda-forge
  libsqlite         3.48.0     hee588c1_1          conda-forge
  libstdcxx         14.2.0     hc0a3c3a_1          conda-forge
  libstdcxx-ng      14.2.0     h4852527_1          conda-forge
  libuuid           2.38.1     h0b41bf4_0          conda-forge
  libxcrypt         4.4.36     hd590300_1          conda-forge
  libzlib           1.3.1      hb9d3cd8_2          conda-forge
  ncurses           6.5        h2d0b736_3          conda-forge
  openssl           3.4.0      h7b32b05_1          conda-forge
  pip               25.0       pyh8b19718_0        conda-forge
  python            3.12.8     h9e4cc4f_1_cpython  conda-forge
  python_abi        3.12       5_cp312             conda-forge
  readline          8.2        h8228510_1          conda-forge
  setuptools        75.8.0     pyhff2d567_0        conda-forge
  sortmerna         4.3.7      py312h8ced662_0     conda-forge
  tk                8.6.13     noxft_h4845f30_101  conda-forge
  tzdata            2025a      h78e105d_0          conda-forge
  wheel             0.45.1     pyhd8ed1ab_1        conda-forge

[biocodz]

Yeah, something is wrong with that conda build. I'm looking into this.

[ck-theory-sc]

Can confirm that I also ran into this issue on 4.3.7 where the conda env ran on some systems but not on others. Using 4.3.6 resolved the issue with successful execution on all systems.

[koriege]

I did not test if this might be caused by not using gcc 11.4 when building the conda package, although specified in conda_build_config.yaml. however, I solved this issue by building it manually. please note, that I had to also resolve jinja2 functions c_stdlib and compiler by adding missing info to conda_build_config.yaml

conda env create -n sortmerna
conda install -n sortmerna conda-build cc_linux-64=11.4 gxx_linux-64=11.4 glib pkg-config cmake pyyaml jinja2 requests ninja
git clone https://github.com/conda-forge/sortmerna-feedstock
cd sortmerna-feedstock
cat <<-EOF >> recipe/conda_build_config.yaml
# resolve jinja2 functions
c_stdlib:
  - sysroot
c_compiler:
  - gcc
cxx_compiler:
  - gxx
EOF
conda activate sortmerna
conda build --no-anaconda-upload recipes
conda install <path/to/conda>/envs/sortmerna/conda-bld/linux-64/sortmerna-4.3.7*.conda

[biocodz]

thanks @koriege. Yep, I also had no problems with local conda builds. Going to add the conda installer built outside the official conda build environment to the release artifacts.

[pinin4fjords]

@biocodz I'm encountering this issue as well.

A colleague of mine managed to package 4.3.7 in a manner that doesn't have this problem (see https://anaconda.org/seqera/sortmerna/files](https://anaconda.org/seqera/sortmerna). I don't know enough to make sense of what the key difference is between that and the conda-forge build, but maybe you do?

Edit: maybe this would do it? https://github.com/conda-forge/sortmerna-feedstock/pull/3

[biocodz]

merged the PR. Let's hope it will fix the problem

[pinin4fjords]

My initial testing at least suggests we're good!

[pinin4fjords]

Further testing confirmed. I think you can close this.

Just trying to get the ARM build going though- could you help @biocodz ? https://github.com/conda-forge/sortmerna-feedstock/pull/4

[biocodz]

sure, i'll have a look over the weekend

[fgvieira]

It seems to have been fixed!

[biocodz]

I'm glad the fix worked (salutations to @pinin4fjords). That fix would be hard to figure out without knowing the intimate details of the conda build system. Hopefully the fix will work for most folks. On my particular machine I still see the illegal instruction error though, so leaving this open for the time being.

[alansill]

This problem is still occurring in the bioconda and conda-forge versions of sortmerna. Is a fix available?

[biocodz]

Tested the latest available on conda-forge OK

cat /etc/os-release
PRETTY_NAME="Ubuntu 24.04.2 LTS"
VERSION="24.04.2 LTS (Noble Numbat)"

conda install sortmerna
conda list sortmerna
# Name                     Version          Build            Channel
sortmerna                  4.3.7            py313h71a826f_2  conda-forge

sortmerna --version
SortMeRNA version 4.3.7
Build Date: Sep  5 2025
sortmerna_build_git_sha:@0@
sortmerna_build_git_date:@2025/09/05 10:43:51@