Bioconda recipe for libstdc++

[vercah]

Hello!

I ran into some issues when installing Fulgor via Bioconda and running it on our HPC cluster - the binary fails to load with a list of missing libstdc++ symbols:

fulgor: /lib64/libstdc++.so.6: version GLIBCXX_3.4.30' not found (required by fulgor) fulgor: /lib64/libstdc++.so.6: version CXXABI_1.3.15' not found (required by fulgor)
fulgor: /lib64/libstdc++.so.6: version GLIBCXX_3.4.29' not found (required by fulgor) fulgor: /lib64/libstdc++.so.6: version GLIBCXX_3.4.22' not found (required by fulgor)
fulgor: /lib64/libstdc++.so.6: version CXXABI_1.3.9' not found (required by fulgor) fulgor: /lib64/libstdc++.so.6: version GLIBCXX_3.4.26' not found (required by fulgor)
fulgor: /lib64/libstdc++.so.6: version GLIBCXX_3.4.20' not found (required by fulgor) fulgor: /lib64/libstdc++.so.6: version GLIBCXX_3.4.21' not found (required by fulgor)
...

Eventually I fixed it on my side, but after consulting with @karel-brinda , it seems the solution differs across OSes, so it's likely something to address in the Fulgor Bioconda recipe. Would it be possible to handle it from your side?

My environment:
Fulgor: installed via Bioconda (version: 4.0.0)
Host OS: CentOS Linux, version 7 (Core)
Conda version 25.9.1

[karel-brinda]

To add more context, I believe that @vercah eventually solved it on her side by a combination of:

• conda install libstdcxx-ng (possible only on Linux IIUC)
• export LD_PRELOAD=$HOME/miniconda3/envs/ism/lib/libstdc++.so.6.0.34

[rob-p]

This is an unfortunate artifact of it being exceedingly difficult to statically link everything in C++ (especially libc).

I presume this isn't unique to Fulgor though, right? It seems like the appropriate libstdc++ isn't being found on the path in the remote machines. Is there a conda environment that is being activated on all of those machines before Fulgor is executed (something that, hopefully, should mimic the export that you describe above)? The need to install libstdcxx-ng explicitly is curious, and it's probably worth us looking to see if there's any way that we can force that easily on our end in the recipe. If it's a dependency, then it should be installed, and the bioconda builds should fail on the runners without it 🤔.

[vercah]

I actually think I didn't have to run conda install libstdcxx-ng (but not 100% sure). I fixed it permanently on my side with the following

mkdir -p $CONDA_PREFIX/etc/conda/activate.d
echo "export LD_PRELOAD=$CONDA_PREFIX/lib/libstdc++.so.6.0.34" \
  > $CONDA_PREFIX/etc/conda/activate.d/libstdcxx.sh

[Alessio-Campa]

Hi everyone,
I think this is probably related to a recent change in bioconda where stdlibc had to be included in the recipe requirements, but it could not compile because of an error on their side. I found a solution on another recipe having the same problem that was to temporarily add

  skip-lints:
    - compiler_needs_stdlib_c

to the recipe. I will try to remove it from the next build and see if it fixes the issue.