helpneeded with samtools install - linking error libstdcxx-ng

[hardingnj]

Hi,

Just looking for some help installing a package that depends on libstdcxx-n

Running into a linking error when installing samtools. Might be as simple as not having a core package installed? Thanks!

 INFO resolvo::solver: ╤══ Install libstdcxx-ng=libstdcxx-ng=13.2.0=h7e041cc_3 at level 31 (required by krb5=krb5=1.17.2=h926e7f8_0)
 WARN rattler::package_cache: validation failed: failed to read 'index.json'
 WARN rattler::package_cache: validation failed: failed to read 'index.json'
 WARN rattler::package_cache: validation failed: failed to read 'index.json'
 WARN rattler::package_cache: validation failed: failed to read 'index.json'
 WARN rattler::package_cache: validation failed: failed to read 'index.json'
 WARN rattler::package_cache: validation failed: failed to read 'index.json'
  × failed to link 'lib/terminfo'
  ├─▶ could not open destination file for writing
  ╰─▶ Is a directory (os error 21)

pixi 0.10.0
pixi global install samtools -c bioconda -c conda-forge -vv

System is Ubuntu 20.04 5.15.0-91-generic

[hardingnj]

 pixi global install libstdcxx-ng -c conda-forge -c bioconda
  × could not find an executable entrypoint in package libstdcxx-ng 13.2.0 h7e041cc_3 from conda-forge, are you sure it exists?

[ruben-arts]

pixi global install currently isn't build to install libraries. That is why you'll get this error. If you want to have libc available you should do it from a pixi project.

[hardingnj]

ok- that's helpful thanks.

[wolfv]

Can you also add -c conda-forge ?

[hardingnj]

Thanks- not following: pixi global install samtools -c bioconda -c conda-forge -vv

Also contains -c conda-forge?

[wolfv]

Sorry, didn't read it properly on mobile. Will have to investigate more

[hadim]

I am having a similar error running pixi install into a dev containter:

$ pixi install
  × failed to link 'share/terminfo/2/2621A'
  ╰─▶ No such file or directory (os error 2)

[hadim]

Ok - that's annoying 😅

So there is no way I can make this work, I guess?

Without switching the macOS disks from APFS to APFS case-sensitive? Which is possible but requires a full reinstallation...

[wolfv]

We will have to fix this in a similar manner as we are working on fixing "clobbering" in rattler (conda/rattler#460)

[baszalmstra]

Im not sure if there is a proper way to fix this. The problem is with the following:

The package ncurses for linux-64 contains the following two files:

• share/terminfo/2/2621A
• share/terminfo/2/2621a

These are written to the cache which is stored in a macOS mounted volume. The mounted volume is case-insensitive which means these two files will clobber each other inside the cache. So the cache will contain either the first or the latter file, not both. You should be able to verify this by looking at the cache directory and finding the extracted ncurses package. Is there indeed only one file or is my reasoning wrong?

Anyway, the linux-64 based image expects a case-sensitive filesystem and thus expects both files to exist. When it's trying to hard-link the file it only finds one of the files which then results in the ╰─▶ No such file or directory (os error 2) error. This is a limitation of docker unfortunately.

Did you confirm that this does indeed work with conda/mamba? I'm very curious how they solved this issue because I think its an inherent problem with docker on macOS.

One way to work around this issue is to not store the cache on your local machine but instead store it in the image itself. By default the cache is stored in your user directory. What happens if you don't mount that part?

[baszalmstra]

I created a small PR in rattler to hopefully diagnose these things better: conda/rattler#461

[hadim]

I finally switched my macOS to case-sensitive. I did a few tests and can confirm that the issue occurs only when the pixi folder is mounted.

I am also not sure if this can be easily fixed since it seems to be a per-package situation and I can imagine some of them requiring case sensitivity.

Maybe the best fix would be to throw a meaningful error message: "your pixi folder seems to be case-insensitive while the package XXXX does not support case-insensitive partition"

[hardingnj]

Not sure I follow the link between my issue and @hadim 's?

I'm not running on macOS- and don't think my issue due to capitalization.

[hadim]

My bad, as I am not sure your issue is indeed related to mine.

[lucascolley]

I think we can close this? FWIW this works for me:

~/sandbox via 🧚 v0.50.2 
❯ pixi init pixi594; cd pixi594; pixi workspace channel add bioconda; pixi add -p linux-64 libstdcxx-ng
✔ Created /Users/lucascolley/sandbox/pixi594/pixi.toml
✔ Added bioconda (https://conda.anaconda.org/bioconda/)
✔ Added libstdcxx-ng >=15.1.0,<16
Added these only for platform(s): linux-64

please shout if you would still like some help @hardingnj !

EDIT: likewise for pixi global install samtools -c conda-forge -c bioconda on my Ubuntu box

[hardingnj]

Happy for it to be closed 🔒

Thanks for checking