Fix broken micromamba FHS environment

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1

Hello!

For about a month I have been using the same shell.nix file (below) to run micromamba in an FHS environment on NixOS. It is based off the script given in the Python wiki pages, but I added that targetpkgs line to allow python to interface with R.

with import <nixpkgs> {}; (pkgs.buildFHSUserEnv { name = "fhs";
          profile = ''
                set -e
                eval "$(micromamba shell hook -s bash)"
                micromamba activate betaspiral
                set +e
  
              '';
      targetPkgs = pkgs: (builtins.concatLists [ [ micromamba ] [] [pkgs.which]]);
}).env

It was working great but starting this week, when I run nix-shell it fails on building libyaml. Here is the error in full:

 
 applying patch /nix/store/1jdigwdc9g4gg9k0dnwakpd851k9xcps-libyaml-cpp-Fix-pc-paths-for-absolute-GNUInstallDirs.patchj
 can't find file to patch at input line 3
 Perhaps you used the wrong -p or --strip option?
 The text leading up to this was:
 --------------------------
 |--- a/yaml-cpp.pc.in
 |+++ b/yaml-cpp.pc.in
 --------------------------
 File to patch: 
 Skip this patch? [y] 
 Skipping patch.
 1 out of 1 hunk ignored
 error: builder for '/nix/store/0ryh5fz3yvs8s56dc1kfifnfrry8i67w-libyaml-cpp-0.6.3.drv' failed with exit code 1;
        last 10 log lines:
        > Perhaps you used the wrong -p or --strip option?
        > The text leading up to this was:
        > --------------------------
        > |--- a/yaml-cpp.pc.in
        > |+++ b/yaml-cpp.pc.in
        > --------------------------
        > File to patch:
        > Skip this patch? [y]
        > Skipping patch.
        > 1 out of 1 hunk ignored
        For full logs, run 'nix log /nix/store/0ryh5fz3yvs8s56dc1kfifnfrry8i67w-libyaml-cpp-0.6.3.drv'.
error: 1 dependencies of derivation '/nix/store/5hiw1ipv6is5j02w8sxx4qqmjazg8f0j-micromamba-0.15.0.drv' failed to build
error: 1 dependencies of derivation '/nix/store/4hkql9p4myhp4dyxxr9vxp7n1wmya8gd-fhs-usr-target.drv' failed to build
error: 1 dependencies of derivation '/nix/store/c1pzs0mc5hl7cs0m1lf4yi4qv1l505mn-fhs-fhs.drv' failed to build
error: 1 dependencies of derivation '/nix/store/x6v6nk3w7cpq7mjl1hjgwxdg3j0vb2s6-fhs-init.drv' failed to build

I was wondering how I could fix/get around this error. I am very new to Nix so any help would be greatly appreciated.

Thank you!

Garrett

2

your not pinning your script, so as your nixpkgs channel advances, so does everything else.

if you can find out a pervious commit of nixpkgs that worked, you should be able to rewind to a time that it worked, it’s not a fix but will get you up and running.

you can read all about it here in this excellent post.

https://nix.dev/tutorials/towards-reproducibility-pinning-nixpkgs

1 Like
3

Thank you so much! By pinning the script I was able to get back into a working state.

Thanks again,

Garrett

1 Like
4

Hi, I’m the maintainer of the package for micromamba. It looks like someone changed libyamlcpp in some way that broke micromamba. I guess I’ll run a bisect later.
In the meatime pin it to 799908d71c4b74c7d0e753c3860f4686790eddc8 , that definitely works.
Definitely pin as much as you can, as nixinator says :slight_smile:

5

Fixed in micromamba: fix libyamlcpp dependency by mausch · Pull Request #149478 · NixOS/nixpkgs · GitHub

6

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^. FIXED!
Things like this is why nix/OS is my favourite linux right now.