nix-shell and nixos-rebuild no longer working build input /nix/store/x5pfxw8jkaifsbqqhf4lahjxlkm5mfqf-update-autotools-gnu-config-scripts-hook does not exist

[malik-n]

Bug description

I can no longer add programs to my shell session with the nix-shell command nor can I rebuild my system. The behaviour started 7 days ago together with the error: cannot connect to socket at '/nix/var/nix/daemon-socket/socket': Connection refused therefore I thought it was related to issue 594.

To Reproduce

Steps to reproduce the behavior:

nix-shell

using nix-shell -p neofetch --command "neofetch" comand causes the respone build input /nix/store/x5pfxw8jkaifsbqqhf4lahjxlkm5mfqf-update-autotools-gnu-config-scripts-hook does not exist

nixos-rebuild

trying to rebuild the system with sudo nixos-rebuild switch --show-trace --flake . causes the following response

error:
       … while calling the 'seq' builtin

         at /nix/store/apchqa88gf3yp1fghqn9aqkg0c2fm962-source/lib/modules.nix:322:18:

          321|         options = checked options;
          322|         config = checked (removeAttrs config [ "_module" ]);
             |                  ^
          323|         _module = checked (config._module);

       … while evaluating a branch condition

         at /nix/store/apchqa88gf3yp1fghqn9aqkg0c2fm962-source/lib/modules.nix:261:9:

          260|       checkUnmatched =
          261|         if config._module.check && config._module.freeformType == null && merged.unmatchedDefns != [] then
             |         ^
          262|           let

       … in the left operand of the AND (&&) operator

         at /nix/store/apchqa88gf3yp1fghqn9aqkg0c2fm962-source/lib/modules.nix:261:72:

          260|       checkUnmatched =
          261|         if config._module.check && config._module.freeformType == null && merged.unmatchedDefns != [] then
             |                                                                        ^
          262|           let

       … in the left operand of the AND (&&) operator

         at /nix/store/apchqa88gf3yp1fghqn9aqkg0c2fm962-source/lib/modules.nix:261:33:

          260|       checkUnmatched =
          261|         if config._module.check && config._module.freeformType == null && merged.unmatchedDefns != [] then
             |                                 ^
          262|           let

       … while evaluating a branch condition

         at /nix/store/apchqa88gf3yp1fghqn9aqkg0c2fm962-source/lib/modules.nix:254:12:

          253|
          254|         in if declaredConfig._module.freeformType == null then declaredConfig
             |            ^
          255|           # Because all definitions that had an associated option ended in

       … from call site

         at /nix/store/apchqa88gf3yp1fghqn9aqkg0c2fm962-source/lib/modules.nix:242:28:

          241|           # For definitions that have an associated option
          242|           declaredConfig = mapAttrsRecursiveCond (v: ! isOption v) (_: v: v.value) options;
             |                            ^
          243|

       … while calling 'mapAttrsRecursiveCond'

         at /nix/store/apchqa88gf3yp1fghqn9aqkg0c2fm962-source/lib/attrsets.nix:1201:5:

         1200|     f:
         1201|     set:
             |     ^
         1202|     let

       … from call site

         at /nix/store/apchqa88gf3yp1fghqn9aqkg0c2fm962-source/lib/modules.nix:234:33:

          233|           ({ inherit lib options config specialArgs; } // specialArgs);
          234|         in mergeModules prefix (reverseList collected);
             |                                 ^
          235|

       … while calling 'reverseList'

         at /nix/store/apchqa88gf3yp1fghqn9aqkg0c2fm962-source/lib/lists.nix:1116:17:

         1115|   */
         1116|   reverseList = xs:
             |                 ^
         1117|     let l = length xs; in genList (n: elemAt xs (l - n - 1)) l;

       … from call site

         at /nix/store/apchqa88gf3yp1fghqn9aqkg0c2fm962-source/lib/modules.nix:229:25:

          228|       merged =
          229|         let collected = collectModules
             |                         ^
          230|           class

       … while calling anonymous lambda

         at /nix/store/apchqa88gf3yp1fghqn9aqkg0c2fm962-source/lib/modules.nix:445:37:

          444|
          445|     in modulesPath: initialModules: args:
             |                                     ^
          446|       filterModules modulesPath (collectStructuredModules unknownModule "" initialModules args);

       … from call site

         at /nix/store/apchqa88gf3yp1fghqn9aqkg0c2fm962-source/lib/modules.nix:446:7:

          445|     in modulesPath: initialModules: args:
          446|       filterModules modulesPath (collectStructuredModules unknownModule "" initialModules args);
             |       ^
          447|

       … while calling 'filterModules'

         at /nix/store/apchqa88gf3yp1fghqn9aqkg0c2fm962-source/lib/modules.nix:413:36:

          412|       # modules recursively. It returns the final list of unique-by-key modules
          413|       filterModules = modulesPath: { disabled, modules }:
             |                                    ^
          414|         let

       … while calling anonymous lambda

         at /nix/store/apchqa88gf3yp1fghqn9aqkg0c2fm962-source/lib/modules.nix:439:31:

          438|           disabledKeys = concatMap ({ file, disabled }: map (moduleKey file) disabled) disabled;
          439|           keyFilter = filter (attrs: ! elem attrs.key disabledKeys);
             |                               ^
          440|         in map (attrs: attrs.module) (builtins.genericClosure {

       … from call site

         at /nix/store/apchqa88gf3yp1fghqn9aqkg0c2fm962-source/lib/modules.nix:400:22:

          399|           let
          400|             module = checkModule (loadModule args parentFile "${parentKey}:anon-${toString n}" x);
             |                      ^
          401|             collectedImports = collectStructuredModules module._file module.key module.imports args;

       … while calling anonymous lambda

         at /nix/store/apchqa88gf3yp1fghqn9aqkg0c2fm962-source/lib/modules.nix:359:11:

          358|         then
          359|           m:
             |           ^
          360|             if m._class != null -> m._class == class

       … from call site

         at /nix/store/apchqa88gf3yp1fghqn9aqkg0c2fm962-source/lib/modules.nix:400:35:

          399|           let
          400|             module = checkModule (loadModule args parentFile "${parentKey}:anon-${toString n}" x);
             |                                   ^
          401|             collectedImports = collectStructuredModules module._file module.key module.imports args;

       … while calling 'loadModule'

         at /nix/store/apchqa88gf3yp1fghqn9aqkg0c2fm962-source/lib/modules.nix:336:53:

          335|       # Like unifyModuleSyntax, but also imports paths and calls functions if necessary
          336|       loadModule = args: fallbackFile: fallbackKey: m:
             |                                                     ^
          337|         if isFunction m then

       … from call site

         at /nix/store/apchqa88gf3yp1fghqn9aqkg0c2fm962-source/lib/modules.nix:337:12:

          336|       loadModule = args: fallbackFile: fallbackKey: m:
          337|         if isFunction m then
             |            ^
          338|           unifyModuleSyntax fallbackFile fallbackKey (applyModuleArgs fallbackKey m args)

       … while calling 'isFunction'

         at /nix/store/apchqa88gf3yp1fghqn9aqkg0c2fm962-source/lib/trivial.nix:929:16:

          928|   */
          929|   isFunction = f: builtins.isFunction f ||
             |                ^
          930|     (f ? __functor && isFunction (f.__functor f));

       … while calling anonymous lambda

         at «string»:25:25:

           24|           inputs = builtins.mapAttrs
           25|             (inputName: inputSpec: allNodes.${resolveInput inputSpec})
             |                         ^
           26|             (node.inputs or {});

       … while calling anonymous lambda

         at «string»:10:13:

            9|     builtins.mapAttrs
           10|       (key: node:
             |             ^
           11|         let

       … from call site

         at «string»:47:21:

           46|
           47|           outputs = flake.outputs (inputs // { self = result; });
             |                     ^
           48|

       … while calling 'outputs'

         at /nix/store/5hp07s3qjv9153dvz5wxfzap5y5j94n6-source/flake.nix:45:5:

           44|   outputs =
           45|     inputs:
             |     ^
           46|     inputs.flake-parts.lib.mkFlake { inherit inputs; } {

       … while calling anonymous lambda

         at «string»:25:25:

           24|           inputs = builtins.mapAttrs
           25|             (inputName: inputSpec: allNodes.${resolveInput inputSpec})
             |                         ^
           26|             (node.inputs or {});

       … while calling anonymous lambda

         at «string»:10:13:

            9|     builtins.mapAttrs
           10|       (key: node:
             |             ^
           11|         let

       error: getting status of '/nix/store/8ql43f4sxqh1dbpqy2q5jz11zdwf9832-source': No such file or directory

WSL version

WSL-Version: 2.1.5.0
Kernelversion: 5.15.146.1-2
WSLg-Version: 1.0.60
MSRDC-Version: 1.2.5105
Direct3D-Version: 1.611.1-81528511
DXCore-Version: 10.0.25131.1002-220531-1700.rs-onecore-base2-hyp
Windows-Version: 10.0.19045.4894

wslgconfig

[system-distro-env]
;disable GPU in system-distro
LIBGL_ALWAYS_SOFTWARE=1
[wsl2]
kernelCommandLine = cgroup_no_v1=all

[malik-n]

I was able to fix the issue with the following command: sudo nix-store --repair --verify --check-contents