Troubleshooting
Search an exact error message or choose an area below. Each diagnosis includes a cause, confirmation commands, and a fix. Full reference
Diagnosis index
Section titled “Diagnosis index”Build & CI
Section titled “Build & CI”- Docker bootstrap build reports invalid Ubuntu package signatures
- ShellCheck rejects the runtime-selected platform environment
- Quality CI fails with
chezmoi: command not found - Cloudflare Pages build failing
Memory & search
Section titled “Memory & search”- cass source build fails with
rustc 1.94.0 is not supportedorE0554 cass searchmisses sessions you know happenedcass indexfails withgraph topology attestation failed- Every
casscommand fails:unable to open database file(but sqlite3 opens it fine) - macOS still asks: “cass would like to access data from other apps”
npm install -gfails withEBUSY … unlink '.nfsXXXX'(qmd upgrade)- qmd is running but its health check cannot connect to
127.0.0.1:8181 - Login-profile fixture intermittently misses QMD startup
Shared homes & storage
Section titled “Shared homes & storage”- Fish reports a missing old PLAT
env.fish - Brew cleanup fails with
Device or resource busy .../.nfs... - Two machines fighting over dotfiles on a shared home
- A symlinked
~/.codexor~/.claudeturned back into a real directory - Duplicate PLAT paths in PATH (both v3 and v4 showing up)
- Migrating off PLAT isolation
Editors & desktop
Section titled “Editors & desktop”- The same VS Code / Cursor extensions report
failon every upgrade run - Cursor reports
ENOENTforUser/settings.jsonand ignores user settings - Cursor computer use reports Ready: no, or screenshots never appear
- Cursor CLI default model reverts to Auto
- Bootstrap upgrade leaves GUI apps outdated
- Cursor skills remain a directory instead of the shared symlink
- A GUI app’s config is permanently dirty in
chezmoi status - Mac App Store reports
No downloads initiated
Agents & integrations
Section titled “Agents & integrations”- Agent shell loops report installed commands as missing
- Bundled skill validation fails with missing yaml
- Agent test commands retry unsupported quiet or filter arguments
- Large tool responses defeat output compression
- Hosted Codex runtime and backup tests fail while local tests pass
- Native OpenCode test cannot find an installed binary
- Local agents default to MLX but localhost:8080 is unavailable
- Upgrade retains an old OpenCode or Ollama package owner
- Codex install fails with
marketplace unavailable: openai-bundled - Codex plugin healthcheck reports a plugin was dropped upstream
- Claude cannot load required remote managed settings
- Claude plugin fails:
Plugin "X" not found in any configured marketplace - Native Codex installed but the shell runs an older npm version
- Skill upgrade reports both “up to date” and committed-digest drift
- Codex background server has incompatible feature settings
- SSH works but the remote Codex desktop cannot initialize its database
codex -p <domain>cannot see its expected MCP tools- Persistent Playwright profile loses login cookies after close
- Google Cloud MCP stops authenticating during a long session
- Codex MCP login times out in an SSH shell after browser sign-in
- Codex MCP OAuth fails: “Authorization server response missing required issuer”
- Remote Codex repeatedly warns about MCP authentication
- Codex MCP login fails with EOF parsing .credentials.json
- Codex lifecycle hook times out after three seconds
- Codex upgrade rejects a valid 0.163.0 package
- Codex disappears after an npm upgrade on NFS
- Codex reconnect collides with an SSH OAuth tunnel
- Codex daemon bootstrap reports an unmanaged app server
- Codex cannot read sessions: No file descriptors available
Shell & PATH
Section titled “Shell & PATH”- Colima intermittently rewrites or breaks
~/.ssh/config - nvm rejects
prefixorglobalconfigin~/.npmrc nvmornodenot available in a script- chezmoi keeps prompting for name/email
- chezmoi diff shows unexpected changes
- PATH order is wrong — wrong binary is resolving
- Lost shell history
- Brew zsh tab completion leaves remnant characters (Linux)
- Copy/paste from a remote SSH session pastes as mojibake (
’,Â,é)
Packages & runtimes
Section titled “Packages & runtimes”- Google status reports the wrong quota project
- Gemini discovery works but a model request fails
- Push validation cannot mount its isolated checkout on NFS
- Bats stalls before listing tests on macOS
- Local secret scanning reports files outside the outgoing branch
- Local fixture tests overwrite a managed tool
- Tool not found after bootstrap
- Brew bundle fails:
No available formula … This command requires the tap - Brew bundle appears stuck after
Usinglines - Python setup waits in NFS locking
- Brew bundle reports
Upgrading X has failed!after installing X - Ruby upgrade writes outside its new keg during
make install - apache-serf cannot find
asm/socket.h - Gecode patch reports that its configure target moved
- Clang cannot load
libz3during an in-progress upgrade - OpenSSH upgrade fails with
inreplace failed ... sshd_config - Brew has the current keg but still uses an older version
- Brew Bundle reports a circular
libtiff, webpdependency - Rust fails after Homebrew says its packages are satisfied
- macOS syntax checks report an unmatched quote in a formula patch
- Mesa PyYAML patch target not found
- systemd patch target not found
- Cargo source build rejects OpenSSL 4
- Cask upgrade fails:
It seems there is already an App at '/Applications/X.app' - A Homebrew package is months behind upstream (Linux)
- Upgrade finishes installing, then the version audit calls newer tools outdated
GLIBC_x.y not foundfrom a Homebrew binary (Linux)NODE_MODULE_VERSIONmismatch /ERR_DLOPEN_FAILEDfrom an npm tool- uv update reports a checksum mismatch because sha256sum cannot start
- A Homebrew binary can’t find
libX.so.Nafter an upgrade nsys/ncuresolve to the CUDA toolkit copy, not the standalone installpythonis Python 2 or cannot import SymPy- WhisperX upgrade fails with SQLAlchemy
duplicate normalized extra name - Python@3.14 build fails on Linux (uuid or test_datetime errors)
import sage.all/ cysignals dies withTypeError: signal handler must be signal.SIG_IGN, signal.SIG_DFL, or a callable object- TinyTeX refuses package installation until tlmgr is updated
pdflatex: command not foundon macOS with MacTeX installedbrew bundleinstalls nothing new and exits 0- Homebrew LLDB installs but fails its runtime checks
- Python tools repeatedly report missing entrypoints
- Python bytecode caching stays disabled after updating dotfiles
- Home directory is near quota despite
install/scratch.shrunning