Codex process fails with SIGKILL then ENOENT after bundled codex binary is removed

[jinsley8]

What happened

Running deepsec process with the Codex backend fails after the bundled Codex executable was killed and then could no longer be spawned. MacOS shows a warning that codex was blocked because it contains malware.

The process first logged Codex Exec exited with signal SIGKILL, then retried and logged spawn .../codex ENOENT. macOS also showed a malware warning for codex, after which the executable appeared to be missing.

Reproduction

cd .deepsec

pnpm deepsec scan
pnpm deepsec process --project-id <project-id> --agent codex --model gpt-5.5

Expected vs actual

Expected: deepsec process should either run the Codex backend successfully or fail with clear guidance that the local Codex executable was killed/removed by the OS.
Actual: deepsec process starts batches, then the Codex backend exits with SIGKILL. On retry, the Codex executable path fails with ENOENT, and batches fail after 3 attempts.

Environment

• deepsec version (pnpm deepsec --version): 2.1.2
• Node version (node --version): 22.22.3
• OS: macOS, Apple Silicon
• Agent backend (claude-agent-sdk / codex): codex
• Model: gpt-5.5

Logs

Processing project <project-id>
  Agent: codex (gpt-5.5)
  Root: /path/to/repo

Batch 1/230: Processing batch 1/230 (5 files, 1 in flight)
Batch 2/230: Processing batch 2/230 (2 files, 2 in flight)
Batch 3/230: Processing batch 3/230 (4 files, 3 in flight)
Batch 4/230: Processing batch 4/230 (3 files, 4 in flight)
Batch 5/230: Processing batch 5/230 (5 files, 5 in flight)
Batch 6/230: Processing batch 6/230 (5 files, 6 in flight)
Batch 7/230: Processing batch 7/230 (5 files, 7 in flight)
Batch 8/230: Processing batch 8/230 (5 files, 8 in flight)
Batch 9/230: Processing batch 9/230 (5 files, 9 in flight)
  > Investigating 5 file(s) with Codex SDK (gpt-5.5, effort=xhigh)
  > Investigating 2 file(s) with Codex SDK (gpt-5.5, effort=xhigh)
  > Investigating 4 file(s) with Codex SDK (gpt-5.5, effort=xhigh)
  > Investigating 3 file(s) with Codex SDK (gpt-5.5, effort=xhigh)
  > Investigating 5 file(s) with Codex SDK (gpt-5.5, effort=xhigh)
  > Investigating 5 file(s) with Codex SDK (gpt-5.5, effort=xhigh)
  > Investigating 5 file(s) with Codex SDK (gpt-5.5, effort=xhigh)
  > Investigating 5 file(s) with Codex SDK (gpt-5.5, effort=xhigh)
  > Investigating 5 file(s) with Codex SDK (gpt-5.5, effort=xhigh)
    Codex SDK error: Codex Exec exited with signal SIGKILL:
    Codex SDK error: Codex Exec exited with signal SIGKILL:
    Codex SDK error: Codex Exec exited with signal SIGKILL:
    Codex SDK error: Codex Exec exited with signal SIGKILL:
    Codex SDK error: Codex Exec exited with signal SIGKILL:
    Codex SDK error: Codex Exec exited with signal SIGKILL:
    Codex SDK error: Codex Exec exited with signal SIGKILL:
    Codex SDK error: Codex Exec exited with signal SIGKILL:
    Codex SDK error: Codex Exec exited with signal SIGKILL:
    Retrying batch after transient error (attempt 2/3): Codex Exec exited with signal SIGKILL:
    Retrying batch after transient error (attempt 2/3): Codex Exec exited with signal SIGKILL:
    Codex SDK error: spawn /path/to/repo/.deepsec/node_modules/.pnpm/@openai+codex@0.125.0-darwin-arm64/node_modules/@openai/codex/vendor/aarch64-apple-darwin/codex/codex ENOENT
    Retrying batch after transient error (attempt 2/3): Codex Exec exited with signal SIGKILL:
    Codex SDK error: spawn /path/to/repo/.deepsec/node_modules/.pnpm/@openai+codex@0.125.0-darwin-arm64/node_modules/@openai/codex/vendor/aarch64-apple-darwin/codex/codex ENOENT
    Retrying batch after transient error (attempt 3/3): spawn /path/to/repo/.deepsec/node_modules/.pnpm/@openai+codex@0.125.0-darwin-arm64/node_modules/@openai/codex/vendor/aarch64-apple-darwin/codex/codex ENOENT
    Codex SDK error: spawn /path/to/repo/.deepsec/node_modules/.pnpm/@openai+codex@0.125.0-darwin-arm64/node_modules/@openai/codex/vendor/aarch64-apple-darwin/codex/codex ENOENT
  Batch 1/230 failed: Codex SDK produced no result after 3 attempt(s). Last error: spawn /path/to/repo/.deepsec/node_modules/.pnpm/@openai+codex@0.125.0-darwin-arm64/node_modules/@openai/codex/vendor/aarch64-apple-darwin/codex/codex ENOENT. (8 in flight, 1/230 done)

Additional context: macOS also showed a system dialog saying "codex" was not opened because it contains malware, and the binary appeared to be missing afterward.

[letroot]

I have the same problem

[Deriul]

    "overrides": {
      "@openai/codex": "0.142.5",
      "@openai/codex-sdk": "0.142.5"
    }

I dropped it to my package.json; that would do until the issue is properly resolved

[Destreyf]

@Deriul I ended up with the same, however i had to add them into specifically into the pnpm.overrides section, I initially tried the top level overrides but it didn't work.

{
  "name": "deepsec-workspace",
  "version": "0.1.0",
  "private": true,
  "description": "deepsec scanning workspace",
  "type": "module",
  "workspaces": [],
  "packageManager": "pnpm@9.15.4",
  "dependencies": {
    "deepsec": "^2.1.2"
  },
  "overrides": {
    "@openai/codex": "0.142.5",
    "@openai/codex-sdk": "0.142.5"
  },
  "pnpm": {
    "overrides": {
      "@openai/codex": "0.142.5",
      "@openai/codex-sdk": "0.142.5"
    }
  }
}

[mvanhorn]

Submitted a fix in #101.

[Destreyf]

@mvanhorn that PR doesn't appear to actually solve this issue though, the deepsec process command will still fail (faster) until the version is updated, something is up with the 0.125.X versions of the codex cli and I wonder if it's somehow related to the axios compromise back in March/April where they told everyone to update their versions because of a developer certificate: https://openai.com/index/axios-developer-tool-compromise/

Apple is detecting the vendored 0.125.0 codex cli as malware and will remove it.

[lukeshumard]

I ran into the same issue today, and this appears to be related to the expired certificate. Running spctl on the executable responds with CSSMERR_TP_CERT_REVOKED. This means that, on macOS, XProtect / Gatekeeper reject the file and remove it when it tries to initially run. Since it's removed, you're getting the ENOET error because the file isn't there anymore. This is why having a later, non-expired override works.