bug: Crash with Uncaught TypeError (NaN) in formatSummary when dataset contains symlinks

[rcruces]

Description

A regression was introduced between v2.0.11 and v2.4.1 causing the validator to crash with an uncaught TypeError: Expected a finite number, got number: NaN.

This seems to happen specifically when evaluating datasets that utilize symlinks.

Context / Dataset Setup

We are currently preparing a dataset for release and utilizing symlinks to map data across different subject IDs (sub-*) to avoid duplicating heavy imaging files on disk.

• Works perfectly in: bids-validator v2.0.11 (Successfully resolves symlinks, reads the 7.53 GB dataset, and returns a clean validation summary).
• Crashes in: bids-validator v2.4.1 (Fails during the formatSummary stage while calculating file/byte metrics).

---

Error Log (v2.4.1)

When executing via Deno or within a Singularity container mounting the dataset, the execution panics at the summary output step:

singularity exec --containall -B "${bids_dir}":"${bids_dir}" "${dcm2bids_img}" deno run --allow-write -ERN jsr:@bids/validator ${bids_dir} --ignoreWarnings --outfile ${bids_dir}/bids_validator_output.txt

╭ Warning
│
│  Ignored build scripts for packages:
│  npm:core-js-pure@3.49.0
│
│  Lifecycle scripts are only supported when using a `node_modules` directory.
│  Enable it in your deno config file:
│  "nodeModulesDir": "auto"
╰─
error: Uncaught (in promise) TypeError: Expected a finite number, got number: NaN
    throw new TypeError(`Expected a finite number, got ${typeof num}: ${num}`);
          ^
    at format ([https://jsr.io/@std/fmt/1.0.10/bytes.ts:123:11](https://jsr.io/@std/fmt/1.0.10/bytes.ts:123:11))
    at formatSummary ([https://jsr.io/@bids/validator/2.4.1/src/utils/output.ts:199:51](https://jsr.io/@bids/validator/2.4.1/src/utils/output.ts:199:51))
    at consoleFormat ([https://jsr.io/@bids/validator/2.4.1/src/utils/output.ts:36:15](https://jsr.io/@bids/validator/2.4.1/src/utils/output.ts:36:15))
    at main ([https://jsr.io/@bids/validator/2.4.1/src/main.ts:45:21](https://jsr.io/@bids/validator/2.4.1/src/main.ts:45:21))
    at async [https://jsr.io/@bids/validator/2.4.1/src/bids-validator.ts:4:16](https://jsr.io/@bids/validator/2.4.1/src/bids-validator.ts:4:16)


## Expected Behavior (Working output in v2.0.11)

Downgrading back to 2.0.11 runs smoothly on the exact same directory structure and generates the expected output report:

```bash
$ deno run --allow-write -ERN jsr:@bids/validator --version
bids-validator 2.0.11

$ deno run --allow-write -ERN jsr:@bids/validator ${bids_dir} --ignoreWarnings --outfile ${bids_dir}/bids_validator_output.txt

This dataset appears to be BIDS compatible.

          Summary:                         Available Tasks:        Available Modalities:
          100 Files, 7.53 GB               rest                    MRI                  
          2 - Subjects 2 - Sessions                                                     

    If you have any questions, please post on [https://neurostars.org/tags/bids](https://neurostars.org/tags/bids).

Suspected Cause

Looking at the stack trace, the crash occurs in src/utils/output.ts line 199 inside formatSummary. It passes a NaN type to Deno's standard library byte formatter (@std/fmt/bytes).

It is highly likely that the file walk logic in newer versions of the validator is failing to correctly resolve the sizes or counts of symlinked files, feeding an undefined/null mathematical value into the total bytes calculator.

Environment Info

• Deno version: Latest stable
• bids-validator version 2.4.1 (bug), 2.0.11 (working)
• OS / Environment: Linux Singularity container environment