GHSA-wj42-v2p3-fq2w: Duplicate Advisory Open Babel Has Out-of-bounds Write Vulnerability

CRITICAL
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CVSS 9.8
CWE-122 CWE-787
Published
Advisory Summary

GHSA-wj42-v2p3-fq2w is a CRITICAL (CVSS 9.8) open babel has out-of-bounds write vulnerability (CWE-122: Heap-based Buffer Overflow) affecting Duplicate Advisory libraries in the PyPI ecosystem. The issue involves open babel has out-of-bounds write in orca natoms parser (second variant). Remediation is available by upgrading affected packages to version 3.2.0.

GHSA-wj42-v2p3-fq2w at a Glance

CVE Identifier N/A
GHSA Identifier GHSA-wj42-v2p3-fq2w
Severity CRITICAL
CVSS v3.1 Base Score 9.8
CWE Classification CWE-122: Heap-based Buffer Overflow
Affected Product Duplicate Advisory
Package Ecosystem PyPI
Published Date
Last Updated

Security Impact

CVSS: 9.8

The security impact metrics below are parsed directly from the CVSS v3.1 vector string (CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:H/I:H/A:H).

Attack Vector Network (AV:N)
Attack Complexity Low (AC:L)
Privileges Required None (PR:N)
User Interaction None (UI:N)
Scope Unchanged (S:U)
Confidentiality High (C:H)
Integrity High (I:H)
Availability High (A:H)

How to Fix GHSA-wj42-v2p3-fq2w

To remediate this vulnerability, upgrade all affected Duplicate Advisory dependencies to a patched release. Both direct and transitive dependencies should be checked, as frameworks or security libraries may pull in vulnerable versions transitively.

openbabel fixed: 3.2.0 
pip install openbabel>=3.2.0
Verify Direct and Transitive Dependencies

Run the following command in your project directory to verify that all resolved dependencies use the patched release: 

pip show openbabel

How to Check if You Are Affected

To determine whether your Python environment is affected by GHSA-wj42-v2p3-fq2w, inspect your installed packages using pip:

pip show openbabel

Analyze the terminal output to locate any version of Duplicate Advisory in your dependency tree. If any resolved version matches the vulnerable ranges listed in the table below (for example, versions earlier than 3.2.0), your application is affected.

Note: The pip show openbabel command checks currently installed packages in your active Python environment.

Technical Details

Vulnerability Mechanism & Technical Analysis

This vulnerability is classified under CWE-122: Heap-based Buffer Overflow, where a heap overflow condition is a buffer overflow, where the buffer that can be overwritten is allocated in the heap portion of memory, generally meaning that the buffer was allocated using a routine such as malloc(). In Duplicate Advisory, software state validation or input boundaries are circumvented during processing. Review the official source advisory statement below for specific affected components, classes, and reproduction details.

Source Advisory Statement

## Duplicate Advisory This advisory has been withdrawn because it is a duplicate of GHSA-5rff-8f7c-8jmw. This link is maintained to preserve external references. ## Original Description Multiple out-of-bounds write vulnerabilities exist in the ORCA format nAtoms functionality of Open Babel 3.1.1 and master commit 530dbfa3. A specially-crafted malformed file can lead to arbitrary code execution. An attacker can provide a malicious file to trigger this vulnerability.The loop that stores the coordinates does not check its index against nAtoms

GHSA-wj42-v2p3-fq2w Affected Duplicate Advisory Versions

1 component(s)
Fixed Versions:
3.2.0
Product / Package Ecosystem Affected Versions Fixed Version
openbabel
pypi/openbabel
PyPI
< 3.2.0
3.2.0

References

NVD — GHSA-wj42-v2p3-fq2w NVD
https://nvd.nist.gov/vuln/detail/CVE-2022-46290
talosintelligence.com/vulnerability_repor... WEB
https://talosintelligence.com/vulnerability_reports/TALOS-2022-1665
www.talosintelligence.com/vulnerability_repor... WEB
https://www.talosintelligence.com/vulnerability_reports/TALOS-2022-1665

Frequently Asked Questions

What is GHSA-wj42-v2p3-fq2w?
GHSA-wj42-v2p3-fq2w is a security vulnerability in Duplicate Advisory involving Open Babel has out-of-bounds write in ORCA nAtoms parser (second variant) under CWE-122: Heap-based Buffer Overflow.
Which Duplicate Advisory versions are affected?
Affected versions include releases prior to 3.2.0 across affected packages: openbabel.
What version fixes GHSA-wj42-v2p3-fq2w?
Upgrading to 3.2.0 (or the latest patched release for your respective branch) resolves the vulnerability.
Is openbabel affected?
Yes, openbabel is affected in releases prior to 3.2.0. Upgrade your dependency to 3.2.0 or later.
What is the CVSS score of GHSA-wj42-v2p3-fq2w?
GHSA-wj42-v2p3-fq2w has a CVSS v3.1 base score of 9.8 (CRITICAL) with vector string CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:H/I:H/A:H.
What CWE is associated with GHSA-wj42-v2p3-fq2w?
GHSA-wj42-v2p3-fq2w is classified under CWE-122: Heap-based Buffer Overflow (A heap overflow condition is a buffer overflow, where the buffer that can be overwritten is allocated in the heap portion of memory, generally meaning that the buffer was allocated using a routine such as malloc().).
How can I check PyPI dependencies for GHSA-wj42-v2p3-fq2w?
Run the dependency tree command: 'pip show openbabel'. This command lists direct and transitive dependencies in your build configuration so you can verify if a vulnerable version is resolved.
Machine-readable OSV JSON OSV v1.5 Schema
Normalized schema output
View Raw JSON 
{
  "schema_version" : "1.4.0",
  "id" : "GHSA-wj42-v2p3-fq2w",
  "modified" : "2026-07-01T17:50:04Z",
  "published" : "2023-07-21T21:30:32Z",
  "withdrawn" : "2026-07-01T17:50:04Z",
  "aliases" : [ ],
  "summary" : "Duplicate Advisory: Open Babel has out-of-bounds write in ORCA nAtoms parser (second variant)",
  "details" : "## Duplicate Advisory\nThis advisory has been withdrawn because it is a duplicate of GHSA-5rff-8f7c-8jmw. This link is maintained to preserve external references.\n\n## Original Description\nMultiple out-of-bounds write vulnerabilities exist in the ORCA format nAtoms functionality of Open Babel 3.1.1 and master commit 530dbfa3. A specially-crafted malformed file can lead to arbitrary code execution. An attacker can provide a malicious file to trigger this vulnerability.The loop that stores the coordinates does not check its index against nAtoms",
  "severity" : [ {
    "type" : "CVSS_V3",
    "score" : "CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:H/I:H/A:H"
  } ],
  "affected" : [ {
    "package" : {
      "ecosystem" : "PyPI",
      "name" : "openbabel"
    },
    "ranges" : [ {
      "type" : "ECOSYSTEM",
      "events" : [ {
        "introduced" : "0"
      }, {
        "fixed" : "3.2.0"
      } ]
    } ]
  } ],
  "references" : [ {
    "type" : "ADVISORY",
    "url" : "https://nvd.nist.gov/vuln/detail/CVE-2022-46290"
  }, {
    "type" : "WEB",
    "url" : "https://talosintelligence.com/vulnerability_reports/TALOS-2022-1665"
  }, {
    "type" : "WEB",
    "url" : "https://www.talosintelligence.com/vulnerability_reports/TALOS-2022-1665"
  } ],
  "database_specific" : {
    "cwe_ids" : [ "CWE-122", "CWE-787" ],
    "severity" : "CRITICAL",
    "github_reviewed" : true,
    "github_reviewed_at" : "2026-07-01T17:50:04Z",
    "nvd_published_at" : "2023-07-21T21:15:10Z"
  }
}