Buffer Overflow in get_reference_pdb() Caused by Insufficient Buffer Size

[TakumiOtagaki]

Summary

When running rnaview -p --pdb 1kpd.pdb, I encountered a crash (Trace/BPT trap) due to a buffer overflow in get_reference_pdb().

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Steps to Reproduce

1. Set RNAVIEW environment variable to a path that, together with "BASEPARS/ref.pdb", exceeds 80 characters (for example, if RNAVIEW points to a deep directory path of length > 60).
2. Run:

$ rnaview -p --pdb 1kpd.pdb

3. The program fails with a message like:

Processing a single file ...

PDB data file name: /Users/ootagakitakumi/myapp/0304test/PseudoknotVisualizer/test/1KPD.pdb_new

########################################################RNA/DNA chain_ID:  A  from residue    1 to   32

The backbone torsion angles are in /Users/ootagakitakumi/myapp/0304test/PseudoknotVisualizer/test/1KPD.pdb_new_torsion.out

Trace/BPT trap: 5

Root Cause

In src/fpair_sub.c, function get_reference_pdb(), there is a buffer declared as:

char **sAtomName, spdb[80];

This buffer holds the concatenation of the RNAVIEW path plus additional strings (like "/BASEPARS/ref.pdb"). If the combined length exceeds 80 characters, it causes a buffer overflow. On macOS or other systems with buffer checks, this triggers a runtime crash (Trace/BPT trap).

Suggested Fix

Increasing the buffer size resolves the crash. For example, changing line 46 in src/fpair_sub.c to:

char **sAtomName, spdb[200];

allowed the program to run correctly when RNAVIEW is set to a longer path.

After modifying and saving the file, recompile with:

cd RNAView
make clean
rm bin/rnaview
make

The program then works without triggering the overflow.

Additional Information

• Environment: (macOS Sequoia, M2 chip, RNAVIEW commit 6349bbd).
• C Compiler: (clang 16.0.0).
• Possible Improvement: Switching from sprintf to snprintf, or using a dynamically allocated buffer, could further safeguard against similar issues.

Thank you for providing this excellent tool! I hope this report helps prevent buffer overflows for others who might install RNAVIEW in a directory with a long path.