[C++] Getting `java.io.IOException: Not enough input bytes` and `java.io.IOException: Missing manifest file` on creating database

[Arpan3323]

Describe the issue

I am using CodeQL CLI to create a database for this repo. The database gets created successfully but I see several messages reporting the following 2 errors in the dataset-import-xxxx.log file:

• java.io.IOException: Missing manifest file
• java.io.IOException: Not enough input bytes

Command I used:

codeql database create codeql_dbs/dealii_db --language=cpp --source-root=repos/dealii/ --build-mode=none --threads=7 --ram=6000

Log file:
dataset-import-20250918.182021.954.log

[jketema]

Hi @Arpan3323,

That's for your report. This likely means that our C/C++ parser is crashing on some of the code. There should be another log files with extractor/parser details. These should contain more details on where the parser might be crashing. Could you share those too?

[Arpan3323]

The other log file that was present after database creation is this one:

database-create-20250918.164558.286.log

Let me know if you were looking for something else

[jketema]

The other log file that was present after database creation is this one:

database-create-20250918.164558.286.log

Let me know if you were looking for something else

Thanks. Not quite what I was looking for, but doing the following:

git clone https://github.com/dealii/dealii
codeql database create dealii-db --language=cpp --source-root=dealii/ --build-mode=none

I indeed observe similar issues to what you are reporting. The issues seem to be coming from our C/C++ frontend, and it segfaulting on some of the source files. I've opened an internal issue to see if we can get this fixed.

The problem seems to be specific to --build-mode=none. You might want to consider switching from none to autobuild or manual.