@hmakholm
This issue is a bit in between the actual cli tool and the C++ extractor - not sure how to debug.

The steps to reproduce:

git clone https://gitlab.com/libeigen/eigen
cd eigen
mkdir build
cd build
cmake ..
codeql database create db --language cpp --command="make buildtests -j8" -j8 -vvvv --logdir=./qllogs --no-cleanup

The make buildtests is reaching 100% and there is no activity, however, there are no logging messages in the terminal as if the extractor doesn't do anything. Inspecting the log:

> tail qllogs/database-create-20200408.103644.678.log 
[2020-04-08 11:32:21] [build] [100%] Linking CXX executable matrix_square_root_5
[2020-04-08 11:32:21] [build] [100%] Built target matrix_square_root_5
[2020-04-08 11:32:23] [build] [100%] Linking CXX executable matrix_square_root_4
[2020-04-08 11:32:23] [build] [100%] Built target matrix_square_root_4
[2020-04-08 11:32:26] [build] [100%] Linking CXX executable gmres_2
[2020-04-08 11:32:26] [build] [100%] Built target gmres_2
[2020-04-08 11:32:48] [build] [100%] Linking CXX executable polynomialsolver_2
[2020-04-08 11:32:48] [build] [100%] Built target polynomialsolver_2
[2020-04-08 11:33:09] [build] [100%] Linking CXX executable sparse_extra_3
[2020-04-08 11:33:09] [build] [100%] Built target sparse_extra_3

The db structure:

> tree db -L 3
db
├── codeql-database.yml
├── log
│   └── build-tracer.log
├── src
│   ├── home
│   │   └── user.name
│   └── usr
│       ├── include
│       └── lib
├── trap
│   └── cpp
│       ├── compilations
│       ├── compiler_mimic_cache
│       ├── source
│       ├── tarballs
│       └── tmp
└── working
    └── tracing
        ├── compiler-tracing2022088708754768740.spec
        └── compiler-tracing2022088708754768740.spec.environment

16 directories, 4 files

If I run the make buildtests -j8 outside of the codeql call, it completes and the process terminates with exit code 0. So the command itself is valid and runnable.

I've waited for a few days thinking that maybe the extractor process has some work to do, but no files are being modified in the db directory over a few days since the make buildtests -j8 reached 100%. Maybe the work is going on, but there is an issue printing logging messages? But it would be very bizarre that it would need more than 2 days to complete creating a database - the project itself is not very big.

I've tried running this both on Linux and MacOS.

Linux:

> lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 18.04.4 LTS
Release:        18.04
Codename:       bionic

MacOS:

> sw_vers -productVersion 
10.15.2
> system_profiler SPSoftwareDataType
      System Version: macOS 10.15.2 (19C57)
      Kernel Version: Darwin 19.2.0

If there is any other piece of information you'd need to help me troubleshoot (compilers present and used and so forth), please let me know.

codeql version
CodeQL command-line toolchain.
Version: 2.1.0.

I've asked @jbj on lgtm.com about header-only projects support and I wonder if this can have anything to do with that?