Some CI tests are flaky or real failures

[ubaidsk]

There are some CI tests that seem to be flaky and fail.

1. Failure in ctest.

Test project /home/runner/work/lpython/lpython
    Start 1: test_stacktrace
1/2 Test #1: test_stacktrace ..................   Passed    0.00 sec
    Start 2: test_lpython
2/2 Test #2: test_lpython .....................Subprocess aborted***Exception:   0.86 sec
[doctest] doctest version is "2.4.8"
[doctest] run with "--help" for options
0 0 0 0 0 0 0 0 0 0 �
test_lpython: /home/runner/micromamba/envs/lp/include/llvm/IR/DataLayout.h:656: uint64_t llvm::StructLayout::getElementOffset(unsigned int) const: Assertion `Idx < NumElements && "Invalid element idx!"' failed.
===============================================================================
/home/runner/work/lpython/lpython/src/lpython/tests/test_llvm.cpp:[15](https://github.com/lcompilers/lpython/actions/runs/13378363981/job/37362241953?pr=2823#step:6:16)56:
TEST CASE:  PythonCompiler classes

/home/runner/work/lpython/lpython/src/lpython/tests/test_llvm.cpp:1556: FATAL ERROR: test case CRASHED: SIGABRT - Abort (abnormal termination) signal

===============================================================================
[doctest] test cases:  55 |  54 passed | 1 failed | [17](https://github.com/lcompilers/lpython/actions/runs/13378363981/job/37362241953?pr=2823#step:6:18) skipped
[doctest] assertions: 486 | 486 passed | 0 failed |
[doctest] Status: FAILURE!


50% tests passed, 1 tests failed out of 2

Total Test time (real) =   0.87 sec

The following tests FAILED:
	  2 - test_lpython (Subprocess aborted)
Errors while running CTest
Error: Process completed with exit code 8.

2. Failure in reference tests

compiler_tester.tester.RunException: Testing with reference output failed.
runtime_errors/test_assert_01.py * run_dbg
The JSON metadata differs against reference results
Reference JSON: tests/reference/run_dbg-test_assert_01-2f34744.json
Output JSON:    tests/output/run_dbg-test_assert_01-2f34744.json
Omitting 9 identical items
Differing items:
{'stderr_hash': '32b0a24f111e577fe4fc5b3f4a5994b951e34dde7986b3fb750c5f5e'} != {'stderr_hash': '4811af471c73572b285e9ea01c8689abdd3cb32c717b3cd4876d2669'}
{'returncode': 134} != {'returncode': 1}
Diff against: tests/reference/run_dbg-test_assert_01-2f34744.stderr
1,7c1,2
<   File "tests/runtime_errors/test_assert_01.py", line 1
<     def test():
<   File "tests/runtime_errors/test_assert_01.py", line 4
<     test()
<   File "tests/runtime_errors/test_assert_01.py", line 2
<     assert False
< AssertionError
---
> *** buffer overflow detected ***: terminated
> Aborted (core dumped)

Error: Process completed with exit code 1.

[ubaidsk]

The above tests kind of fail randomly. I will probably comment out these two tests for now and get the CI to pass (which will unblock merging PRs). We can then fix these tests iteratively in subsequent PRs.

[ubaidsk]

Failure in reference tests

Seems like all the run_with_dbg reference tests are failing/flaky as of now. Following the steps at the CI, they work fine for me locally.

[ubaidsk]

Also integration_tests/test_str_01.py fails with the above (> *** buffer overflow detected ***: terminated).

I think these are real failures that we need to fix.

[kmr-srbh]

I think a fix for this buffer overflow error might be the same as lfortran/lfortran#6003.

The CI failures started occurring when the GCC compiler was updated on the CI. The PRs which fixed them incrementally were:

• ci: resolve failures lfortran/lfortran#5983
• fix: allocate space for null terminator in string allocations lfortran/lfortran#6003
• fix: initialize variables to avoid undefined behavior lfortran/lfortran#6004

[swamishiju]

lpython/src/libasr/runtime/lfortran_intrinsics.c

Lines 2306 to 2308 in 7eb2bea

	char* dest_char = (char*)malloc(s_len);
	strcpy(dest_char, s);

It does look like the same issue for test_str_01