Extractor exiting with code 4: assertion failed at: "decls.c", line 18401 in add_src_seq_end_of_variable_if_needed

[intrigus-lgtm]

We tried to build a CodeQL DB for https://github.com/category-labs/monad/.
Unfortunately the DB is missing many important files.

This is because the extractor chokes ("catastrophic error") on the bits/alloc_traits.h header file of libstdc++ 15.
The problem appears to be related to macros?

(I will create additional issues for non-catastrophic errors that are also in the build-tracer.log: #20640)

Minimized reproducer

struct __allocator_traits_base {
  template < typename >
  static constexpr int __can_construct_at{
# 1
  };
};

Error log extract

[E 23:52:43 2164329] Finished compilation TRAP /tmp/tmp.NzaonYxdn4/trap/cpp/compilations/33/52125401_0.trap.zst
CodeQL C++ extractor: Current location: minimal.cpp:5,4
CodeQL C++ extractor: Current physical location: minimal.cpp:5,4
"minimal.cpp", line 1: internal error: assertion failed at: "decls.c", line 18401 in add_src_seq_end_of_variable_if_needed

    };
     ^

[E 23:52:43 2164329] Warning[extractor-c++]: In construct_text_message: "minimal.cpp", line 1: internal error: assertion failed at: "decls.c", line 18401 in add_src_seq_end_of_variable_if_needed

    };
     ^


1 catastrophic error detected in the compilation of "minimal.cpp".

build-tracer-cut.log

"Original" reproducer

#include <bits/alloc_traits.h>

OS information

• CodeQL v2.23.2
• Ubuntu 25:04
• libstdc++-15
• clang-19

Please let me know if you need anything else!

[jketema]

Hi @intrigus-lgtm

Thanks for the report. Slightly higher up in the build-tracer.log file there will be a line that says: "Processed command line". Would you be able to share that line too? Feel free to strip out any paths from that line in case they are confidential.

[two-heart]

With gcc-15, but the same error, the processed command is:

[E 11:14:42 118016] Processed command line: /home/nine/localTools/codeql/cpp/tools/linux64/extractor --trapfolder /home/nine/Documents/monad/monad-codeql-h/trap/cpp --src_archive /home/nine/Documents/monad/monad-codeql-h/src --object_filename CMakeFiles/ethash.dir/primes.c.o --no_warnings_and_discretionary_errors --error_limit 1000 --disable_system_macros --variadic_macros --incognito --c18 --gcc --clang_version 190107 --gnu_version 40801 --has_feature_vector 1111111111111111000000000000000000000000000000000000000000000000000011 --clang --target linux_x86_64 -D_LP64=1 -D__ATOMIC_ACQUIRE=2 -D__ATOMIC_ACQ_REL=4 -D__ATOMIC_CONSUME=1 -D__ATOMIC_RELAXED=0 -D__ATOMIC_RELEASE=3 -D__ATOMIC_SEQ_CST=5 -D__AVX2__=1 -D__AVX__=1 -D__BIGGEST_ALIGNMENT__=16 -D__BITINT_MAXWIDTH__=8388608 -D__BMI2__=1 -D__BMI__=1 -D__BOOL_WIDTH__=8 -D__BYTE_ORDER__=__ORDER_LITTLE_ENDIAN__ -D__CHAR_BIT__=8 -D__CLANG_ATOMIC_BOOL_LOCK_FREE=2 -D__CLANG_ATOMIC_CHAR16_T_LOCK_FREE=2 -D__CLANG_ATOMIC_CHAR32_T_LOCK_FREE=2 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-D__ORDER_BIG_ENDIAN__=4321 -D__ORDER_LITTLE_ENDIAN__=1234 -D__ORDER_PDP_ENDIAN__=3412 -D__PCLMUL__=1 -D__PIC__=2 -D__PIE__=2 -D__POINTER_WIDTH__=64 -D__POPCNT__=1 -D__PRAGMA_REDEFINE_EXTNAME=1 '-D__PTRDIFF_FMTd__="ld"' '-D__PTRDIFF_FMTi__="li"' -D__PTRDIFF_MAX__=9223372036854775807L '-D__PTRDIFF_TYPE__=long int' -D__PTRDIFF_WIDTH__=64 -D__RDRND__=1 -D__REGISTER_PREFIX__= -D__SCHAR_MAX__=127 -D__SEG_FS=1 -D__SEG_GS=1 -D__SHRT_MAX__=32767 -D__SHRT_WIDTH__=16 -D__SIG_ATOMIC_MAX__=2147483647 -D__SIG_ATOMIC_WIDTH__=32 -D__SIZEOF_DOUBLE__=8 -D__SIZEOF_FLOAT128__=16 -D__SIZEOF_FLOAT__=4 -D__SIZEOF_INT128__=16 -D__SIZEOF_INT__=4 -D__SIZEOF_LONG_DOUBLE__=16 -D__SIZEOF_LONG_LONG__=8 -D__SIZEOF_LONG__=8 -D__SIZEOF_POINTER__=8 -D__SIZEOF_PTRDIFF_T__=8 -D__SIZEOF_SHORT__=2 -D__SIZEOF_SIZE_T__=8 -D__SIZEOF_WCHAR_T__=4 -D__SIZEOF_WINT_T__=4 '-D__SIZE_FMTX__="lX"' '-D__SIZE_FMTo__="lo"' '-D__SIZE_FMTu__="lu"' '-D__SIZE_FMTx__="lx"' -D__SIZE_MAX__=18446744073709551615UL '-D__SIZE_TYPE__=long unsigned 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-I/home/nine/Documents/monad/third_party/ethash/include -I/usr/lib/llvm-19/lib/clang/19/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include -- /home/nine/Documents/monad/third_party/ethash/lib/ethash/primes.c

[jketema]

@two-heart Thanks!

[jketema]

I'm able to reproduce the problem. I've opened an internal issue to track this.

[intrigus-lgtm]

(Apologies for forgetting that crucial information, too early in the "morning")
For completeness, the full extractor.log and script I used to reduce the testcase (cvise --sllooww -n 96 ./interestingness-test.sh minimal.cpp:

exctractor.log

[E 12:11:49 2252375] CodeQL C/C++ Extractor 2.23.2
[E 12:11:49 2252375] Current directory: /home/sg/foobar
[E 12:11:49 2252375] Command: /home/sg/.local/share/gh/extensions/gh-codeql/dist/release/v2.23.2/cpp/tools/linux64/extractor --mimic /usr/lib/llvm-19/bin/clang '-std=gnu++23' -c minimal.cpp
[E 12:11:49 2252375] Checking whether C compilation already happened.
[E 12:11:49 2252375] Checking for tag c-compilation-happened
[E 12:11:49 2252375] Checking CODEQL_TRACER_DB_ID 0000000000225E53_0000000000000003
[E 12:11:49 2252375] Locking DB /tmp/tmp.kvigeH0Gcy/working/tags.db
[E 12:11:49 2252375] Locked DB /tmp/tmp.kvigeH0Gcy/working/tags.db
[E 12:11:49 2252375] Unlocking DB
[E 12:11:49 2252375] Unlocked DB
[E 12:11:49 2252375] Looks like C compilation didn't already happen.
[E 12:11:49 2252375] Checking whether C compilation has been attempted.
[E 12:11:49 2252375] Checking for tag c-compilation-attempted
[E 12:11:49 2252375] Checking CODEQL_TRACER_DB_ID 0000000000225E53_0000000000000003
[E 12:11:49 2252375] Locking DB /tmp/tmp.kvigeH0Gcy/working/tags.db
[E 12:11:49 2252375] Locked DB /tmp/tmp.kvigeH0Gcy/working/tags.db
[E 12:11:49 2252375] Unlocking DB
[E 12:11:49 2252375] Unlocked DB
[E 12:11:49 2252375] Marking C compilation as attempted.
[E 12:11:49 2252375] Setting tag c-compilation-attempted
[E 12:11:49 2252375] Starting from CODEQL_TRACER_DB_ID 0000000000225E53_0000000000000003
[E 12:11:49 2252375] Locking DB /tmp/tmp.kvigeH0Gcy/working/tags.db
[E 12:11:49 2252375] Locked DB /tmp/tmp.kvigeH0Gcy/working/tags.db
[E 12:11:49 2252375] Set tag for 0000000000225E53_0000000000000003
[E 12:11:49 2252375] Set tag for 0000000000225E53_0000000000000002
[E 12:11:49 2252375] Set tag for root
[E 12:11:49 2252375] Unlocking DB
[E 12:11:49 2252375] Unlocked DB
[E 12:11:50 2252375] Processed command line: /home/sg/.local/share/gh/extensions/gh-codeql/dist/release/v2.23.2/cpp/tools/linux64/extractor --trapfolder /tmp/tmp.kvigeH0Gcy/trap/cpp --src_archive /tmp/tmp.kvigeH0Gcy/src --no_warnings_and_discretionary_errors --error_limit 1000 --disable_system_macros --variadic_macros --incognito '--c++23' '--g++' --clang_version 190107 --gnu_version 40801 --has_feature_vector 1111111100000011011111110111111111111111111011111111111110111111111111 --clang --target linux_x86_64 -D_GNU_SOURCE=1 -D_LP64=1 -D__ATOMIC_ACQUIRE=2 -D__ATOMIC_ACQ_REL=4 -D__ATOMIC_CONSUME=1 -D__ATOMIC_RELAXED=0 -D__ATOMIC_RELEASE=3 -D__ATOMIC_SEQ_CST=5 -D__BIGGEST_ALIGNMENT__=16 -D__BITINT_MAXWIDTH__=8388608 -D__BOOL_WIDTH__=8 -D__BYTE_ORDER__=__ORDER_LITTLE_ENDIAN__ -D__CHAR_BIT__=8 -D__CLANG_ATOMIC_BOOL_LOCK_FREE=2 -D__CLANG_ATOMIC_CHAR16_T_LOCK_FREE=2 -D__CLANG_ATOMIC_CHAR32_T_LOCK_FREE=2 -D__CLANG_ATOMIC_CHAR8_T_LOCK_FREE=2 -D__CLANG_ATOMIC_CHAR_LOCK_FREE=2 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-D__linux=1 -D__linux__=1 -D__llvm__=1 -D__pic__=2 -D__pie__=2 -D__private_extern__=extern '-D__seg_fs=__attribute__((address_space(257)))' '-D__seg_gs=__attribute__((address_space(256)))' -D__tune_k8__=1 -D__unix=1 -D__unix__=1 -D__x86_64=1 -D__x86_64__=1 -Dlinux=1 -Dunix=1 '-I/usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14' '-I/usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/x86_64-linux-gnu/c++/14' '-I/usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/backward' -I/usr/lib/llvm-19/lib/clang/19/include -I/usr/local/include -I/usr/include/x86_64-linux-gnu -I/usr/include -- minimal.cpp
[E 12:11:50 2252375] CODEQL_EXTRACTOR_CPP_TRAP_CACHING is not set
[E 12:11:50 2252375] CODEQL_EXTRACTOR_CPP_OPTION_TRAP_CACHE_WRITE is not set
[E 12:11:50 2252375] CODEQL_EXTRACTOR_CPP_OPTION_TRAP_CACHE_DIR is not set
[E 12:11:50 2252375] Initialising TRAP cache at path: 85/9844/44133f98f14442203f59aebe4e0c
[E 12:11:50 2252375] Not using TRAP cache
[E 12:11:50 2252375] TRAP cache miss
[E 12:11:50 2252375] Starting compilation TRAP /tmp/tmp.kvigeH0Gcy/trap/cpp/compilations/35/18360135_0.trap.zst
[E 12:11:50 2252375] Archiving /tmp/tmp.kvigeH0Gcy/src/home/sg/foobar/minimal.cpp
[E 12:11:50 2252375] Finished compilation TRAP /tmp/tmp.kvigeH0Gcy/trap/cpp/compilations/35/18360135_0.trap.zst
[E 12:11:50 2252375] Warning[extractor-c++]: In construct_text_message: "minimal.cpp", line 1: internal error: assertion failed at: "decls.c", line 18401 in add_src_seq_end_of_variable_if_needed

    };
     ^


[E 12:11:50 2252375] Marking C compilation as happened.
[E 12:11:50 2252375] Setting tag c-compilation-happened
[E 12:11:50 2252375] Starting from CODEQL_TRACER_DB_ID 0000000000225E53_0000000000000003
[E 12:11:50 2252375] Locking DB /tmp/tmp.kvigeH0Gcy/working/tags.db
[E 12:11:50 2252375] Locked DB /tmp/tmp.kvigeH0Gcy/working/tags.db
[E 12:11:50 2252375] Set tag for 0000000000225E53_0000000000000003
[E 12:11:50 2252375] Set tag for 0000000000225E53_0000000000000002
[E 12:11:50 2252375] Set tag for root
[E 12:11:50 2252375] Unlocking DB
[E 12:11:50 2252375] Unlocked DB
[E 12:11:50 2252375] Warning[extractor-c++]: In main: Extractor exiting with code 4

interestingness-test.sh

#!/bin/bash

set -e

cleanup() {
    rm -rf "$mytmpdir"
}
trap cleanup EXIT

mytmpdir=$(mktemp -d 2>/dev/null || mktemp -d -t 'mytmpdir')
codeql database create "$mytmpdir" --language=cpp --command="/usr/lib/llvm-19/bin/clang -std=gnu++23 -c minimal.cpp" --overwrite
cat "$mytmpdir/log/build-tracer.log" | grep 'error: assertion failed at: "decls.c", line 18401 in add_src_seq_end_of_variable_if_needed'
status=$?
exit $status

[intrigus-lgtm]

For other folks who might find the issue and don't want to wait for an extractor fix:
as a workaround you can patch the /usr/include/c++/15/bits/alloc_traits.h file:
(This might break stuff in surprising ways so only do in docker or a dedicated environment)

141c141
< #if __cpp_constexpr_dynamic_alloc
---
> //#if __cpp_constexpr_dynamic_alloc
143,145c143,145
< #else
<           ::new((void*)__p) _Tp(std::forward<_Args>(__args)...);
< #endif
---
> //#else
> //          ::new((void*)__p) _Tp(std::forward<_Args>(__args)...);
> //#endif