Today I was offered an Eclipse update, so I installed it and re-tested the LSP editor. I no longer see the errors in the log that I saw before, also the commands in compile-commands.json look more complete (see fragment below). However, I am now getting a new error in the log file, which may be related to the original one because it's also a system include extraction problem. Here is the error message:

I[11:33:24.391] --> $/progress
I[11:33:24.391] --> $/progress
E[11:33:24.429] System include extraction: start marker not found: Using built-in specs.

COLLECT_GCC=C:/Program Files (x86)/Arm GNU Toolchain arm-none-eabi/13.2 Rel1/bin/arm-none-eabi-gcc.exe

Target: arm-none-eabi

Configured with: /data/jenkins/workspace/GNU-toolchain/arm-13/src/gcc/configure --target=arm-none-eabi --prefix=/data/jenkins/workspace/GNU-toolchain/arm-13/build-mingw-arm-none-eabi/install --with-gmp=/data/jenkins/workspace/GNU-toolchain/arm-13/build-mingw-arm-none-eabi/host-tools --with-mpfr=/data/jenkins/workspace/GNU-toolchain/arm-13/build-mingw-arm-none-eabi/host-tools --with-mpc=/data/jenkins/workspace/GNU-toolchain/arm-13/build-mingw-arm-none-eabi/host-tools --with-isl=/data/jenkins/workspace/GNU-toolchain/arm-13/build-mingw-arm-none-eabi/host-tools --disable-shared --disable-nls --disable-threads --disable-tls --enable-checking=release --enable-languages=c,c++,fortran --with-newlib --with-gnu-as --with-headers=yes --with-gnu-ld --with-native-system-header-dir=/include --with-sysroot=/data/jenkins/workspace/GNU-toolchain/arm-13/build-mingw-arm-none-eabi/install/arm-none-eabi --with-multilib-list=aprofile,rmprofile --with-libiconv-prefix=/data/jenkins/workspace/GNU-toolchain/arm-13/build-mingw-arm-none-eabi/host-tools --host=i686-w64-mingw32 --with-pkgversion='Arm GNU Toolchain 13.2.rel1 (Build arm-13.7)' --with-bugurl=https://bugs.linaro.org/

Thread model: single

Supported LTO compression algorithms: zlib

gcc version 13.2.1 20231009 (Arm GNU Toolchain 13.2.rel1 (Build arm-13.7)) 

COLLECT_GCC_OPTIONS='-E' '-v' '-mcpu=arm7tdmi' '-mfloat-abi=soft' '-marm' '-mlibarch=armv4t' '-march=armv4t'

COMPILER_PATH=C:/Program Files (x86)/Arm GNU Toolchain arm-none-eabi/13.2 Rel1/bin/../libexec/gcc/arm-none-eabi/13.2.1/;C:/Program Files (x86)/Arm GNU Toolchain arm-none-eabi/13.2 Rel1/bin/../libexec/gcc/;C:/Program Files (x86)/Arm GNU Toolchain arm-none-eabi/13.2 Rel1/bin/../lib/gcc/arm-none-eabi/13.2.1/../../../../arm-none-eabi/bin/

LIBRARY_PATH=C:/Program Files (x86)/Arm GNU Toolchain arm-none-eabi/13.2 Rel1/bin/../lib/gcc/arm-none-eabi/13.2.1/;C:/Program Files (x86)/Arm GNU Toolchain arm-none-eabi/13.2 Rel1/bin/../lib/gcc/;C:/Program Files (x86)/Arm GNU Toolchain arm-none-eabi/13.2 Rel1/bin/../lib/gcc/arm-none-eabi/13.2.1/../../../../arm-none-eabi/lib/;C:/Program Files (x86)/Arm GNU Toolchain arm-none-eabi/13.2 Rel1/bin/../arm-none-eabi/lib/

COLLECT_GCC_OPTIONS='-E' '-v' '-mcpu=arm7tdmi' '-mfloat-abi=soft' '-marm' '-mlibarch=armv4t' '-march=armv4t'


I[11:33:24.432] --> $/progress
I[11:33:24.870] Indexed C:/Eclipse/Firmware-3.6/RepRapFirmware/src/Hardware/Spi/SpiDevice.cpp (4411 symbols, 43944 refs, 273 files)
I[11:33:24.968] Indexed C:/Eclipse/Firmware-3.6/RepRapFirmware/src/GCodes/GCodeException.cpp (7136 symbols, 50665 refs, 300 files)

The GCC options that it lists in the above log entry are not correct for my project.

Here is an extract from compile-commands.json:

[
  {
    "directory": "C:/Eclipse/Firmware-3.6/Duet3Expansion/EXP1HCL",
    "command": "\"C:/Program Files (x86)/Arm GNU Toolchain arm-none-eabi/13.2 Rel1/bin/arm-none-eabi-g++.exe\" -std\u003dgnu++17 -D__SAME51G19A__ -D__ARM_ARCH_7EM__\u003d1 -DEXP1HCL -DRTOS \"-IC:\\\\Eclipse\\\\Firmware-3.6\\\\CoreN2G\" \"-IC:\\\\Eclipse\\\\Firmware-3.6\\\\FreeRTOS\" \"-IC:\\\\Eclipse\\\\Firmware-3.6\\\\Duet3Expansion\\\\src\" \"-IC:\\\\Eclipse\\\\Firmware-3.6\\\\CoreN2G\\\\src\" \"-IC:\\\\Eclipse\\\\Firmware-3.6\\\\CoreN2G\\\\src\\\\SAME5x_C21\" \"-IC:\\\\Eclipse\\\\Firmware-3.6\\\\CoreN2G\\\\src\\\\SAME5x_C21\\\\SAME5x\\\\hal\\\\include\" \"-IC:\\\\Eclipse\\\\Firmware-3.6\\\\CoreN2G\\\\src\\\\SAME5x_C21\\\\SAME5x\\\\hal\\\\utils\\\\include\" \"-IC:\\\\Eclipse\\\\Firmware-3.6\\\\CoreN2G\\\\src\\\\SAME5x_C21\\\\SAME5x\\\\hri\" \"-IC:\\\\Eclipse\\\\Firmware-3.6\\\\CoreN2G\\\\src\\\\arm\\\\CMSIS\\\\5.4.0\\\\CMSIS\\\\Core\\\\Include\" \"-IC:\\\\Eclipse\\\\Firmware-3.6\\\\CoreN2G\\\\src\\\\atmel\\\\SAME51_DFP\\\\1.1.139\\\\include\" \"-IC:\\\\Eclipse\\\\Firmware-3.6\\\\RRFLibraries\\\\src\" \"-IC:\\\\Eclipse\\\\Firmware-3.6\\\\CANlib\\\\src\" \"-IC:\\\\Eclipse\\\\Firmware-3.6\\\\FreeRTOS\\\\src\\\\include\" \"-IC:\\\\Eclipse\\\\Firmware-3.6\\\\FreeRTOS\\\\src\\\\portable\\\\GCC\\\\ARM_CM4F\" -O3 -Wall -c -mcpu\u003dcortex-m4 -mthumb -fno-math-errno -mfpu\u003dfpv4-sp-d16 -mfloat-abi\u003dhard -mfp16-format\u003dieee -ffunction-sections -fdata-sections -fno-threadsafe-statics -fno-rtti -fno-exceptions -nostdlib -Wundef -Wdouble-promotion -Werror\u003dreturn-type -fsingle-precision-constant -Wa,-al\u003d$*.s -o C:/Eclipse/Firmware-3.6/Duet3Expansion/EXP1HCL/src/CAN/CanInterface.o C:/Eclipse/Firmware-3.6/Duet3Expansion/src/CAN/CanInterface.cpp",
    "file": "C:/Eclipse/Firmware-3.6/Duet3Expansion/src/CAN/CanInterface.cpp"
  },
  {
    "directory": "C:/Eclipse/Firmware-3.6/Duet3Expansion/EXP1HCL",
    "command": "\"C:/Program Files (x86)/Arm GNU Toolchain arm-none-eabi/13.2 Rel1/bin/arm-none-eabi-g++.exe\" -std\u003dgnu++17 -D__SAME51G19A__ -D__ARM_ARCH_7EM__\u003d1 -DEXP1HCL -DRTOS \"-IC:\\\\Eclipse\\\\Firmware-3.6\\\\CoreN2G\" \"-IC:\\\\Eclipse\\\\Firmware-3.6\\\\FreeRTOS\" \"-IC:\\\\Eclipse\\\\Firmware-3.6\\\\Duet3Expansion\\\\src\" \"-IC:\\\\Eclipse\\\\Firmware-3.6\\\\CoreN2G\\\\src\" \"-IC:\\\\Eclipse\\\\Firmware-3.6\\\\CoreN2G\\\\src\\\\SAME5x_C21\" \"-IC:\\\\Eclipse\\\\Firmware-3.6\\\\CoreN2G\\\\src\\\\SAME5x_C21\\\\SAME5x\\\\hal\\\\include\" \"-IC:\\\\Eclipse\\\\Firmware-3.6\\\\CoreN2G\\\\src\\\\SAME5x_C21\\\\SAME5x\\\\hal\\\\utils\\\\include\" \"-IC:\\\\Eclipse\\\\Firmware-3.6\\\\CoreN2G\\\\src\\\\SAME5x_C21\\\\SAME5x\\\\hri\" \"-IC:\\\\Eclipse\\\\Firmware-3.6\\\\CoreN2G\\\\src\\\\arm\\\\CMSIS\\\\5.4.0\\\\CMSIS\\\\Core\\\\Include\" \"-IC:\\\\Eclipse\\\\Firmware-3.6\\\\CoreN2G\\\\src\\\\atmel\\\\SAME51_DFP\\\\1.1.139\\\\include\" \"-IC:\\\\Eclipse\\\\Firmware-3.6\\\\RRFLibraries\\\\src\" \"-IC:\\\\Eclipse\\\\Firmware-3.6\\\\CANlib\\\\src\" \"-IC:\\\\Eclipse\\\\Firmware-3.6\\\\FreeRTOS\\\\src\\\\include\" \"-IC:\\\\Eclipse\\\\Firmware-3.6\\\\FreeRTOS\\\\src\\\\portable\\\\GCC\\\\ARM_CM4F\" -O3 -Wall -c -mcpu\u003dcortex-m4 -mthumb -fno-math-errno -mfpu\u003dfpv4-sp-d16 -mfloat-abi\u003dhard -mfp16-format\u003dieee -ffunction-sections -fdata-sections -fno-threadsafe-statics -fno-rtti -fno-exceptions -nostdlib -Wundef -Wdouble-promotion -Werror\u003dreturn-type -fsingle-precision-constant -Wa,-al\u003d$*.s -o C:/Eclipse/Firmware-3.6/Duet3Expansion/EXP1HCL/src/CAN/CanMessageQueue.o C:/Eclipse/Firmware-3.6/Duet3Expansion/src/CAN/CanMessageQueue.cpp",
    "file": "C:/Eclipse/Firmware-3.6/Duet3Expansion/src/CAN/CanMessageQueue.cpp"
  },

#1130 was closed but the issue is still present #1382

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