compile_commands.json doesnt find system headers.

[Zeed-gn]

I'm using https://github.com/bazel-contrib/toolchains_llvm to set up the toolchain the project should use and making sure everything looks right. Everything compiles, and the compile_commands.json seems to generated, mostly correct. Except that the system headers (libc, libc++, etc) are being pulled from the host instead from the bazel-.../external/toolchain_ path. So C++20 headers are not found.

There is no sysroot flag on the compile_commands, so I will assume that make clangd use whatever the host is using.

Is there something else I need to set?

[Zeed-gn]

Actually just tried with the host(gcc), seems like the certain paths are available, but the C++ header path is not properly added into the compile_commands.json.
While bazel resolves evertyhing nicely, the compile commands for a sample binary:

cc_binary(
     name = "foo",
     srcs = ["foo.cc"]
  )

foo.cc

#include <vector>
int main(int, char**) { return 0;}

Generates the following compile_commands.json

  {
  "file": "foo.cc",
  "arguments": [
    "/usr/bin/gcc",
    "-xc++",
    "-U_FORTIFY_SOURCE",
    "-fstack-protector",
    "-Wall",
    "-Wunused-but-set-parameter",
    "-Wno-free-nonheap-object",
    "-fno-omit-frame-pointer",
    "-std=c++14",
    "-MD",
    "-MF",
    "bazel-out/k8-fastbuild/bin/_objs/foo/foo.pic.d",
    "-frandom-seed=bazel-out/k8-fastbuild/bin/_objs/foo/foo.pic.o",
    "-fPIC",
    "-iquote",
    ".",
    "-iquote",
    "bazel-out/k8-fastbuild/bin",
    "-std=c++20",
    "-Wall",
    "-Werror",
    "-Wextra",
    "-Wextra-semi",
    "-Wconversion",
    "-Wno-unused-parameter",
    "-Wold-style-cast",
    "-Wwrite-strings",
    "-Wimplicit-fallthrough",
    "-fno-exceptions",
    "-fno-rtti",
    "-fomit-frame-pointer",
    "-funwind-tables",
    "-Wno-builtin-macro-redefined",
    "-D__DATE__=\"redacted\"",
    "-D__TIMESTAMP__=\"redacted\"",
    "-D__TIME__=\"redacted\"",
    "-c",
    "foo.cc",
    "-o",
    "bazel-out/k8-fastbuild/bin/_objs/foo/foo.pic.o"
  ],
  "directory": "/home/user/repos/new_repo"
},

Now clangd fail to find though <c++/13/vector> exists.

[Zeed-gn]

Curerrent compile command commit: "1e08f8e0507b6b6b1f4416a9a22cf5c28beaba93" (HEAD)
Current bazel version: "7.3.1"

[Zeed-gn]

Hacking out a local repo, that injects -isystem for each builtin directory seems to work. Though have to strip nested external, since it seems that external repositories that depend on each other end up generating nested external paths.
repo1 being llvm_toolchain and repo2 being llvm_toolchain_llvm, in the llvm_toolchain mod. There is probably a less hacky way to do this.

external/repo1/external/repo2/path_to_bin.

external/toolchains_llvm~~llvm~llvm_toolchain/bin/cc_wrapper.sh -xc++ -U_FORTIFY_SOURCE --target=x86_64-unknown-linux-gnu -U_FORTIFY_SOURCE -fstack-protector -fno-omit-frame-pointer -fcolor-diagnostics -Wall -Wthread-safety -Wself-assign -std=c++17 -stdlib=libc++ -Xclang -fno-cxx-modules -MD -MF bazel-out/k8-fastbuild/bin/_objs/foo/foo.pic.d -frandom-seed=bazel-out/k8-fastbuild/bin/_objs/foo/foo.pic.o -fPIC -iquote . -iquote bazel-out/k8-fastbuild/bin -iquote external/bazel_tools -iquote bazel-out/k8-fastbuild/bin/external/bazel_tools -std=c++20 -Wall -Werror -Wextra -Wextra-semi -Wconversion -Wno-unused-parameter -Wold-style-cast -Wwrite-strings -Wimplicit-fallthrough -fno-exceptions -fno-rtti -fomit-frame-pointer -funwind-tables -no-canonical-prefixes -Wno-builtin-macro-redefined "-D__DATE__=\"redacted\"" "-D__TIMESTAMP__=\"redacted\"" "-D__TIME__=\"redacted\"" -c -o bazel-out/k8-fastbuild/bin/_objs/foo/foo.pic.o -Iexternal/toolchains_llvm~~llvm~llvm_toolchain_llvm/include/c++/v1 -Iexternal/toolchains_llvm~~llvm~llvm_toolchain_llvm/include/x86_64-unknown-linux-gnu/c++/v1 -Iexternal/toolchains_llvm~~llvm~llvm_toolchain_llvm/lib/clang/19.1.0/include -Iexternal/toolchains_llvm~~llvm~llvm_toolchain_llvm/lib/clang/19.1.0/share -Iexternal/toolchains_llvm~~llvm~llvm_toolchain_llvm/lib64/clang/19.1.0/include -Iexternal/toolchains_llvm~~llvm~llvm_toolchain_llvm/lib/clang/19/include -Iexternal/toolchains_llvm~~llvm~llvm_toolchain_llvm/lib/clang/19/share -Iexternal/toolchains_llvm~~llvm~llvm_toolchain_llvm/lib64/clang/19/include -I/usr/include -I/usr/local/include -resource-dir=/hom_path/.cache/bazel/_bazel_user/85ee35e2f2022d11c5822a0c418173da/external/toolchains_llvm~~llvm~llvm_toolchain_llvm/lib/clang/19 -- /path_to_repo/foo.cc