bear fails with erro

[ghost]

Describe the bug

bear is unable to produce compile_commands.json, fails with GLIBC error

Steps To Reproduce

Steps to reproduce the behavior:
executing bear -- make all inside a nix results in the following error
/usr/bin/env: /lib/x86_64-linux-gnu/libc.so.6: version 'GLIBC_2.38' not found (required by /nix/store/dghjv6hfz0s0z4kffa5ahyw2mhp79215-gcc-12.3.0-lib/lib/libstdc++.so.6)

Notify maintainers

@babariviere
@alyssais

Metadata

[user@system:~]$ nix-shell -p nix-info --run "nix-info -m"
this path will be fetched (0.00 MiB download, 0.00 MiB unpacked):
  /nix/store/zzjrl1zzc0lbwlc8dvs98l5k906cwd7z-nix-info
copying path '/nix/store/zzjrl1zzc0lbwlc8dvs98l5k906cwd7z-nix-info' from 'https://cache.nixos.org'...
 - system: `"x86_64-linux"`
 - host os: `Linux 5.15.133.1-microsoft-standard-WSL2, Debian GNU/Linux, 12 (bookworm), nobuild`
 - multi-user?: `no`
 - sandbox: `no`
 - version: `nix-env (Nix) 2.8.0`
 - channels(root): `"nixos-23.11-23.11, nixpkgs"`
 - channels(ah): `""`
 - nixpkgs: `/nix/var/nix/profiles/per-user/root/channels/nixpkgs`

[DieracDelta]

#238531 this fix gets bear working for me fwiw

[laggron42]

This is still happening for me, using 23.11 or unstable.

[DieracDelta]

@laggron42 looks like the backport is still open. The patch that fixes the problem hasn't made its way from master into 23.11 or unstable. #279035 (comment)

[laggron42]

@DieracDelta Thanks for your answer! I have pulled from master, but the problem still happens for me:

epita@rayquaza ~/tc $ nix develop --ignore-environment
bash-5.2$ bear -- make
  GEN      src/version.stamp
/bin/sh: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_ABI_DT_RELR' not found (required by /nix/store/ksk3rnb0ljx8gngzk19jlmbjyvac4hw6-glibc-2.38-44/lib/libdl.so.2)
/bin/sh: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by /nix/store/pp0jsd045xvfsz60kpbkfxbs9pbpk8z5-gcc-13.2.0-lib/lib/libstdc++.so.6)
/bin/sh: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.36' not found (required by /nix/store/pp0jsd045xvfsz60kpbkfxbs9pbpk8z5-gcc-13.2.0-lib/lib/libstdc++.so.6)
/bin/sh: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_ABI_DT_RELR' not found (required by /nix/store/ksk3rnb0ljx8gngzk19jlmbjyvac4hw6-glibc-2.38-44/lib/libm.so.6)
make: *** [Makefile:2300: src/version.stamp] Error 1

The output of nix derivation show seems to indicate that my environment holds the patched bear by the presence of ./fix-functional-tests.patch and the additional CMake flags:

Output of nix derivation show

epita@rayquaza ~/tc $ nix develop
bash-5.2$ which bear
/nix/store/j0hm34ln27wpx05l0zbv7c4mria926xc-bear-3.1.3/bin/bear

nix derivation show /nix/store/j0hm34ln27wpx05l0zbv7c4mria926xc-bear-3.1.3

{
  "/nix/store/w86rc4js58760n5qr8fimizap85547g3-bear-3.1.3.drv": {
    "args": [
      "-e",
      "/nix/store/v6x3cs394jgqfbi0a42pam708flxaphh-default-builder.sh"
    ],
    "builder": "/nix/store/4vzal97iq3dmrgycj8r0gflrh51p8w1s-bash-5.2p26/bin/bash",
    "env": {
      "__structuredAttrs": "",
      "buildInputs": "/nix/store/nl6dmqmbcliwaqmzcsyh8q09aa8r4s11-grpc-1.62.0 /nix/store/5g29ind1alcyqa7r820jvhmcpyi5i8pb-protobuf-24.4 /nix/store/xpz5n8nd9minrr31yw2d63xwg0941xb7-openssl-3.0.13-dev /nix/store/fnc247gqx35njq660m7aylf7cf0shxb4-nlohmann_json-3.11.3 /nix/store/zbbp7rpnlv7jk8ynj07zjrqsli9jm7y6-gtest-1.14.0-dev /nix/store/7k5dkgi4hqcqpzr9zsr2g5favzqndsan-spdlog-1.13.0-dev /nix/store/w3cv7kvp2ax8mh06vk3w234wh4ir105a-c-ares-1.27.0-dev /nix/store/hlirwi0zfhna90xp2j2mnyplyjz437h5-zlib-1.3.1-dev /nix/store/17iz09krgkygjb4dkl2r76y5dnw8r7yk-sqlite-3.45.1-dev /nix/store/20brkr5zibka9wjn44dspp1jibrc1scl-re2-2024-02-01-dev",
      "builder": "/nix/store/4vzal97iq3dmrgycj8r0gflrh51p8w1s-bash-5.2p26/bin/bash",
      "cmakeFlags": "-DCMAKE_INSTALL_BINDIR=bin -DCMAKE_INSTALL_LIBDIR=lib -DENABLE_UNIT_TESTS:BOOL=FALSE -DENABLE_FUNC_TESTS:BOOL=FALSE",
      "configureFlags": "",
      "depsBuildBuild": "",
      "depsBuildBuildPropagated": "",
      "depsBuildTarget": "",
      "depsBuildTargetPropagated": "",
      "depsHostHost": "",
      "depsHostHostPropagated": "",
      "depsTargetTarget": "",
      "depsTargetTargetPropagated": "",
      "doCheck": "",
      "doInstallCheck": "",
      "mesonFlags": "",
      "name": "bear-3.1.3",
      "nativeBuildInputs": "/nix/store/9walp7knvqvmnpp9pqwjsdpnx2524ack-cmake-3.28.3 /nix/store/d6bvhfhg3aw2lj0nyb08y0ahlj5md6p8-ninja-1.11.1 /nix/store/a3752l19hc76dmzh1wgrxbsxh6lfx67z-pkg-config-wrapper-0.29.2 /nix/store/j3rcmgzjg61h94fgcjj4kpysvr0miz6l-python3.11-lit-17.0.6 /nix/store/3v2ch16fkl50i85n05h5ckss8pxx6836-python3-3.11.8",
      "out": "/nix/store/j0hm34ln27wpx05l0zbv7c4mria926xc-bear-3.1.3",
      "outputs": "out",
      "patches": "/nix/store/aym0v0a1c7wix8fywy2bg0likz5q100s-fix-functional-tests.patch",
      "pname": "bear",
      "postPatch": "patchShebangs test/bin\n\n# /usr/bin/env is used in test commands and embedded scripts.\nfind test -name '*.sh' \\\n  -exec sed -ie 's|/usr/bin/env|/nix/store/mb488rr560vq1xnl10hinnyfflcrd51n-coreutils-9.4/bin/env|g' {} +\n",
      "propagatedBuildInputs": "",
      "propagatedNativeBuildInputs": "",
      "src": "/nix/store/blwxxfk6dk91xms2pxgchpscv54izg0y-source",
      "stdenv": "/nix/store/v099hqvw5z87423p4hz1vfhzaqa07dii-stdenv-linux",
      "strictDeps": "",
      "system": "x86_64-linux",
      "version": "3.1.3"
    },
    "inputDrvs": {
      "/nix/store/092s4n6d7dhm1xcfl5m1q4qybnnwn1lw-gtest-1.14.0.drv": {
        "dynamicOutputs": {},
        "outputs": [
          "dev"
        ]
      },
      "/nix/store/28dkg1wfig3f7vwf7gxbi90kppzdcngy-nlohmann_json-3.11.3.drv": {
        "dynamicOutputs": {},
        "outputs": [
          "out"
        ]
      },
      "/nix/store/2gp6pdljs2b8rv7spyqn1zx62hpp3q4m-re2-2024-02-01.drv": {
        "dynamicOutputs": {},
        "outputs": [
          "dev"
        ]
      },
      "/nix/store/4risxx9frn02fraphwrb0jbcpcx78a0g-ninja-1.11.1.drv": {
        "dynamicOutputs": {},
        "outputs": [
          "out"
        ]
      },
      "/nix/store/66j28a1lxf21cl3fbsynqc2ac79dgzag-cmake-3.28.3.drv": {
        "dynamicOutputs": {},
        "outputs": [
          "out"
        ]
      },
      "/nix/store/77827b36qz2s0713m61z12w73sr3dzlz-python3.11-lit-17.0.6.drv": {
        "dynamicOutputs": {},
        "outputs": [
          "out"
        ]
      },
      "/nix/store/8brdx72cmmmjrap80d8x4k58f69h4247-stdenv-linux.drv": {
        "dynamicOutputs": {},
        "outputs": [
          "out"
        ]
      },
      "/nix/store/9by54ylsfw1a617njnldvhn8dr5j01wx-pkg-config-wrapper-0.29.2.drv": {
        "dynamicOutputs": {},
        "outputs": [
          "out"
        ]
      },
      "/nix/store/bnkny1qgs16q84kshlmfqdnc8a154nzy-coreutils-9.4.drv": {
        "dynamicOutputs": {},
        "outputs": [
          "out"
        ]
      },
      "/nix/store/bzik9pfby875yv5xzchcs9ad3mvaahc1-grpc-1.62.0.drv": {
        "dynamicOutputs": {},
        "outputs": [
          "out"
        ]
      },
      "/nix/store/ccxb8wmah8w11x94n58hxzi5z25nkrc9-openssl-3.0.13.drv": {
        "dynamicOutputs": {},
        "outputs": [
          "dev"
        ]
      },
      "/nix/store/gp8zp58fh5rfrz4ypqqq460dlihaldk7-sqlite-3.45.1.drv": {
        "dynamicOutputs": {},
        "outputs": [
          "dev"
        ]
      },
      "/nix/store/ha2jqykyvnszwdd40x58bpswfqlp956b-zlib-1.3.1.drv": {
        "dynamicOutputs": {},
        "outputs": [
          "dev"
        ]
      },
      "/nix/store/i8lcijxxjy4akf79741l8m6aasg2cw9g-spdlog-1.13.0.drv": {
        "dynamicOutputs": {},
        "outputs": [
          "dev"
        ]
      },
      "/nix/store/kpgpdkllqj1jp4fq1ky418axbfxf8v7x-c-ares-1.27.0.drv": {
        "dynamicOutputs": {},
        "outputs": [
          "dev"
        ]
      },
      "/nix/store/kqbwi7q7b4nq8m4xh7m5d08yiijfdvsj-python3-3.11.8.drv": {
        "dynamicOutputs": {},
        "outputs": [
          "out"
        ]
      },
      "/nix/store/p4hkq7hz2y80b43rz9nn3253ki69l73z-protobuf-24.4.drv": {
        "dynamicOutputs": {},
        "outputs": [
          "out"
        ]
      },
      "/nix/store/pmrqjyxrwr4m19pah4l698xkx8z9cwni-source.drv": {
        "dynamicOutputs": {},
        "outputs": [
          "out"
        ]
      },
      "/nix/store/y1j406svnfr5i2i78z4ybg8rg30ngmkj-bash-5.2p26.drv": {
        "dynamicOutputs": {},
        "outputs": [
          "out"
        ]
      }
    },
    "inputSrcs": [
      "/nix/store/aym0v0a1c7wix8fywy2bg0likz5q100s-fix-functional-tests.patch",
      "/nix/store/v6x3cs394jgqfbi0a42pam708flxaphh-default-builder.sh"
    ],
    "name": "bear-3.1.3",
    "outputs": {
      "out": {
        "path": "/nix/store/j0hm34ln27wpx05l0zbv7c4mria926xc-bear-3.1.3"
      }
    },
    "system": "x86_64-linux"
  }
}

If this helps, here's the metadata on my machine

epita@rayquaza ~/tc $ nix-shell -p nix-info --run "nix-info -m"
 - system: `"x86_64-linux"`
 - host os: `Linux 5.15.0-91-generic, Ubuntu, 22.04.3 LTS (Jammy Jellyfish), nobuild`
 - multi-user?: `yes`
 - sandbox: `yes`
 - version: `nix-env (Nix) 2.18.1`
 - channels(epita): `"home-manager"`
 - channels(root): `"nixpkgs"`
 - nixpkgs: `/nix/var/nix/profiles/per-user/root/channels/nixpkgs`

[DieracDelta]

Ack, yeah it's broken for me too (with the same error). Not sure how to fix that...

[DieracDelta]

So, it's a mismatch between the glibc in nix-23.11 and nixos-unstable/master. If I rebuild my own config with nixos-unstable then nix run nixpkgs#bear -- make, compile_commands are generated and I get no errors.

[siraben]

Closing because it's due to nixpkgs versioning mismatch, and works on unstable.

[ro6]

Still doesn't work for me. Is there some requirement that that Bear be built against an older version of glibc than what you run it with? In that case, I may need to pin an older version since I'm running on CentOS 7 with glibc 2.17. Or maybe I just need to set up the environment so bear dynamically links against a glibc from the nix store at runtime? I don't know bear internals enough to know how it interacts with the program being wrapped, and whether their glibc versions need to be compatible.

I'm still getting errors like:

make: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by /nix/store/f4szlnrx9x7nhm026qg0nraxw4v5d304-bear-3.1.4/lib/bear/libexec.so)
make: /lib64/libc.so.6: version `GLIBC_2.33' not found (required by /nix/store/f4szlnrx9x7nhm026qg0nraxw4v5d304-bear-3.1.4/lib/bear/libexec.so)
make: /lib64/libc.so.6: version `GLIBC_2.36' not found (required by /nix/store/wlffq5p6mxxgfap10sav3ij936jzqm59-glibc-2.39-52/lib/libdl.so.2)
make: /lib64/libc.so.6: version `GLIBC_ABI_DT_RELR' not found (required by /nix/store/wlffq5p6mxxgfap10sav3ij936jzqm59-glibc-2.39-52/lib/libdl.so.2)
make: /lib64/libc.so.6: version `GLIBC_2.38' not found (required by /nix/store/zx9zgvy2nsxcmpn0fzx277m5lk352cdf-gcc-13.3.0-lib/lib/libstdc++.so.6)
make: /lib64/libc.so.6: version `GLIBC_2.26' not found (required by /nix/store/zx9zgvy2nsxcmpn0fzx277m5lk352cdf-gcc-13.3.0-lib/lib/libstdc++.so.6)
make: /lib64/libc.so.6: version `GLIBC_2.33' not found (required by /nix/store/zx9zgvy2nsxcmpn0fzx277m5lk352cdf-gcc-13.3.0-lib/lib/libstdc++.so.6)
make: /lib64/libc.so.6: version `GLIBC_2.25' not found (required by /nix/store/zx9zgvy2nsxcmpn0fzx277m5lk352cdf-gcc-13.3.0-lib/lib/libstdc++.so.6)
make: /lib64/libc.so.6: version `GLIBC_2.18' not found (required by /nix/store/zx9zgvy2nsxcmpn0fzx277m5lk352cdf-gcc-13.3.0-lib/lib/libstdc++.so.6)
make: /lib64/libc.so.6: version `GLIBC_2.32' not found (required by /nix/store/zx9zgvy2nsxcmpn0fzx277m5lk352cdf-gcc-13.3.0-lib/lib/libstdc++.so.6)
make: /lib64/libc.so.6: version `GLIBC_2.36' not found (required by /nix/store/zx9zgvy2nsxcmpn0fzx277m5lk352cdf-gcc-13.3.0-lib/lib/libstdc++.so.6)
make: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by /nix/store/zx9zgvy2nsxcmpn0fzx277m5lk352cdf-gcc-13.3.0-lib/lib/libstdc++.so.6)
make: /lib64/libc.so.6: version `GLIBC_2.36' not found (required by /nix/store/wlffq5p6mxxgfap10sav3ij936jzqm59-glibc-2.39-52/lib/libm.so.6)
make: /lib64/libc.so.6: version `GLIBC_ABI_DT_RELR' not found (required by /nix/store/wlffq5p6mxxgfap10sav3ij936jzqm59-glibc-2.39-52/lib/libm.so.6)
make: /lib64/libc.so.6: version `GLIBC_2.35' not found (required by /nix/store/zx9zgvy2nsxcmpn0fzx277m5lk352cdf-gcc-13.3.0-lib/lib/libgcc_s.so.1)
make: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by /nix/store/zx9zgvy2nsxcmpn0fzx277m5lk352cdf-gcc-13.3.0-lib/lib/libgcc_s.so.1)