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nanoporetech / modkit

A bioinformatics tool for working with modified bases
https://nanoporetech.com/
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Install failed: fatal error: '-fuse-linker-plugin', but liblto_plugin.so not found #291

Open liuyang2006 opened 4 days ago

liuyang2006 commented 4 days ago

I cannot install the software based on README file:

Here is my command used:

cargo install --path .

Error message:

(cargo) [yliu8962@d05-10 modkit]$ cargo install --path .

  Installing mod_kit v0.4.1 (/project/sli68423_1316/users/yang/tools/modkit)
    Updating crates.io index
     Locking 270 packages to latest compatible versions
      Adding bio v1.6.0 (latest: v2.0.3)
      Adding bit-set v0.5.3 (latest: v0.8.0)
      Adding bit-vec v0.6.3 (latest: v0.8.0)
      Adding charming v0.3.1 (latest: v0.4.0)
      Adding derive-new v0.5.9 (latest: v0.7.0)
      Adding derive-new v0.6.0 (latest: v0.7.0)
      Adding destructure_traitobject v0.2.0 (latest: v0.3.0)
      Adding encode_unicode v0.3.6 (latest: v1.0.0)
      Adding fixedbitset v0.4.2 (latest: v0.5.7)
      Adding flume v0.10.14 (latest: v0.11.1)
      Adding generic-array v0.14.7 (latest: v1.1.0)
      Adding handlebars v4.5.0 (latest: v6.2.0)
      Adding hashbrown v0.13.2 (latest: v0.15.0)
      Adding heck v0.4.1 (latest: v0.5.0)
      Adding hermit-abi v0.3.9 (latest: v0.4.0)
      Adding idna v0.5.0 (latest: v1.0.2)
      Adding itertools v0.11.0 (latest: v0.13.0)
      Adding itertools v0.12.1 (latest: v0.13.0)
      Adding libdeflate-sys v0.12.0 (latest: v1.22.0)
      Adding libdeflater v0.12.0 (latest: v1.22.0)
      Adding linux-raw-sys v0.4.14 (latest: v0.6.5)
      Adding lru v0.9.0 (latest: v0.12.5)
      Adding multimap v0.9.1 (latest: v0.10.0)
      Adding nalgebra v0.29.0 (latest: v0.33.1)
      Adding nalgebra-macros v0.1.0 (latest: v0.2.2)
      Adding ndarray v0.15.6 (latest: v0.16.1)
      Adding ordered-float v2.10.1 (latest: v4.4.0)
      Adding ordered-float v3.9.2 (latest: v4.4.0)
      Adding peroxide v0.32.1 (latest: v0.37.9)
      Adding puruspe v0.2.5 (latest: v0.3.0)
      Adding quick-error v1.2.3 (latest: v2.0.1)
      Adding radium v0.7.0 (latest: v1.1.0)
      Adding rust-htslib v0.46.0 (latest: v0.47.0)
      Adding rustc-hash v1.1.0 (latest: v2.0.0)
      Adding rustc_version v0.1.7 (latest: v0.4.1)
      Adding rv v0.16.0 (latest: v0.17.0)
      Adding semver v0.1.20 (latest: v1.0.23)
      Adding simba v0.6.0 (latest: v0.9.0)
      Adding special v0.10.3 (latest: v0.11.2)
      Adding statrs v0.16.1 (latest: v0.17.1)
      Adding strum v0.25.0 (latest: v0.26.3)
      Adding strum_macros v0.25.3 (latest: v0.26.4)
      Adding syn v1.0.109 (latest: v2.0.85)
      Adding term v0.7.0 (latest: v1.0.0)
      Adding thread-id v4.2.2 (latest: v5.0.0)
      Adding unicode-width v0.1.14 (latest: v0.2.0)
      Adding wasi v0.11.0+wasi-snapshot-preview1 (latest: v0.13.3+wasi-0.2.2)
      Adding windows-core v0.52.0 (latest: v0.58.0)
      Adding windows-sys v0.52.0 (latest: v0.59.0)
      Adding wyz v0.5.1 (latest: v0.6.1)
      Adding zerocopy v0.7.35 (latest: v0.8.7)
      Adding zerocopy-derive v0.7.35 (latest: v0.8.7)
   Compiling libc v0.2.161
error: linking with `/project/sli68423_1316/users/yang/conda/envs/cargo/bin/x86_64-conda-linux-gnu-cc` failed: exit status: 1
  |
  = note: LC_ALL="C" PATH="/project/sli68423_1316/users/yang/conda/envs/cargo/lib/rustlib/x86_64-unknown-linux-gnu/bin:/project/sli68423_1316/users/yang/conda/envs/cargo/lib/rustlib/x86_64-unknown-linux-gnu/bin:/project/sli68423_1316/users/yang/conda/envs/cargo/lib/rustlib/x86_64-unknown-linux-gnu/bin:/project/sli68423_1316/users/yang/conda/envs/cargo/bin:/spack/2206/apps/linux-centos7-x86_64_v3/gcc-11.3.0/rust-1.60.0-273igj4/bin:/spack/2206/apps/linux-centos7-x86_64_v3/gcc-11.3.0/tmux-3.3a-m5kg7vt/bin:/spack/2206/apps/linux-centos7-x86_64_v3/gcc-11.3.0/pmix-3.2.3-o4owkss/bin:/spack/2206/apps/linux-centos7-x86_64_v3/gcc-11.3.0/openmpi-4.1.4-4w23jca/bin:/spack/2206/apps/linux-centos7-x86_64_v3/gcc-11.3.0/openblas-0.3.21-afcoykn/bin:/spack/apps/gcc/11.3.0/bin:/spack/utilities:/spack/conda/miniforge3/24.3.0/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/project/sli68423_1316/users/yang/scripts:/home1/yliu8962/.local/bin:/home1/yliu8962/bin" VSLANG="1033" "/project/sli68423_1316/users/yang/conda/envs/cargo/bin/x86_64-conda-linux-gnu-cc" "-m64" "/tmp/SLURM_26690861/rustcX4pZFu/symbols.o" "/project/sli68423_1316/users/yang/tools/modkit/target/release/build/libc-44655db41e767daf/build_script_build-44655db41e767daf.build_script_build.89f7cbb8a3b77216-cgu.0.rcgu.o" "/project/sli68423_1316/users/yang/tools/modkit/target/release/build/libc-44655db41e767daf/build_script_build-44655db41e767daf.build_script_build.89f7cbb8a3b77216-cgu.1.rcgu.o" "/project/sli68423_1316/users/yang/tools/modkit/target/release/build/libc-44655db41e767daf/build_script_build-44655db41e767daf.build_script_build.89f7cbb8a3b77216-cgu.2.rcgu.o" "/project/sli68423_1316/users/yang/tools/modkit/target/release/build/libc-44655db41e767daf/build_script_build-44655db41e767daf.build_script_build.89f7cbb8a3b77216-cgu.3.rcgu.o" "/project/sli68423_1316/users/yang/tools/modkit/target/release/build/libc-44655db41e767daf/build_script_build-44655db41e767daf.215r0kdgl730yxmhzgg8twriu.rcgu.o" "-Wl,--as-needed" "-L" "/project/sli68423_1316/users/yang/tools/modkit/target/release/deps" "-L" "/project/sli68423_1316/users/yang/conda/envs/cargo/lib/rustlib/x86_64-unknown-linux-gnu/lib" "-Wl,-Bstatic" "/project/sli68423_1316/users/yang/conda/envs/cargo/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd-1c4b19562077c20d.rlib" "/project/sli68423_1316/users/yang/conda/envs/cargo/lib/rustlib/x86_64-unknown-linux-gnu/lib/libpanic_unwind-85a631ebc91746e0.rlib" "/project/sli68423_1316/users/yang/conda/envs/cargo/lib/rustlib/x86_64-unknown-linux-gnu/lib/libobject-fdace1a0b4cda412.rlib" "/project/sli68423_1316/users/yang/conda/envs/cargo/lib/rustlib/x86_64-unknown-linux-gnu/lib/libmemchr-e5c28d21823e9a85.rlib" "/project/sli68423_1316/users/yang/conda/envs/cargo/lib/rustlib/x86_64-unknown-linux-gnu/lib/libaddr2line-1e0edbcd516a8cce.rlib" "/project/sli68423_1316/users/yang/conda/envs/cargo/lib/rustlib/x86_64-unknown-linux-gnu/lib/libgimli-77a1dc5e8fb357d6.rlib" "/project/sli68423_1316/users/yang/conda/envs/cargo/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_demangle-8c9d2edb6dff139f.rlib" "/project/sli68423_1316/users/yang/conda/envs/cargo/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd_detect-ecadd85ae8bacc0c.rlib" "/project/sli68423_1316/users/yang/conda/envs/cargo/lib/rustlib/x86_64-unknown-linux-gnu/lib/libhashbrown-67895a0c8dd8130b.rlib" "/project/sli68423_1316/users/yang/conda/envs/cargo/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_alloc-5b4263e767961458.rlib" "/project/sli68423_1316/users/yang/conda/envs/cargo/lib/rustlib/x86_64-unknown-linux-gnu/lib/libminiz_oxide-4f03d5a171522141.rlib" "/project/sli68423_1316/users/yang/conda/envs/cargo/lib/rustlib/x86_64-unknown-linux-gnu/lib/libadler-9e4e8543de06315e.rlib" "/project/sli68423_1316/users/yang/conda/envs/cargo/lib/rustlib/x86_64-unknown-linux-gnu/lib/libunwind-7fc51dfce9c057eb.rlib" "/project/sli68423_1316/users/yang/conda/envs/cargo/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcfg_if-7ec98a9b1cc1792f.rlib" "/project/sli68423_1316/users/yang/conda/envs/cargo/lib/rustlib/x86_64-unknown-linux-gnu/lib/liblibc-2f9b4333f6d32438.rlib" "/project/sli68423_1316/users/yang/conda/envs/cargo/lib/rustlib/x86_64-unknown-linux-gnu/lib/liballoc-b6fe0262c36c500a.rlib" "/project/sli68423_1316/users/yang/conda/envs/cargo/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_core-2a862c0b1c86f483.rlib" "/project/sli68423_1316/users/yang/conda/envs/cargo/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcore-500f37ee5bcf0ffe.rlib" "/project/sli68423_1316/users/yang/conda/envs/cargo/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcompiler_builtins-06dfbf1de02fde3b.rlib" "-Wl,-Bdynamic" "-lgcc_s" "-lutil" "-lrt" "-lpthread" "-lm" "-ldl" "-lc" "-Wl,--eh-frame-hdr" "-Wl,-z,noexecstack" "-L" "/project/sli68423_1316/users/yang/conda/envs/cargo/lib/rustlib/x86_64-unknown-linux-gnu/lib" "-o" "/project/sli68423_1316/users/yang/tools/modkit/target/release/build/libc-44655db41e767daf/build_script_build-44655db41e767daf" "-Wl,--gc-sections" "-pie" "-Wl,-z,relro,-z,now" "-Wl,--strip-debug" "-nodefaultlibs"
  = note: x86_64-conda-linux-gnu-cc: fatal error: '-fuse-linker-plugin', but liblto_plugin.so not found
          compilation terminated.

error: could not compile `libc` (build script) due to 1 previous error
error: failed to compile `mod_kit v0.4.1 (/project/sli68423_1316/users/yang/tools/modkit)`, intermediate artifacts can be found at `/project/sli68423_1316/users/yang/tools/modkit/target`.
To reuse those artifacts with a future compilation, set the environment variable `CARGO_TARGET_DIR` to that path.
ArtRand commented 3 days ago

Hello @liuyang2006,

Could you tell me how you installed rust and cargo as well as the platform you're running on?. From a quick internet search, I found this SO thread, it might be helpful. If you're on linux, do the pre-compiled binaries work?