installation of SCENIC+ failure

[daccachejoe]

Hi Seppe-

I went to install SCENIC+ as always and ran into an error when scatac_fragment_tools was being built. Can you seem to tell what the issue may be? I've went and installed rust and cmake in this conda environment and the error persists.

Thanks! Joe

Error:

  error: subprocess-exited-with-error

  × Building wheel for scatac-fragment-tools (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [62 lines of output]
      Running `maturin pep517 build-wheel -i /gpfs/home/jd5457/naiklink/jd5457/.conda/envs/sc-multiome-pipeline-env/bin/python3.8 --compatibility off`
      🍹 Building a mixed python/rust project
      🔗 Found pyo3 bindings
      🐍 Found CPython 3.8 at /gpfs/home/jd5457/naiklink/jd5457/.conda/envs/sc-multiome-pipeline-env/bin/python3.8
      📡 Using build options features from pyproject.toml
         Compiling libc v0.2.152
         Compiling pkg-config v0.3.28
         Compiling proc-macro2 v1.0.76
         Compiling unicode-ident v1.0.12
         Compiling vcpkg v0.2.15
         Compiling quote v1.0.35
         Compiling jobserver v0.1.26
         Compiling target-lexicon v0.12.13
         Compiling syn v1.0.109
         Compiling cc v1.0.83
         Compiling autocfg v1.1.0
         Compiling once_cell v1.19.0
         Compiling crossbeam-utils v0.8.19
         Compiling openssl-src v300.2.1+3.2.0
         Compiling pyo3-build-config v0.19.2
         Compiling cmake v0.1.50
         Compiling syn v2.0.48
         Compiling libz-sys v1.1.14
         Compiling openssl-sys v0.9.98
      error: failed to run custom build command for `libz-sys v1.1.14`

      Caused by:
        process didn't exit successfully: `/tmp/pip-install-w5h0p2ed/scatac-fragment-tools_3373270f56694ff78070c136f7030faa/rust/target/release/build/libz-sys-1bfea9d25fd4e33d/build-script-build` (exit status: 101)
        --- stdout
        cargo:rerun-if-env-changed=LIBZ_SYS_STATIC
        cargo:rerun-if-changed=build.rs
        CMAKE_TOOLCHAIN_FILE_x86_64-unknown-linux-gnu = None
        CMAKE_TOOLCHAIN_FILE_x86_64_unknown_linux_gnu = None
        HOST_CMAKE_TOOLCHAIN_FILE = None
        CMAKE_TOOLCHAIN_FILE = None
        CMAKE_GENERATOR_x86_64-unknown-linux-gnu = None
        CMAKE_GENERATOR_x86_64_unknown_linux_gnu = None
        HOST_CMAKE_GENERATOR = None
        CMAKE_GENERATOR = None
        CMAKE_PREFIX_PATH_x86_64-unknown-linux-gnu = None
        CMAKE_PREFIX_PATH_x86_64_unknown_linux_gnu = None
        HOST_CMAKE_PREFIX_PATH = None
        CMAKE_PREFIX_PATH = None
        CMAKE_x86_64-unknown-linux-gnu = None
        CMAKE_x86_64_unknown_linux_gnu = None
        HOST_CMAKE = None
        CMAKE = None
        running: cd "/tmp/pip-install-w5h0p2ed/scatac-fragment-tools_3373270f56694ff78070c136f7030faa/rust/target/release/build/libz-sys-85f2d12f3bcd2304/out/build" && CMAKE_PREFIX_PATH="" "cmake" "/gpfs/home/jd5457/.cargo/registry/src/index.crates.io-6f17d22bba15001f/libz-sys-1.1.14/src/zlib-ng" "-DBUILD_SHARED_LIBS=OFF" "-DZLIB_COMPAT=ON" "-DZLIB_ENABLE_TESTS=OFF" "-DWITH_GZFILEOP=ON" "-DCMAKE_INSTALL_PREFIX=/tmp/pip-install-w5h0p2ed/scatac-fragment-tools_3373270f56694ff78070c136f7030faa/rust/target/release/build/libz-sys-85f2d12f3bcd2304/out" "-DCMAKE_C_FLAGS= -ffunction-sections -fdata-sections -fPIC -m64" "-DCMAKE_C_COMPILER=/usr/bin/cc" "-DCMAKE_CXX_FLAGS= -ffunction-sections -fdata-sections -fPIC -m64" "-DCMAKE_CXX_COMPILER=/usr/bin/c++" "-DCMAKE_ASM_FLAGS= -ffunction-sections -fdata-sections -fPIC -m64" "-DCMAKE_ASM_COMPILER=/usr/bin/cc" "-DCMAKE_BUILD_TYPE=Release"

        --- stderr
        cmake: error while loading shared libraries: librhash.so.0: cannot open shared object file: No such file or directory
        thread 'main' panicked at /gpfs/home/jd5457/.cargo/registry/src/index.crates.io-6f17d22bba15001f/cmake-0.1.50/src/lib.rs:1098:5:

        command did not execute successfully, got: exit status: 127

        build script failed, must exit now
        note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
      warning: build failed, waiting for other jobs to finish...
      💥 maturin failed
        Caused by: Failed to build a native library through cargo
        Caused by: Cargo build finished with "exit status: 101": `env -u CARGO PYO3_ENVIRONMENT_SIGNATURE="cpython-3.8-64bit" PYO3_PYTHON="/gpfs/home/jd5457/naiklink/jd5457/.conda/envs/sc-multiome-pipeline-env/bin/python3.8" PYTHON_SYS_EXECUTABLE="/gpfs/home/jd5457/naiklink/jd5457/.conda/envs/sc-multiome-pipeline-env/bin/python3.8" "cargo" "rustc" "--features" "pyo3/extension-module" "--message-format" "json-render-diagnostics" "--manifest-path" "/tmp/pip-install-w5h0p2ed/scatac-fragment-tools_3373270f56694ff78070c136f7030faa/rust/Cargo.toml" "--release" "--lib"`
      Error: command ['maturin', 'pep517', 'build-wheel', '-i', '/gpfs/home/jd5457/naiklink/jd5457/.conda/envs/sc-multiome-pipeline-env/bin/python3.8', '--compatibility', 'off'] returned non-zero exit status 1
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for scatac-fragment-tools
Successfully built scenicplus loomxpy pyscenic pycistarget pycisTopic
Failed to build scatac-fragment-tools
ERROR: Could not build wheels for scatac-fragment-tools, which is required to install pyproject.toml-based projects

[ghuls]

Do you have cmake installed correctly? Does cmake --version work?

[daccachejoe]

Hi- That seemed to be the issue! Not sure why the cmake installation I had failed like that but sorting it out had installation work well.

Thanks

[ghuls]

Now you can also directly install a precompiled version from PyPi:

pip install scatac_fragment_tools