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Pip install still failing. Error is now: #94

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tito-abbo opened this issue Dec 12, 2024 · 1 comment
Open

Pip install still failing. Error is now: #94

tito-abbo opened this issue Dec 12, 2024 · 1 comment

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@tito-abbo
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          Pip install still failing. Error is now:
     error: failed to run custom build command for `d4-hts v0.3.5`
      
      Caused by:
        process didn't exit successfully: `/tmp/pip-install-3kya479p/pyd4_c078b6dd33b54f9f9f02cefe521e2e41/target/release/build/d4-hts-1b44fec096ee500a/build-script-build` (exit status: 101)
        --- stderr
        + pushd /tmp/pip-install-3kya479p/pyd4_c078b6dd33b54f9f9f02cefe521e2e41/target/release/build/d4-hts-8e2eee3158639a84/out
        + HTSLIB_VERSION=1.11
        + rm -rf /tmp/pip-install-3kya479p/pyd4_c078b6dd33b54f9f9f02cefe521e2e41/target/release/build/d4-hts-8e2eee3158639a84/out/htslib
        + git clone -b 1.11 https://github.com/samtools/htslib.git
        Note: checking out 'a7a90fe913f8a466f32f6e284cf46653944acd6f'.
      
        You are in 'detached HEAD' state. You can look around, make experimental
        changes and commit them, and you can discard any commits you make in this
        state without impacting any branches by performing another checkout.
      
        If you want to create a new branch to retain commits you create, you may
        do so (now or later) by using -b with the checkout command again. Example:
      
          git checkout -b new_branch_name
      
        + cd htslib
        + cat
        + perl -i -pe 's/hfile_libcurl\.o//g' Makefile
        + is_musl
        ++ echo x86_64-unknown-linux-gnu
        ++ grep musl
        + '[' '!' -z ']'
        + return 1
        + curl https://zlib.net/zlib-1.2.11.tar.gz
        + tar xz
          % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                         Dload  Upload   Total   Spent    Left  Speed
      
        0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
      100   315  100   315    0     0    722      0 --:--:-- --:--:-- --:--:--   724
      
        gzip: stdin: not in gzip format
        tar: Child returned status 1
        tar: Error is not recoverable: exiting now
        thread 'main' panicked at 'assertion failed: Command::new(\"bash\").args(&[\"build_htslib.sh\",\n                            &version]).stdout(std::process::Stdio::null()).spawn().expect(\"Unable to build htslib\").wait().unwrap().success()', /n/home12/tsackton/.cargo/registry/src/github.com-1ecc6299db9ec823/d4-hts-0.3.5/build.rs:34:5
        note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
      warning: build failed, waiting for other jobs to finish...
      error: build failed
      error: cargo failed with code: 101
      
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for pyd4
Failed to build pyd4
ERROR: Could not build wheels for pyd4, which is required to install pyproject.toml-based projects

I think the problem is that zlib is now at version 1.2.12, so the hard-coded url does not work.

Originally posted by @tsackton in #48 (comment)

@tito-abbo
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I am experiencing the exact error above while trying to install pyd4

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