pip install fails
tsackton opened this issue · comments
I can install the Python API successfully by cloning the git repo, but using pip install fails:
[tsackton@holylogin02 d4test]$ python -m pip install pyd4
Collecting pyd4
Using cached pyd4-0.3.1.2.tar.gz (15 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting numpy
Using cached numpy-1.22.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.8 MB)
Building wheels for collected packages: pyd4
Building wheel for pyd4 (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for pyd4 (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [83 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.10
creating build/lib.linux-x86_64-3.10/pyd4
copying pyd4/__init__.py -> build/lib.linux-x86_64-3.10/pyd4
running egg_info
writing pyd4.egg-info/PKG-INFO
writing dependency_links to pyd4.egg-info/dependency_links.txt
writing requirements to pyd4.egg-info/requires.txt
writing top-level names to pyd4.egg-info/top_level.txt
reading manifest file 'pyd4.egg-info/SOURCES.txt'
writing manifest file 'pyd4.egg-info/SOURCES.txt'
running build_ext
running build_rust
error: failed to get `d4` as a dependency of package `pyd4 v0.1.13 (/tmp/pip-install-ow4cacbp/pyd4_1c42aedb701a4779a0da42389c2ab244)`
Caused by:
failed to load source for dependency `d4`
Caused by:
Unable to update /tmp/pip-install-ow4cacbp/d4
Caused by:
failed to read `/tmp/pip-install-ow4cacbp/d4/Cargo.toml`
Caused by:
No such file or directory (os error 2)
Traceback (most recent call last):
File "/n/home12/tsackton/sw/mambaforge/envs/d4/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in <module>
main()
File "/n/home12/tsackton/sw/mambaforge/envs/d4/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/n/home12/tsackton/sw/mambaforge/envs/d4/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 261, in build_wheel
return _build_backend().build_wheel(wheel_directory, config_settings,
File "/tmp/pip-build-env-3dnx28re/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 244, in build_wheel
return self._build_with_temp_dir(['bdist_wheel'], '.whl',
File "/tmp/pip-build-env-3dnx28re/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 229, in _build_with_temp_dir
self.run_setup()
File "/tmp/pip-build-env-3dnx28re/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 174, in run_setup
exec(compile(code, __file__, 'exec'), locals())
File "setup.py", line 34, in <module>
setup(
File "/tmp/pip-build-env-3dnx28re/overlay/lib/python3.10/site-packages/setuptools/__init__.py", line 155, in setup
return distutils.core.setup(**attrs)
File "/tmp/pip-build-env-3dnx28re/overlay/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 148, in setup
return run_commands(dist)
File "/tmp/pip-build-env-3dnx28re/overlay/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 163, in run_commands
dist.run_commands()
File "/tmp/pip-build-env-3dnx28re/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 967, in run_commands
self.run_command(cmd)
File "/tmp/pip-build-env-3dnx28re/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 986, in run_command
cmd_obj.run()
File "/tmp/pip-build-env-3dnx28re/overlay/lib/python3.10/site-packages/wheel/bdist_wheel.py", line 299, in run
self.run_command('build')
File "/tmp/pip-build-env-3dnx28re/overlay/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/tmp/pip-build-env-3dnx28re/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 986, in run_command
cmd_obj.run()
File "/tmp/pip-build-env-3dnx28re/overlay/lib/python3.10/site-packages/setuptools/_distutils/command/build.py", line 135, in run
self.run_command(cmd_name)
File "/tmp/pip-build-env-3dnx28re/overlay/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/tmp/pip-build-env-3dnx28re/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 986, in run_command
cmd_obj.run()
File "/tmp/pip-build-env-3dnx28re/overlay/lib/python3.10/site-packages/setuptools_rust/setuptools_ext.py", line 132, in run
build_rust.run()
File "/tmp/pip-build-env-3dnx28re/overlay/lib/python3.10/site-packages/setuptools_rust/command.py", line 101, in run
self.run_for_extension(ext)
File "/tmp/pip-build-env-3dnx28re/overlay/lib/python3.10/site-packages/setuptools_rust/build.py", line 108, in run_for_extension
dylib_paths = self.build_extension(ext, self.target)
File "/tmp/pip-build-env-3dnx28re/overlay/lib/python3.10/site-packages/setuptools_rust/build.py", line 139, in build_extension
target_dir = _base_cargo_target_dir(ext)
File "/tmp/pip-build-env-3dnx28re/overlay/lib/python3.10/site-packages/setuptools_rust/build.py", line 673, in _base_cargo_target_dir
target_directory = ext._metadata()["target_directory"]
File "/tmp/pip-build-env-3dnx28re/overlay/lib/python3.10/site-packages/setuptools_rust/extension.py", line 200, in _metadata
self._cargo_metadata = json.loads(subprocess.check_output(metadata_command))
File "/n/home12/tsackton/sw/mambaforge/envs/d4/lib/python3.10/subprocess.py", line 420, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File "/n/home12/tsackton/sw/mambaforge/envs/d4/lib/python3.10/subprocess.py", line 524, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['cargo', 'metadata', '--manifest-path', 'Cargo.toml', '--format-version', '1']' returned non-zero exit status 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
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.
Thanks for reporting this. This is due to the zlib website removed one file that D4 depends on.
Got this fixed on pypi already. Please let me know if the error persists. Cheers!