install failed

[yuzhenpeng]

Dear author,

When I installed this software on my computer, I got an error warning. Could you give me some suggestion.

$pip install ./reat/
Processing ./reat
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting 2passtools@ git+https://github.com/bartongroup/2passtools.git#d4378d0
  Cloning https://github.com/bartongroup/2passtools.git to /tmp/pip-install-kp6uo_p_/2passtools_98265f384cdc42daab3aaf786f9fdf76
  Running command git clone --filter=blob:none --quiet https://github.com/bartongroup/2passtools.git /tmp/pip-install-kp6uo_p_/2passtools_98265f384cdc42daab3aaf786f9fdf76
  fatal: unable to access 'https://github.com/bartongroup/2passtools.git/': HTTP/2 stream 1 was not closed cleanly before end of the underlying stream
  error: subprocess-exited-with-error

  × git clone --filter=blob:none --quiet https://github.com/bartongroup/2passtools.git /tmp/pip-install-kp6uo_p_/2passtools_98265f384cdc42daab3aaf786f9fdf76 did not run successfully.
  │ exit code: 128
  ╰─> See above for output.

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× git clone --filter=blob:none --quiet https://github.com/bartongroup/2passtools.git /tmp/pip-install-kp6uo_p_/2passtools_98265f384cdc42daab3aaf786f9fdf76 did not run successfully.
│ exit code: 128
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

Thank you, Zhen-peng

[gemygk]

Dear @yuzhenpeng

Thanks for reporting the issue and providing the error log.

Can you please check if you can access the GitHub link - https://github.com/bartongroup/2passtools.git?

As you can see in the above error log, it says:

fatal: unable to access 'https://github.com/bartongroup/2passtools.git/': HTTP/2 stream 1 was not closed cleanly before end of the underlying stream error: subprocess-exited-with-error

It looks like a git config issue.

Thanks, Gemy

[yuzhenpeng]

Dear @gemygk

Thanks for your reply. It seems very well.

[gemygk]

Dear @yuzhenpeng

Thanks for testing it.

I have just tried to install REAT myself (in another location for testing using --prefix, please see below) and it works fine. I have used mamba to install dependencies a bit faster (I will update the documentation to use mamba)

$ cd /path/to/software
$ git clone git@github.com:EI-CoreBioinformatics/reat.git
$ wget https://github.com/broadinstitute/cromwell/releases/download/62/cromwell-62.jar
$ mamba env create -f reat/reat.yml --prefix /path/to/software/reat/x86_64
$ conda activate /path/to/software/reat/x86_64
(/path/to/software/reat/x86_64) $ pip install reat/
(/path/to/software/reat/x86_64) $ which reat
/path/to/software/reat/x86_64/bin/reat
(/path/to/software/reat/x86_64) $ reat --help

For reference, I am adding the pip 2passtools log below which works fine at our end and it should be similar when you try:

...
...
Collecting 2passtools@ git+https://github.com/bartongroup/2passtools.git#d4378d0
  Cloning https://github.com/bartongroup/2passtools.git to /tmp/pip-install-xpwzm_xv/2passtools_a1469f8bb1a34c4eb08433a62db13bfb
  Running command git clone --filter=blob:none --quiet https://github.com/bartongroup/2passtools.git /tmp/pip-install-xpwzm_xv/2passtools_a1469f8bb1a34c4eb08433a62db13bfb
  Resolved https://github.com/bartongroup/2passtools.git to commit d4378d0f4a780b5b89399161ed8eac6ca5092128
  Preparing metadata (setup.py) ... done
...
...

Can you please try the above steps and let me know how it goes?

Thanks, Gemy

[yuzhenpeng]

Dear @gemygk,

Thanks for your kind help. I followed your new pipeline to install REAT. Unfortunately, I got a new error warning shown as followed.

`Processing ./reat Installing build dependencies ... done Getting requirements to build wheel ... done Preparing metadata (pyproject.toml) ... done Collecting 2passtools@ git+https://github.com/bartongroup/2passtools.git#d4378d0 Cloning https://github.com/bartongroup/2passtools.git to /tmp/pip-install-1hofbgo8/2passtools_1b35d4d60c2c41caa7efd63e2936d30c Running command git clone --filter=blob:none --quiet https://github.com/bartongroup/2passtools.git /tmp/pip-install-1hofbgo8/2passtools_1b35d4d60c2c41caa7efd63e2936d30c Resolved https://github.com/bartongroup/2passtools.git to commit d4378d0f4a780b5b89399161ed8eac6ca5092128 Preparing metadata (setup.py) ... done Collecting parasail~=1.2.4 Using cached parasail-1.2.4-py2.py3-none-manylinux2010_x86_64.whl (14.1 MB) Requirement already satisfied: biopython~=1.78 in /root/data1/yuzhenpeng2021/miniconda3/envs/REAT/lib/python3.9/site-packages (from reat==0.6.1) (1.79) Collecting jsonschema~=3.2.0 Using cached jsonschema-3.2.0-py2.py3-none-any.whl (56 kB) Collecting mikado~=2.3.0 Using cached Mikado-2.3.4.tar.gz (24.7 MB) Installing build dependencies ... done Getting requirements to build wheel ... error error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully. │ exit code: 1 ╰─> [15 lines of output] Traceback (most recent call last): File "/root/data1/yuzhenpeng2021/miniconda3/envs/REAT/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in main() File "/root/data1/yuzhenpeng2021/miniconda3/envs/REAT/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/root/data1/yuzhenpeng2021/miniconda3/envs/REAT/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 130, in get_requires_for_build_wheel return hook(config_settings) File "/tmp/pip-build-env-bj8uibuh/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 338, in get_requires_for_build_wheel return self._get_build_requires(config_settings, requirements=['wheel']) File "/tmp/pip-build-env-bj8uibuh/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 320, in _get_build_requires self.run_setup() File "/tmp/pip-build-env-bj8uibuh/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 335, in run_setup exec(code, locals()) File "", line 15, in ModuleNotFoundError: No module named 'scipy._build_utils' [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully. │ exit code: 1 ╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip. `

[gemygk]

@yuzhenpeng

Can you please try pip with --no-cache-dir

See below the full list of commands:

$ cd /path/to/software
$ git clone git@github.com:EI-CoreBioinformatics/reat.git
$ wget https://github.com/broadinstitute/cromwell/releases/download/62/cromwell-62.jar
$ mamba env create -f reat/reat.yml --prefix /path/to/software/reat/x86_64
$ conda activate /path/to/software/reat/x86_64
(/path/to/software/reat/x86_64) $ pip install --no-cache-dir ./reat
(/path/to/software/reat/x86_64) $ which reat
/path/to/software/reat/x86_64/bin/reat
(/path/to/software/reat/x86_64) $ reat --help

[gemygk]

@yuzhenpeng

Just came across a similar error with pip in StackOverflow - https://stackoverflow.com/q/71009659, and it was caused due the latest pip and python 3.10

May I know the version of pip you were using?

I was using pip 21.1.3 with python 3.9.5.

[yuzhenpeng]

Hi, @gemygk

Thank your suggestion. The version of pip and python on my computer are Python 3.9.9 and pip 22.2.2.

I run the command like you pip install --no-cache-dir ./reat. But I still obtained an error Getting requirements to build wheel ... error.

I guess it may be the network problems, likely HTTPs/HTTP.

Processing ./reat Installing build dependencies ... done Getting requirements to build wheel ... done Preparing metadata (pyproject.toml) ... done Collecting 2passtools@ git+https://github.com/bartongroup/2passtools.git#d4378d0 Cloning https://github.com/bartongroup/2passtools.git to /tmp/pip-install-g1coajy7/2passtools_809c5530699646a8821172e4e7740967 Running command git clone --filter=blob:none --quiet https://github.com/bartongroup/2passtools.git /tmp/pip-install-g1coajy7/2passtools_809c5530699646a8821172e4e7740967 Resolved https://github.com/bartongroup/2passtools.git to commit d4378d0f4a780b5b89399161ed8eac6ca5092128 Preparing metadata (setup.py) ... done Collecting pyyaml~=5.4.1 Downloading PyYAML-5.4.1-cp39-cp39-manylinux1_x86_64.whl (630 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 630.1/630.1 kB 804.7 kB/s eta 0:00:00 Collecting jsonschema~=3.2.0 Downloading jsonschema-3.2.0-py2.py3-none-any.whl (56 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 56.3/56.3 kB 7.9 MB/s eta 0:00:00 Collecting pyfaidx~=0.5.8 Downloading pyfaidx-0.5.9.5.tar.gz (32 kB) Preparing metadata (setup.py) ... done Collecting parasail~=1.2.4 Downloading parasail-1.2.4-py2.py3-none-manylinux2010_x86_64.whl (14.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 14.1/14.1 MB 4.2 MB/s eta 0:00:00 Requirement already satisfied: biopython~=1.78 in ./reat/x86_64/lib/python3.9/site-packages (from reat==0.6.1) (1.79) Collecting mikado~=2.3.0 Downloading Mikado-2.3.4.tar.gz (24.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 24.7/24.7 MB 4.7 MB/s eta 0:00:00 Installing build dependencies ... done Getting requirements to build wheel ... error error: subprocess-exited-with-error × Getting requirements to build wheel did not run successfully. │ exit code: 1 ╰─> [15 lines of output] Traceback (most recent call last): File "/root/data1/yuzhenpeng2021/biosoft/reat/x86_64/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in main() File "/root/data1/yuzhenpeng2021/biosoft/reat/x86_64/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/root/data1/yuzhenpeng2021/biosoft/reat/x86_64/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 130, in get_requires_for_build_wheel return hook(config_settings) File "/tmp/pip-build-env-32h_44jl/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 338, in get_requires_for_build_wheel return self._get_build_requires(config_settings, requirements=['wheel']) File "/tmp/pip-build-env-32h_44jl/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 320, in _get_build_requires self.run_setup() File "/tmp/pip-build-env-32h_44jl/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 335, in run_setup exec(code, locals()) File "", line 15, in ModuleNotFoundError: No module named 'scipy._build_utils' [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. error: subprocess-exited-with-error × Getting requirements to build wheel did not run successfully. │ exit code: 1 ╰─> See above for output. note: This error originates from a subprocess, and is likely not a problem with pip.

[gemygk]

@yuzhenpeng

My suggestion would be to downgrade pip and give it a go

pip install pip==21.3.1

[yuzhenpeng]

@yuzhenpeng

My suggestion would be to downgrade pip and give it a go

pip install pip==21.3.1

Thank you for your suggestion.

I set the pip mirror. pip config set global.index-url https://pypi.tuna.tsinghua.edu.cn/simple

Now, it worked very well.

Thank you.

[gemygk]

Thanks @yuzhenpeng

I am marking the issue as closed.

Please let us know if you have any queries.

[dadrasarmin]

Hi,

We had a similar problem. The solution suggested here could not solve the problem:

pip install pip==21.3.1

But, we have changed something in the setup.py file according to the Mikado Github page and it worked:

'mikado @ git+https://github.com/EI-CoreBioinformatics/mikado@fix_install'

Also, we fixed the python and pip version in the reat.yml as follows:

- pip=21.3.1
- python=3.9.9

After these changes, this command successfully installed reat:

pip install --no-cache-dir ./reat

It was tested on a Debian machine, and dependencies were installed via mamba.