[BUG] pip install ultra-bioinformatics => Could not build wheels for edlib

Question

[BUG] pip install ultra-bioinformatics => Could not build wheels for edlib

nick-youngblut opened this issue 7 months ago · 7 comments

nick-youngblut commented 7 months ago

Is there an existing issue for this?

I have searched the existing issues

Have you loaded the SQANTI3.env conda environment?

I have loaded the SQANTI3.env conda environment

Problem description

Whether pip install ultra-bioinformatics is run independently or within conda env create -f SQANTI3.conda_env.yml, the error is:

Collecting ultra-bioinformatics
  Using cached ultra_bioinformatics-0.1-py3-none-any.whl
Collecting parasail (from ultra-bioinformatics)
  Using cached parasail-1.3.4-py2.py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (21 kB)
Requirement already satisfied: pysam in /home/nickyoungblut/miniforge3/envs/SQANTI3.env/lib/python3.12/site-packages (from ultra-bioinformatics) (0.22.1)
Collecting dill (from ultra-bioinformatics)
  Using cached dill-0.3.8-py3-none-any.whl.metadata (10 kB)
Collecting intervaltree (from ultra-bioinformatics)
  Using cached intervaltree-3.1.0-py2.py3-none-any.whl
Collecting gffutils (from ultra-bioinformatics)
  Using cached gffutils-0.13-py3-none-any.whl.metadata (1.5 kB)
Collecting edlib (from ultra-bioinformatics)
  Using cached edlib-1.3.9.tar.gz (91 kB)
  Preparing metadata (setup.py) ... done
Collecting pyfaidx>=0.5.5.2 (from gffutils->ultra-bioinformatics)
  Using cached pyfaidx-0.8.1.1-py3-none-any.whl.metadata (25 kB)
Collecting argh>=0.26.2 (from gffutils->ultra-bioinformatics)
  Using cached argh-0.31.2-py3-none-any.whl.metadata (7.3 kB)
Requirement already satisfied: argcomplete>=1.9.4 in /home/nickyoungblut/miniforge3/envs/SQANTI3.env/lib/python3.12/site-packages (from gffutils->ultra-bioinformatics) (3.4.0)
Collecting simplejson (from gffutils->ultra-bioinformatics)
  Using cached simplejson-3.19.2-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.1 kB)
Collecting sortedcontainers<3.0,>=2.0 (from intervaltree->ultra-bioinformatics)
  Using cached sortedcontainers-2.4.0-py2.py3-none-any.whl.metadata (10 kB)
Requirement already satisfied: numpy in /home/nickyoungblut/miniforge3/envs/SQANTI3.env/lib/python3.12/site-packages (from parasail->ultra-bioinformatics) (1.26.4)
Requirement already satisfied: setuptools in /home/nickyoungblut/miniforge3/envs/SQANTI3.env/lib/python3.12/site-packages (from pyfaidx>=0.5.5.2->gffutils->ultra-bioinformatics) (70.1.1)
Collecting importlib-metadata (from pyfaidx>=0.5.5.2->gffutils->ultra-bioinformatics)
  Using cached importlib_metadata-7.2.1-py3-none-any.whl.metadata (4.6 kB)
Collecting zipp>=0.5 (from importlib-metadata->pyfaidx>=0.5.5.2->gffutils->ultra-bioinformatics)
  Using cached zipp-3.19.2-py3-none-any.whl.metadata (3.6 kB)
Using cached dill-0.3.8-py3-none-any.whl (116 kB)
Using cached gffutils-0.13-py3-none-any.whl (1.6 MB)
Using cached parasail-1.3.4-py2.py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (15.6 MB)
Using cached argh-0.31.2-py3-none-any.whl (44 kB)
Using cached pyfaidx-0.8.1.1-py3-none-any.whl (28 kB)
Using cached sortedcontainers-2.4.0-py2.py3-none-any.whl (29 kB)
Using cached simplejson-3.19.2-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (152 kB)
Using cached importlib_metadata-7.2.1-py3-none-any.whl (25 kB)
Using cached zipp-3.19.2-py3-none-any.whl (9.0 kB)
Building wheels for collected packages: edlib
  Building wheel for edlib (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [14 lines of output]
      running bdist_wheel
      running build
      running build_ext
      building 'edlib' extension
      creating build
      creating build/temp.linux-x86_64-cpython-312
      creating build/temp.linux-x86_64-cpython-312/edlib
      creating build/temp.linux-x86_64-cpython-312/edlib/src
      gcc -pthread -B /home/nickyoungblut/miniforge3/envs/SQANTI3.env/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/nickyoungblut/miniforge3/envs/SQANTI3.env/include -fPIC -O2 -isystem /home/nickyoungblut/miniforge3/envs/SQANTI3.env/include -fPIC -Iedlib/include -I/home/nickyoungblut/miniforge3/envs/SQANTI3.env/include/python3.12 -c edlib.bycython.cpp -o build/temp.linux-x86_64-cpython-312/edlib.bycython.o -O3 -std=c++11
      edlib.bycython.cpp:198:12: fatal error: longintrepr.h: No such file or directory
        198 |   #include "longintrepr.h"
            |            ^~~~~~~~~~~~~~~
      compilation terminated.
      error: command '/usr/bin/gcc' failed with exit code 1
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for edlib
  Running setup.py clean for edlib
Failed to build edlib
ERROR: Could not build wheels for edlib, which is required to install pyproject.toml-based projects

conda install compilers did not help.

I've created an issue in the edlib repo: Martinsos/edlib#222

Code sample

No response

Error

No response

Anything else?

For now, I'm just going to skip edlib: pip install dill intervaltree gffutils parasail

You might want to consider setting python in SQANTI3.conda_env.yml to python<=3.11, given Martinsos/edlib#221

Answer 1 · 2024-06-25T18:36:02.000Z

Setting python=3.11 in SQANTI3.conda_env.yml avoided the edlib issue.

Note: at least for mamba, the defaults channel should NOT be used (see here)

Answer 2 · 2024-06-25T18:42:55.000Z

At least for my install, running sqanti3_qc.py throws the error:

ModuleNotFoundError: No module named 'pandas'

...since pandas is not included in SQANTI3.conda_env.yml, and thus not in my conda env.

So, another dependency issue.

Answer 3 · 2024-06-26T10:12:22.000Z

Hi @nick-youngblut,

Yes, the issue with the latest Python version was mentioned in #310. Everything is working well with 3.11, so I will update the dependencies in the yml.

I think you may have had some problems with your installation because pandas is included in the yml.

Alejandro.

Answer 4 · 2024-06-26T14:43:26.000Z

I think you may have had some problems with your installation because pandas is included in the yml.

SQANTI3.conda_env.yml in https://github.com/ConesaLab/SQANTI3/archive/refs/tags/v5.2.1.tar.gz does not include pandas:

name: SQANTI3.env
channels:
  - conda-forge
  - bioconda
  - anaconda
  - r
  - defaults
dependencies:
  - bcbio-gff
  - bedtools
  - biopython<=1.81
  - bioconductor-noiseq
  - bioconductor-busparse
  - bx-python
  - cython
  - desalt
  - gffread
  - gmap
  - kallisto=0.48.0
  - minimap2
  - numpy
  - openssl
  - pandoc
  - perl
  - pip
  - psutil
  - pybedtools
  - pysam
  - python>=3.7.6
  - r>=4.3.0
  - r-biocmanager
  - r-caret
  - r-dplyr
  - r-dt
  - r-devtools
  - r-e1071
  - r-forcats
  - r-ggplot2>=3.4.0
  - r-ggplotify
  - r-gridbase
  - r-gridextra
  - r-htmltools
  - r-jsonlite
  - r-optparse
  - r-plotly
  - r-plyr
  - r-pROC
  - r-purrr
  - r-rmarkdown
  - r-reshape
  - r-readr
  - r-randomForest
  - r-scales
  - r-stringi
  - r-stringr
  - r-tibble
  - r-tidyr
  - samtools
  - scipy<=1.11.4
  - seqtk
  - star
  - slamem
  - pip:
    - ultra-bioinformatics

I see that you just recently added pandas. Apparently, that update is not yet in the tarball.

Answer 5 · 2024-06-27T07:07:38.000Z

Yes, you are right. It has been a while since the last release.

Answer 6 · 2024-06-27T12:50:04.000Z

I had the same issue and I managed to circumvent that by replacing the contents of the envrionement.yaml in the tarball with those in the git repo.

Answer 7 · 2024-07-30T16:18:56.000Z

Please update the tarball, this error still occurs in todays download (July 30 2024). I downloaded using git clone to get the correct .yml file