install failure: bedGraphToBigWig "utf-8 codec"

[darked89]

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Hello,

I got a rather strange error message while trying to install RGT package:

  File "/scratch/dkedra/.conda/envs/rgt_thor/lib/python3.9/site-packages/pkg_resources/__init__.py", line 1420, in get_metadata
    return value.decode('utf-8')
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa9 in position 25: invalid start byte in scripts/bedGraphToBigWig file at path: /mnt/beegfs/scratch/dkedra/.conda/envs/rgt_thor/lib/python3.9/site-packages/RGT-0.13.2-py3.9.egg/EGG-INFO/scripts/bedGraphToBigWig

The bedGraphToBigWig is a compiled executable:

./reg-gen-RGT-0.13.2/build/scripts-3.9/bedGraphToBigWig: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.18, BuildID[sha1]=2cae34bf6ef3752a8422d35a79a2d70b47609415, not stripped

clearly a binary, not a text script file with an encoding to check.

I have seen that there may be a problem with the setuptools ver > 58, but I am on a fairly closed HPC setup where apart from installing software from the source or using conda I can not install Python libs using pip.

Many thanks for your help,

Darek Kedra

steps to reproduce

conda create --name rgt_thor
conda activate rgt_thor 
conda install -c anaconda cython
conda install -c anaconda scipy

cd /scratch/dkedra/soft/tmp_all/
mkdir thor_20220520
cd thor_20220520/

tar xf RGT-0.13.2.tar.gz 
cd reg-gen-RGT-0.13.2/

python3 setup.py build
python3 setup.py install --prefix=/scratch/dkedra/.conda/envs/rgt_thor/

conda env

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main    anaconda
_openmp_mutex             4.5                       1_gnu    anaconda
blas                      1.0                         mkl    anaconda
ca-certificates           2022.4.26            h06a4308_0    anaconda
certifi                   2021.10.8        py39h06a4308_2    anaconda
cython                    0.29.28          py39h295c915_0    anaconda
intel-openmp              2021.4.0          h06a4308_3561    anaconda
ld_impl_linux-64          2.35.1               h7274673_9    anaconda
libffi                    3.3                  he6710b0_2    anaconda
libgcc-ng                 9.3.0               h5101ec6_17    anaconda
libgfortran-ng            7.5.0               ha8ba4b0_17    anaconda
libgfortran4              7.5.0               ha8ba4b0_17    anaconda
libgomp                   9.3.0               h5101ec6_17    anaconda
libstdcxx-ng              9.3.0               hd4cf53a_17    anaconda
mkl                       2021.4.0           h06a4308_640    anaconda
mkl-service               2.4.0            py39h7f8727e_0    anaconda
mkl_fft                   1.3.1            py39hd3c417c_0    anaconda
mkl_random                1.2.2            py39h51133e4_0    anaconda
ncurses                   6.3                  h7f8727e_2    anaconda
numpy                     1.21.5           py39he7a7128_2    anaconda
numpy-base                1.21.5           py39hf524024_2    anaconda
openssl                   1.1.1n               h7f8727e_0    anaconda
pip                       21.2.4           py39h06a4308_0    anaconda
python                    3.9.12               h12debd9_0    anaconda
readline                  8.1.2                h7f8727e_1    anaconda
scipy                     1.7.3            py39hc147768_0    anaconda
setuptools                61.2.0           py39h06a4308_0    anaconda
six                       1.16.0             pyhd3eb1b0_1    anaconda
sqlite                    3.38.2               hc218d9a_0    anaconda
tk                        8.6.11               h1ccaba5_0    anaconda
tzdata                    2022a                hda174b7_0    anaconda
wheel                     0.37.1             pyhd3eb1b0_0    anaconda
xz                        5.2.5                h7b6447c_0    anaconda
zlib                      1.2.12               h7f8727e_2    anaconda