install problem in conda env

[thierryjanssens]

I cannot install gff3tool in a freshly created conda env (including python=2.7 and perl):

(gff3tool_env) [user@XXX]$ pip install gff3tool
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Collecting gff3tool
Using cached https://files.pythonhosted.org/packages/cf/33/8cd85764a601bf3a5e0116f8b457c308294ec9c25139aacade6e21860335/gff3tool-1.4.4.tar.gz
Building wheels for collected packages: gff3tool
Building wheel for gff3tool (setup.py) ... error
ERROR: Complete output from command /mnt/scratch_dir/user/conda/envs/gff3tool_env/bin/python -u -c 'import setuptools, tokenize;file='"'"'/tmp/pip-install-m6SnWy/gff3tool/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-Ev8vXP --python-tag cp27:
ERROR: running bdist_wheel
running build
error: [Errno url error] invalid proxy for https: 'xx-xxxx:8080'

ERROR: Failed building wheel for gff3tool
Running setup.py clean for gff3tool
Failed to build gff3tool
Installing collected packages: gff3tool
Running setup.py install for gff3tool ... error
ERROR: Complete output from command /mnt/scratch_dir/userconda/envs/gff3tool_env/bin/python -u -c 'import setuptools, tokenize;file='"'"'/tmp/pip-install-m6SnWy/gff3tool/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-R72i2q/install-record.txt --single-version-externally-managed --compile:
ERROR: running install
running build
error: [Errno 17] File exists: '/tmp/pip-install-m6SnWy/gff3tool/gff3tool/lib/ncbi-blast+'
----------------------------------------
ERROR: Command "/mnt/scratch_dir/user/conda/envs/gff3tool_env/bin/python -u -c 'import setuptools, tokenize;file='"'"'/tmp/pip-install-m6SnWy/gff3tool/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-R72i2q/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-m6SnWy/gff3tool/

[thierryjanssens]

$ conda list

packages in environment at /mnt/scratch_dir/user/conda/envs/gff3tool_env:

Name Version Build Channel

_libgcc_mutex 0.1 main
bzip2 1.0.8 h516909a_0 conda-forge
ca-certificates 2019.6.16 hecc5488_0 conda-forge
certifi 2019.6.16 py27_1 conda-forge
libffi 3.2.1 he1b5a44_1006 conda-forge
libgcc-ng 9.1.0 hdf63c60_0
libstdcxx-ng 9.1.0 hdf63c60_0
ncurses 6.1 hf484d3e_1002 conda-forge
openssl 1.1.1c h516909a_0 conda-forge
perl 5.26.2 h516909a_1006 conda-forge
pip 19.1.1 py27_0 conda-forge
python 2.7.15 h5a48372_1009 conda-forge
readline 8.0 hf8c457e_0 conda-forge
setuptools 41.0.1 py27_0 conda-forge
sqlite 3.29.0 hcee41ef_0 conda-forge
tk 8.6.9 hed695b0_1002 conda-forge
wheel 0.33.4 py27_0 conda-forge
xz 5.2.4 h14c3975_1001 conda-forge
zlib 1.2.11 h516909a_1005 conda-forge

[tony006469]

Hey @thierryjanssens
I created a new virtual environment (myenv) using conda.
conda create --name myenv python=2.7
conda activate myenv

I tried to pip install gff3tool. Gff3tool seems to be successfully installed.
Would you mind re-establishing a virtual environment?
The following is my virtual environment variable for your reference.
$ conda list

If it still doesn't work, can you try to install gff3tool directly without using conda in a python2 environment?

Thank you for your question.

[mpoelchau]

Hi @thierryjanssens, just checking in - did the above suggestion solve your problem?