CocoMlle
commented
3 years ago sorry i answered here if it can help you : i found what is wrong for the UnicodeEncodeError: 'latin-1' codec can't encode character '\u2013' in position 985: ordinal not in range(256)
in this file : miniconda3/lib/python3.6/site-packages/hicexplorer/list_tools.py "Nucleic Acids Research, Volume 46, Issue W1, 2 July 2018, Pages W11-W16, doi: https://doi.org/10.1093/nar/gky504" => there were originally some "<" around W11 and W16 and some extra character, i removed all and just add some "-" and it's working fine!
lldelisle
Hi, i was trying to install HiCExplorer by all the way but with no success:
i tried conda: conda install hicexplorer -c bioconda -c conda-forge Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
ResolvePackageNotFound:
then pip :
pip3 install hicexplorer Traceback (most recent call last): File "/work/gad/shared/bin/miniconda3/bin/pip3", line 7, in
from pip._internal.cli.main import main
File "/work/gad/shared/bin/miniconda3/lib/python3.6/site-packages/pip/_internal/cli/main.py", line 8, in
from pip._internal.cli.autocompletion import autocomplete
File "/work/gad/shared/bin/miniconda3/lib/python3.6/site-packages/pip/_internal/cli/autocompletion.py", line 9, in
from pip._internal.cli.main_parser import create_main_parser
File "/work/gad/shared/bin/miniconda3/lib/python3.6/site-packages/pip/_internal/cli/main_parser.py", line 7, in
from pip._internal.cli import cmdoptions
File "/work/gad/shared/bin/miniconda3/lib/python3.6/site-packages/pip/_internal/cli/cmdoptions.py", line 22, in
from pip._internal.cli.progress_bars import BAR_TYPES
File "/work/gad/shared/bin/miniconda3/lib/python3.6/site-packages/pip/_internal/cli/progress_bars.py", line 9, in
from pip._internal.utils.logging import get_indentation
File "/work/gad/shared/bin/miniconda3/lib/python3.6/site-packages/pip/_internal/utils/logging.py", line 14, in
from pip._internal.utils.misc import ensure_dir
File "/work/gad/shared/bin/miniconda3/lib/python3.6/site-packages/pip/_internal/utils/misc.py", line 29, in
from pip._internal.locations import get_major_minor_version, site_packages, user_site
File "/work/gad/shared/bin/miniconda3/lib/python3.6/site-packages/pip/_internal/locations/init.py", line 14, in
from . import _distutils, _sysconfig
File "/work/gad/shared/bin/miniconda3/lib/python3.6/site-packages/pip/_internal/locations/_sysconfig.py", line 8, in
from pip._internal.exceptions import InvalidSchemeCombination, UserInstallationInvalid
ImportError: cannot import name 'InvalidSchemeCombination'
and i tried with the github repo, it's kind of working but with the same bug than already reported, i can't launch hicexplorer:
./hicexplorer Traceback (most recent call last): File "./hicexplorer", line 11, in
main(args)
File "/work/gad/shared/bin/miniconda3/lib/python3.6/site-packages/hicexplorer/list_tools.py", line 93, in main
process_args(args)
File "/work/gad/shared/bin/miniconda3/lib/python3.6/site-packages/hicexplorer/list_tools.py", line 85, in process_args
args = parse_arguments().parse_args(args)
File "/work/gad/shared/bin/miniconda3/lib/python3.6/argparse.py", line 1734, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/work/gad/shared/bin/miniconda3/lib/python3.6/argparse.py", line 1766, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/work/gad/shared/bin/miniconda3/lib/python3.6/argparse.py", line 1972, in _parse_known_args
start_index = consume_optional(start_index)
File "/work/gad/shared/bin/miniconda3/lib/python3.6/argparse.py", line 1912, in consume_optional
take_action(action, args, option_string)
File "/work/gad/shared/bin/miniconda3/lib/python3.6/argparse.py", line 1840, in take_action
action(self, namespace, argument_values, option_string)
File "/work/gad/shared/bin/miniconda3/lib/python3.6/argparse.py", line 1024, in call
parser.print_help()
File "/work/gad/shared/bin/miniconda3/lib/python3.6/argparse.py", line 2366, in print_help
self._print_message(self.format_help(), file)
File "/work/gad/shared/bin/miniconda3/lib/python3.6/argparse.py", line 2372, in _print_message
file.write(message)
UnicodeEncodeError: 'latin-1' codec can't encode character '\u2013' in position 985: ordinal not in range(256)
do you have any idea what can i do more ?
i'm working on server with rhel fedora 7 and python 3.6 is the current version installed. thanks for your help !