conda踩坑记录1.An unexpected error h
2021-06-07 本文已影响0人
小狼小狼_e211
想更新deeptools，但是发现无论如何都下载不了，并且有以下报错
(atac) vip9t07@tpm9-desktop:~/project/atac/new$ conda update -n atac deeptools
Collecting package metadata (current_repodata.json): failed
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/home/data/vip9t07/miniconda3/lib/python3.6/site-packages/conda/core/subdir_data.py", line 375, in _load
repodata_fn=self.repodata_fn)
File "/home/data/vip9t07/miniconda3/lib/python3.6/site-packages/conda/core/subdir_data.py", line 808, in fetch_repodata_remote_request
raise Response304ContentUnchanged()
conda.core.subdir_data.Response304ContentUnchanged
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/data/vip9t07/miniconda3/lib/python3.6/site-packages/conda/exceptions.py", line 1079, in __call__
return func(*args, **kwargs)
File "/home/data/vip9t07/miniconda3/lib/python3.6/site-packages/conda/cli/main.py", line 84, in _main
exit_code = do_call(args, p)
File "/home/data/vip9t07/miniconda3/lib/python3.6/site-packages/conda/cli/conda_argparse.py", line 83, in do_call
return getattr(module, func_name)(args, parser)
File "/home/data/vip9t07/miniconda3/lib/python3.6/site-packages/conda/cli/main_update.py", line 20, in execute
install(args, parser, 'update')
File "/home/data/vip9t07/miniconda3/lib/python3.6/site-packages/conda/cli/install.py", line 265, in install
should_retry_solve=(_should_retry_unfrozen or repodata_fn != repodata_fns[-1]),
File "/home/data/vip9t07/miniconda3/lib/python3.6/site-packages/conda/core/solve.py", line 117, in solve_for_transaction
should_retry_solve)
File "/home/data/vip9t07/miniconda3/lib/python3.6/site-packages/conda/core/solve.py", line 158, in solve_for_diff
force_remove, should_retry_solve)
File "/home/data/vip9t07/miniconda3/lib/python3.6/site-packages/conda/core/solve.py", line 262, in solve_final_state
ssc = self._collect_all_metadata(ssc)
File "/home/data/vip9t07/miniconda3/lib/python3.6/site-packages/conda/common/io.py", line 88, in decorated
return f(*args, **kwds)
File "/home/data/vip9t07/miniconda3/lib/python3.6/site-packages/conda/core/solve.py", line 425, in _collect_all_metadata
index, r = self._prepare(prepared_specs)
File "/home/data/vip9t07/miniconda3/lib/python3.6/site-packages/conda/core/solve.py", line 1021, in _prepare
self.subdirs, prepared_specs, self._repodata_fn)
File "/home/data/vip9t07/miniconda3/lib/python3.6/site-packages/conda/core/index.py", line 289, in get_reduced_index
repodata_fn=repodata_fn)
File "/home/data/vip9t07/miniconda3/lib/python3.6/site-packages/conda/core/subdir_data.py", line 140, in query_all
result = tuple(concat(executor.map(subdir_query, channel_urls)))
File "/home/data/vip9t07/miniconda3/lib/python3.6/concurrent/futures/_base.py", line 556, in result_iterator
yield future.result()
File "/home/data/vip9t07/miniconda3/lib/python3.6/concurrent/futures/_base.py", line 398, in result
return self.__get_result()
File "/home/data/vip9t07/miniconda3/lib/python3.6/concurrent/futures/_base.py", line 357, in __get_result
raise self._exception
File "/home/data/vip9t07/miniconda3/lib/python3.6/concurrent/futures/thread.py", line 55, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/data/vip9t07/miniconda3/lib/python3.6/site-packages/conda/core/subdir_data.py", line 133, in <lambda>
package_ref_or_match_spec))
File "/home/data/vip9t07/miniconda3/lib/python3.6/site-packages/conda/core/subdir_data.py", line 145, in query
self.load()
File "/home/data/vip9t07/miniconda3/lib/python3.6/site-packages/conda/core/subdir_data.py", line 209, in load
_internal_state = self._load()
File "/home/data/vip9t07/miniconda3/lib/python3.6/site-packages/conda/core/subdir_data.py", line 390, in _load
mod_etag_headers.get('_mod'))
File "/home/data/vip9t07/miniconda3/lib/python3.6/site-packages/conda/core/subdir_data.py", line 438, in _read_local_repdata
_internal_state = self._process_raw_repodata_str(raw_repodata_str)
File "/home/data/vip9t07/miniconda3/lib/python3.6/site-packages/conda/core/subdir_data.py", line 476, in _process_raw_repodata_str
json_obj = json.loads(raw_repodata_str or '{}')
File "/home/data/vip9t07/miniconda3/lib/python3.6/json/__init__.py", line 354, in loads
return _default_decoder.decode(s)
File "/home/data/vip9t07/miniconda3/lib/python3.6/json/decoder.py", line 339, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/home/data/vip9t07/miniconda3/lib/python3.6/json/decoder.py", line 355, in raw_decode
obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Unterminated string starting at: line 150276 column 17 (char 4718399)
`$ /home/data/vip9t07/miniconda3/bin/conda update -n atac deeptools`
environment variables:
CIO_TEST=<not set>
CONDA_DEFAULT_ENV=atac
CONDA_EXE=/home/data/vip9t07/miniconda3/bin/conda
CONDA_PREFIX=/home/data/vip9t07/miniconda3/envs/atac
CONDA_PREFIX_1=/home/data/vip9t07/miniconda3
CONDA_PROMPT_MODIFIER=(atac)
CONDA_PYTHON_EXE=/home/data/vip9t07/miniconda3/bin/python
CONDA_ROOT=/home/data/vip9t07/miniconda3
CONDA_SHLVL=2
CURL_CA_BUNDLE=<not set>
JAVA_LD_LIBRARY_PATH=/home/data/vip9t07/miniconda3/envs/atac/lib/server
PATH=/home/data/vip9t07/miniconda3/bin:/home/data/vip9t07/miniconda3/envs/a
tac/bin:/home/data/vip9t07/miniconda3/condabin:/usr/local/sbin:/usr/lo
cal/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/sna
p/bin:/home/data/vip9t07/biosoft/bowtie2/bowtie2-2.4.2-linux-x86_64:/h
ome/data/vip9t07/biosoft/samtools/samtools-1.12
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
active environment : atac
active env location : /home/data/vip9t07/miniconda3/envs/atac
shell level : 2
user config file : /home/data/vip9t07/.condarc
populated config files : /home/data/vip9t07/.condarc
conda version : 4.10.1
conda-build version : not installed
python version : 3.6.2.final.0
virtual packages : __linux=5.8.0=0
__glibc=2.31=0
__unix=0=0
__archspec=1=x86_64
base environment : /home/data/vip9t07/miniconda3 (writable)
conda av data dir : /home/data/vip9t07/miniconda3/etc/conda
conda av metadata url : https://repo.anaconda.com/pkgs/main
channel URLs : https://mirrors.ustc.edu.cn/anaconda/cloud/bioconda/linux-64
https://mirrors.ustc.edu.cn/anaconda/cloud/bioconda/noarch
https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/linux-64
https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/noarch
https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64
https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch
https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64
https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/data/vip9t07/miniconda3/pkgs
/home/data/vip9t07/.conda/pkgs
envs directories : /home/data/vip9t07/miniconda3/envs
/home/data/vip9t07/.conda/envs
platform : linux-64
user-agent : conda/4.10.1 requests/2.25.1 CPython/3.6.2 Linux/5.8.0-50-generic ubuntu/20.04.2 glibc/2.31
UID:GID : 1012:1014
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers?
[y/N]: y
Upload successful.
Thank you for helping to improve conda.
Opt-in to always sending reports (and not see this message again)
by running
$ conda config --set report_errors true
按照conda install安装不了任何包，报一大段错误_E_vens怡宝-CSDN博客
方法，还是不行，并且出现了新的报错
(atac) vip9t07@tpm9-desktop:~/project/atac/new$ conda clean -i
(atac) vip9t07@tpm9-desktop:~/project/atac/new$ conda install -c bioconda deeptools
Collecting package metadata (current_repodata.json): failed
CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch/current_repodata.json>
Elapsed: -
An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.
'https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch'
(atac) vip9t07@tpm9-desktop:~$ conda config --remove channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
(atac) vip9t07@tpm9-desktop:~$ conda config --set show_channel_urls yes
光删除了conda-forge的镜像源依然不能解决问题
继续
CondaHTTPError: HTTP 000 CONNECTION FAILED for url ＜https://mirrors.tuna.tsinghua.edu.cn/anaconda/_titake的博客-CSDN博客
将中科大的镜像源加入并删除其他清华镜像源及default
(atac) vip9t07@tpm9-desktop:~$ vim ~/.condarc
(atac) vip9t07@tpm9-desktop:~$ cat ~/.condarc
channels:
- https://mirrors.ustc.edu.cn/anaconda/pkgs/free/
- https://mirrors.ustc.edu.cn/anaconda/cloud/bioconda/
show_channel_urls: true
可以了！
(当然这只是我以为的可以了，实际上后续还经历了一系列醉生梦死的艰辛求知路……）
