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ERROR conda update conda #1108

Open RachelXNguyen opened 5 years ago

RachelXNguyen commented 5 years ago

Hi, I installed and reinstalled miniconda3, then installed anaconda3. Then run conda update conda and got the TypeError: 'NoneType' object does not support item assignment Is it due to not remove completely miniconda3? I removed by rm -rf ~/miniconda3. I know there is an issue #7870 but I can't get it at all. Please someone help me? Below is the error details c_n031@lsp-bioinfo03:~$ conda list

packages in environment at /home/c_n031/anaconda3:

#

Name Version Build Channel

_ipyw_jlab_nb_ext_conf 0.1.0 py37_0
alabaster 0.7.11 py37_0
anaconda 5.3.0 py37_0
anaconda-client 1.7.2 py37_0
anaconda-navigator 1.9.2 py37_0
anaconda-project 0.8.2 py37_0
appdirs 1.4.3 py37h28b3542_0
asn1crypto 0.24.0 py37_0
astroid 2.0.4 py37_0
astropy 3.0.4 py37h14c3975_0
atomicwrites 1.2.1 py37_0
attrs 18.2.0 py37h28b3542_0
automat 0.7.0 py37_0
babel 2.6.0 py37_0
backcall 0.1.0 py37_0
backports 1.0 py37_1
backports.shutil_get_terminal_size 1.0.0 py37_2
beautifulsoup4 4.6.3 py37_0
bitarray 0.8.3 py37h14c3975_0
bkcharts 0.2 py37_0
blas 1.0 mkl
blaze 0.11.3 py37_0
bleach 2.1.4 py37_0
blosc 1.14.4 hdbcaa40_0
bokeh 0.13.0 py37_0
boto 2.49.0 py37_0
bottleneck 1.2.1 py37h035aef0_1
bzip2 1.0.6 h14c3975_5
ca-certificates 2018.03.07 0
cairo 1.14.12 h8948797_3
certifi 2018.8.24 py37_1
cffi 1.11.5 py37he75722e_1
chardet 3.0.4 py37_1
click 6.7 py37_0
cloudpickle 0.5.5 py37_0
clyent 1.2.2 py37_1
colorama 0.3.9 py37_0
conda 4.5.11 py37_0
conda-build 3.15.1 py37_0
conda-env 2.6.0 1
constantly 15.1.0 py37h28b3542_0
contextlib2 0.5.5 py37_0
cryptography 2.3.1 py37hc365091_0
curl 7.61.0 h84994c4_0
cycler 0.10.0 py37_0
cython 0.28.5 py37hf484d3e_0
cytoolz 0.9.0.1 py37h14c3975_1
dask 0.19.1 py37_0
dask-core 0.19.1 py37_0
datashape 0.5.4 py37_1
dbus 1.13.2 h714fa37_1
decorator 4.3.0 py37_0
defusedxml 0.5.0 py37_1
distributed 1.23.1 py37_0
docutils 0.14 py37_0
entrypoints 0.2.3 py37_2
et_xmlfile 1.0.1 py37_0
expat 2.2.6 he6710b0_0
fastcache 1.0.2 py37h14c3975_2
filelock 3.0.8 py37_0
flask 1.0.2 py37_1
flask-cors 3.0.6 py37_0
fontconfig 2.13.0 h9420a91_0
freetype 2.9.1 h8a8886c_1
fribidi 1.0.5 h7b6447c_0
get_terminal_size 1.0.0 haa9412d_0
gevent 1.3.6 py37h7b6447c_0
glib 2.56.2 hd408876_0
glob2 0.6 py37_0
gmp 6.1.2 h6c8ec71_1
gmpy2 2.0.8 py37h10f8cd9_2
graphite2 1.3.12 h23475e2_2
greenlet 0.4.15 py37h7b6447c_0
gst-plugins-base 1.14.0 hbbd80ab_1
gstreamer 1.14.0 hb453b48_1
h5py 2.8.0 py37h989c5e5_3
harfbuzz 1.8.8 hffaf4a1_0
hdf5 1.10.2 hba1933b_1
heapdict 1.0.0 py37_2
html5lib 1.0.1 py37_0
hyperlink 18.0.0 py37_0
icu 58.2 h9c2bf20_1
idna 2.7 py37_0
imageio 2.4.1 py37_0
imagesize 1.1.0 py37_0
incremental 17.5.0 py37_0
intel-openmp 2019.0 118
ipykernel 4.9.0 py37_1
ipython 6.5.0 py37_0
ipython_genutils 0.2.0 py37_0
ipywidgets 7.4.1 py37_0
isort 4.3.4 py37_0
itsdangerous 0.24 py37_1
jbig 2.1 hdba287a_0
jdcal 1.4 py37_0
jedi 0.12.1 py37_0
jeepney 0.3.1 py37_0
jinja2 2.10 py37_0
jpeg 9b h024ee3a_2
jsonschema 2.6.0 py37_0
jupyter 1.0.0 py37_7
jupyter_client 5.2.3 py37_0
jupyter_console 5.2.0 py37_1
jupyter_core 4.4.0 py37_0
jupyterlab 0.34.9 py37_0
jupyterlab_launcher 0.13.1 py37_0
keyring 13.2.1 py37_0
kiwisolver 1.0.1 py37hf484d3e_0
lazy-object-proxy 1.3.1 py37h14c3975_2
libcurl 7.61.0 h1ad7b7a_0
libedit 3.1.20170329 h6b74fdf_2
libffi 3.2.1 hd88cf55_4
libgcc-ng 8.2.0 hdf63c60_1
libgfortran-ng 7.3.0 hdf63c60_0
libpng 1.6.34 hb9fc6fc_0
libsodium 1.0.16 h1bed415_0
libssh2 1.8.0 h9cfc8f7_4
libstdcxx-ng 8.2.0 hdf63c60_1
libtiff 4.0.9 he85c1e1_2
libtool 2.4.6 h544aabb_3
libuuid 1.0.3 h1bed415_2
libxcb 1.13 h1bed415_1
libxml2 2.9.8 h26e45fe_1
libxslt 1.1.32 h1312cb7_0
llvmlite 0.24.0 py37hdbcaa40_0
locket 0.2.0 py37_1
lxml 4.2.5 py37hefd8a0e_0
lzo 2.10 h49e0be7_2
markupsafe 1.0 py37h14c3975_1
matplotlib 2.2.3 py37hb69df0a_0
mccabe 0.6.1 py37_1
mistune 0.8.3 py37h14c3975_1
mkl 2019.0 118
mkl-service 1.1.2 py37h90e4bf4_5
mkl_fft 1.0.4 py37h4414c95_1
mkl_random 1.0.1 py37h4414c95_1
more-itertools 4.3.0 py37_0
mpc 1.1.0 h10f8cd9_1
mpfr 4.0.1 hdf1c602_3
mpmath 1.0.0 py37_2
msgpack-python 0.5.6 py37h6bb024c_1
multipledispatch 0.6.0 py37_0
navigator-updater 0.2.1 py37_0
nbconvert 5.4.0 py37_1
nbformat 4.4.0 py37_0
ncurses 6.1 hf484d3e_0
networkx 2.1 py37_0
nltk 3.3.0 py37_0
nose 1.3.7 py37_2
notebook 5.6.0 py37_0
numba 0.39.0 py37h04863e7_0
numexpr 2.6.8 py37hd89afb7_0
numpy 1.15.1 py37h1d66e8a_0
numpy-base 1.15.1 py37h81de0dd_0
numpydoc 0.8.0 py37_0
odo 0.5.1 py37_0
olefile 0.46 py37_0
openpyxl 2.5.6 py37_0
openssl 1.0.2p h14c3975_0
packaging 17.1 py37_0
pandas 0.23.4 py37h04863e7_0
pandoc 1.19.2.1 hea2e7c5_1
pandocfilters 1.4.2 py37_1
pango 1.42.4 h049681c_0
parso 0.3.1 py37_0
partd 0.3.8 py37_0
patchelf 0.9 hf484d3e_2
path.py 11.1.0 py37_0
pathlib2 2.3.2 py37_0
patsy 0.5.0 py37_0
pcre 8.42 h439df22_0
pep8 1.7.1 py37_0
pexpect 4.6.0 py37_0
pickleshare 0.7.4 py37_0
pillow 5.2.0 py37heded4f4_0
pip 10.0.1 py37_0
pixman 0.34.0 hceecf20_3
pkginfo 1.4.2 py37_1
pluggy 0.7.1 py37h28b3542_0
ply 3.11 py37_0
prometheus_client 0.3.1 py37h28b3542_0
prompt_toolkit 1.0.15 py37_0
psutil 5.4.7 py37h14c3975_0
ptyprocess 0.6.0 py37_0
py 1.6.0 py37_0
pyasn1 0.4.4 py37h28b3542_0
pyasn1-modules 0.2.2 py37_0
pycodestyle 2.4.0 py37_0
pycosat 0.6.3 py37h14c3975_0
pycparser 2.18 py37_1
pycrypto 2.6.1 py37h14c3975_9
pycurl 7.43.0.2 py37hb7f436b_0
pyflakes 2.0.0 py37_0
pygments 2.2.0 py37_0
pylint 2.1.1 py37_0
pyodbc 4.0.24 py37he6710b0_0
pyopenssl 18.0.0 py37_0
pyparsing 2.2.0 py37_1
pyqt 5.9.2 py37h05f1152_2
pysocks 1.6.8 py37_0
pytables 3.4.4 py37ha205bf6_0
pytest 3.8.0 py37_0
pytest-arraydiff 0.2 py37h39e3cac_0
pytest-astropy 0.4.0 py37_0
pytest-doctestplus 0.1.3 py37_0
pytest-openfiles 0.3.0 py37_0
pytest-remotedata 0.3.0 py37_0
python 3.7.0 hc3d631a_0
python-dateutil 2.7.3 py37_0
pytz 2018.5 py37_0
pywavelets 1.0.0 py37hdd07704_0
pyyaml 3.13 py37h14c3975_0
pyzmq 17.1.2 py37h14c3975_0
qt 5.9.6 h8703b6f_2
qtawesome 0.4.4 py37_0
qtconsole 4.4.1 py37_0
qtpy 1.5.0 py37_0
readline 7.0 h7b6447c_5
requests 2.19.1 py37_0
rope 0.11.0 py37_0
ruamel_yaml 0.15.46 py37h14c3975_0
scikit-image 0.14.0 py37hf484d3e_1
scikit-learn 0.19.2 py37h4989274_0
scipy 1.1.0 py37hfa4b5c9_1
seaborn 0.9.0 py37_0
secretstorage 3.1.0 py37_0
send2trash 1.5.0 py37_0
service_identity 17.0.0 py37h28b3542_0
setuptools 40.2.0 py37_0
simplegeneric 0.8.1 py37_2
singledispatch 3.4.0.3 py37_0
sip 4.19.8 py37hf484d3e_0
six 1.11.0 py37_1
snappy 1.1.7 hbae5bb6_3
snowballstemmer 1.2.1 py37_0
sortedcollections 1.0.1 py37_0
sortedcontainers 2.0.5 py37_0
sphinx 1.7.9 py37_0
sphinxcontrib 1.0 py37_1
sphinxcontrib-websupport 1.1.0 py37_1
spyder 3.3.1 py37_1
spyder-kernels 0.2.6 py37_0
sqlalchemy 1.2.11 py37h7b6447c_0
sqlite 3.24.0 h84994c4_0
statsmodels 0.9.0 py37h035aef0_0
sympy 1.2 py37_0
tblib 1.3.2 py37_0
terminado 0.8.1 py37_1
testpath 0.3.1 py37_0
tk 8.6.8 hbc83047_0
toolz 0.9.0 py37_0
tornado 5.1 py37h14c3975_0
tqdm 4.26.0 py37h28b3542_0
traitlets 4.3.2 py37_0
twisted 18.7.0 py37h14c3975_1
unicodecsv 0.14.1 py37_0
unixodbc 2.3.7 h14c3975_0
urllib3 1.23 py37_0
wcwidth 0.1.7 py37_0
webencodings 0.5.1 py37_1
werkzeug 0.14.1 py37_0
wheel 0.31.1 py37_0
widgetsnbextension 3.4.1 py37_0
wrapt 1.10.11 py37h14c3975_2
xlrd 1.1.0 py37_1
xlsxwriter 1.1.0 py37_0
xlwt 1.3.0 py37_0
xz 5.2.4 h14c3975_4
yaml 0.1.7 had09818_2
zeromq 4.2.5 hf484d3e_1
zict 0.1.3 py37_0
zlib 1.2.11 ha838bed_2
zope 1.0 py37_1
zope.interface 4.5.0 py37h14c3975_0
c_n031@lsp-bioinfo03:~$ conda update conda Solving environment: failed

>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

Traceback (most recent call last):
  File "/home/c_n031/anaconda3/lib/python3.7/site-packages/conda/exceptions.py", line 819, in __call__
    return func(*args, **kwargs)
  File "/home/c_n031/anaconda3/lib/python3.7/site-packages/conda/cli/main.py", line 78, in _main
    exit_code = do_call(args, p)
  File "/home/c_n031/anaconda3/lib/python3.7/site-packages/conda/cli/conda_argparse.py", line 77, in do_call
    exit_code = getattr(module, func_name)(args, parser)
  File "/home/c_n031/anaconda3/lib/python3.7/site-packages/conda/cli/main_update.py", line 14, in execute
    install(args, parser, 'update')
  File "/home/c_n031/anaconda3/lib/python3.7/site-packages/conda/cli/install.py", line 235, in install
    force_reinstall=context.force,
  File "/home/c_n031/anaconda3/lib/python3.7/site-packages/conda/core/solve.py", line 518, in solve_for_transaction
    force_remove, force_reinstall)
  File "/home/c_n031/anaconda3/lib/python3.7/site-packages/conda/core/solve.py", line 451, in solve_for_diff
    final_precs = self.solve_final_state(deps_modifier, prune, ignore_pinned, force_remove)
  File "/home/c_n031/anaconda3/lib/python3.7/site-packages/conda/core/solve.py", line 180, in solve_final_state
    index, r = self._prepare(prepared_specs)
  File "/home/c_n031/anaconda3/lib/python3.7/site-packages/conda/core/solve.py", line 592, in _prepare
    self.subdirs, prepared_specs)
  File "/home/c_n031/anaconda3/lib/python3.7/site-packages/conda/core/index.py", line 215, in get_reduced_index
    new_records = query_all(spec)
  File "/home/c_n031/anaconda3/lib/python3.7/site-packages/conda/core/index.py", line 184, in query_all
    return tuple(concat(future.result() for future in as_completed(futures)))
  File "/home/c_n031/anaconda3/lib/python3.7/site-packages/conda/core/subdir_data.py", line 95, in query
    self.load()
  File "/home/c_n031/anaconda3/lib/python3.7/site-packages/conda/core/subdir_data.py", line 149, in load
    _internal_state = self._load()
  File "/home/c_n031/anaconda3/lib/python3.7/site-packages/conda/core/subdir_data.py", line 218, in _load
    mod_etag_headers.get('_mod'))
  File "/home/c_n031/anaconda3/lib/python3.7/site-packages/conda/core/subdir_data.py", line 280, in _read_local_repdata
    _internal_state = self._process_raw_repodata_str(raw_repodata_str)
  File "/home/c_n031/anaconda3/lib/python3.7/site-packages/conda/core/subdir_data.py", line 369, in _process_raw_repodata_str
    info['fn'] = fn
TypeError: 'NoneType' object does not support item assignment

$ /home/c_n031/anaconda3/bin/conda update conda

environment variables: CIO_TEST= CONDA_DEFAULT_ENV=base CONDA_EXE=/home/c_n031/anaconda3/bin/conda CONDA_PREFIX=/home/c_n031/anaconda3 CONDA_PROMPT_MODIFIER= CONDA_PYTHON_EXE=/home/c_n031/anaconda3/bin/python CONDA_ROOT=/home/c_n031/anaconda3 CONDA_SHLVL=1 MANPATH=/home/c_n031/.nvm/versions/node/v10.12.0/share/man:/home/c_n031/anacon da3/man:/usr/share/man:/usr/local/man:/usr/local/share/man PATH=/home/c_n031/anaconda3/bin:/home/c_n031/bin/anaconda3/bin:/home/c_n031 /bin/miniconda3/bin:/home/c_n031/bin/miniconda3/bin:/home/c_n031/.nvm/ versions/node/v10.12.0/bin:/home/c_n031/bin/anaconda3/bin:/home/c_n031 /bin/miniconda3/bin:/home/c_n031/bin/anaconda3/bin:/home/c_n031/bin/an aconda2/bin:/home/c_n031/bin/miniconda3/bin:/home/c_n031/bin/miniconda 3/bin:/home/c_n031/bin/miniconda2/bin:/home/c_n031/bin/miniconda3/bin: /home/c_n031/miniconda3/bin:/home/c_n031/anaconda3/bin:/bin:/usr/bin:/ usr/local/bin REQUESTS_CA_BUNDLE= SSL_CERT_FILE=

 active environment : base
active env location : /home/c_n031/anaconda3
        shell level : 1
   user config file : /home/c_n031/.condarc

populated config files : /home/c_n031/.condarc conda version : 4.5.11 conda-build version : 3.15.1 python version : 3.7.0.final.0 base environment : /home/c_n031/anaconda3 (writable) channel URLs : https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch https://conda.anaconda.org/anaconda/linux-64 https://conda.anaconda.org/anaconda/noarch https://conda.anaconda.org/bioconda/linux-64 https://conda.anaconda.org/bioconda/noarch https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/free/linux-64 https://repo.anaconda.com/pkgs/free/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch https://repo.anaconda.com/pkgs/pro/linux-64 https://repo.anaconda.com/pkgs/pro/noarch https://conda.anaconda.org/biocore/linux-64 https://conda.anaconda.org/biocore/noarch package cache : /home/c_n031/anaconda3/pkgs /home/c_n031/.conda/pkgs envs directories : /home/c_n031/anaconda3/envs /home/c_n031/.conda/envs platform : linux-64 user-agent : conda/4.5.11 requests/2.19.1 CPython/3.7.0 Linux/4.8.0-59-generic ubuntu/16.10 glibc/2.24 UID:GID : 82481:1513 netrc file : None offline mode : False

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