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Conda Deletes All Modules During Update #8842

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cgivre opened this issue Jun 28, 2019 · 45 comments

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@cgivre
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commented Jun 28, 2019

Current Behavior

I attempt to do a conda update --all and it informs me that conda wants to remove nearly every module. This can't be correct.

conda update --all
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /anaconda3


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    libtiff-4.0.10             |    hcb84e12_1001         396 KB
    ------------------------------------------------------------
                                           Total:         396 KB

The following packages will be REMOVED:

  alabaster-0.7.12-py37_0
  anaconda-custom-py37_0
  anaconda-project-0.8.3-py_0
  appscript-1.1.0-py37h1de35cc_0
  astroid-2.2.5-py37_0
  astropy-3.2.1-py37h1de35cc_0
  atomicwrites-1.3.0-py37_1
  babel-2.7.0-py_0
  backports.os-0.1.1-py37_0
  backports.shutil_get_terminal_size-1.0.0-py37_2
  bitarray-0.9.3-py37h1de35cc_0
  bkcharts-0.2-py37_0
  blas-1.0-mkl
  blosc-1.16.3-hd9629dc_0
  bokeh-1.2.0-py37_0
  boto-2.49.0-py37_0
  bottleneck-1.2.1-py37h1d22016_1
  cloudpickle-1.1.1-py_0
  colorama-0.4.1-py37_0
  contextlib2-0.5.5-py37_0
  curl-7.64.1-ha441bb4_0
  cycler-0.10.0-py37_0
  cython-0.29.10-py37h0a44026_0
  cytoolz-0.9.0.1-py37h1de35cc_1
  dask-2.0.0-py_0
  dask-core-2.0.0-py_0
  distributed-2.0.1-py_0
  docutils-0.14-py37_0
  et_xmlfile-1.0.1-py37_0
  fastcache-1.1.0-py37h1de35cc_0
  flask-1.0.3-py37_0
  get_terminal_size-1.0.0-h7520d66_0
  gevent-1.4.0-py37h1de35cc_0
  gmp-6.1.2-hb37e062_1
  gmpy2-2.0.8-py37h6ef4df4_2
  greenlet-0.4.15-py37h1de35cc_0
  h5py-2.9.0-py37h3134771_0
  hdf5-1.10.4-hfa1e0ec_0
  heapdict-1.0.0-py37_2
  html5lib-1.0.1-py37_0
  imageio-2.5.0-py37_0
  imagesize-1.1.0-py37_0
  importlib_metadata-0.17-py37_1
  intel-openmp-2019.4-233
  isort-4.3.20-py37_0
  itsdangerous-1.1.0-py37_0
  jbig-2.1-h4d881f8_0
  jdcal-1.4.1-py_0
  joblib-0.13.2-py37_0
  jupyter-1.0.0-py37_7
  jupyter_console-6.0.0-py37_0
  keyring-18.0.0-py37_0
  kiwisolver-1.1.0-py37h0a44026_0
  krb5-1.16.1-hddcf347_7
  lazy-object-proxy-1.4.1-py37h1de35cc_0
  libcurl-7.64.1-h051b688_0
  libgfortran-3.0.1-h93005f0_2
  libssh2-1.8.2-ha12b0ac_0
  libxslt-1.1.33-h33a18ac_0
  llvm-openmp-4.0.1-hcfea43d_1
  llvmlite-0.29.0-py37h98b8051_0
  locket-0.2.0-py37_1
  lxml-4.3.3-py37hef8c89e_0
  matplotlib-3.1.0-py37h54f8f79_0
  mccabe-0.6.1-py37_1
  mkl-2019.4-233
  mkl-service-2.0.2-py37h1de35cc_0
  mkl_fft-1.0.12-py37h5e564d8_0
  mkl_random-1.0.2-py37h27c97d8_0
  mock-3.0.5-py37_0
  more-itertools-7.0.0-py37_0
  mpc-1.1.0-h6ef4df4_1
  mpfr-4.0.1-h3018a27_3
  mpmath-1.1.0-py37_0
  msgpack-python-0.6.1-py37h04f5b5a_1
  multipledispatch-0.6.0-py37_0
  networkx-2.3-py_0
  nltk-3.4.1-py37_0
  nose-1.3.7-py37_2
  numba-0.44.1-py37h6440ff4_0
  numexpr-2.6.9-py37h7413580_0
  numpy-1.16.4-py37hacdab7b_0
  numpy-base-1.16.4-py37h6575580_0
  numpydoc-0.9.1-py_0
  openpyxl-2.6.2-py_0
  packaging-19.0-py37_0
  pandas-0.24.2-py37h0a44026_0
  partd-0.3.10-py37_1
  path.py-12.0.1-py_0
  pathlib2-2.3.3-py37_0
  patsy-0.5.1-py37_0
  pep8-1.7.1-py37_0
  pluggy-0.12.0-py_0
  ply-3.11-py37_0
  py-1.8.0-py37_0
  pycodestyle-2.5.0-py37_0
  pycrypto-2.6.1-py37h1de35cc_9
  pycurl-7.43.0.2-py37ha12b0ac_0
  pyflakes-2.1.1-py37_0
  pylint-2.3.1-py37_0
  pyodbc-4.0.26-py37h0a44026_0
  pyparsing-2.4.0-py_0
  pytables-3.5.2-py37h5bccee9_1
  pytest-4.6.2-py37_0
  pytest-arraydiff-0.3-py37h39e3cac_0
  pytest-astropy-0.5.0-py37_0
  pytest-doctestplus-0.3.0-py37_0
  pytest-openfiles-0.3.2-py37_0
  pytest-remotedata-0.3.1-py37_0
  pywavelets-1.0.3-py37h1d22016_1
  qtawesome-0.5.7-py37_1
  qtconsole-4.5.1-py_0
  rope-0.14.0-py_0
  scikit-image-0.15.0-py37h0a44026_0
  scikit-learn-0.21.2-py37h27c97d8_0
  scipy-1.2.1-py37h1410ff5_0
  seaborn-0.9.0-py37_0
  simplegeneric-0.8.1-py37_2
  singledispatch-3.4.0.3-py37_0
  snappy-1.1.7-he62c110_3
  snowballstemmer-1.2.1-py37_0
  sortedcollections-1.1.2-py37_0
  sortedcontainers-2.1.0-py37_0
  sphinx-2.1.0-py_0
  sphinxcontrib-1.0-py37_1
  sphinxcontrib-applehelp-1.0.1-py_0
  sphinxcontrib-devhelp-1.0.1-py_0
  sphinxcontrib-htmlhelp-1.0.2-py_0
  sphinxcontrib-jsmath-1.0.1-py_0
  sphinxcontrib-qthelp-1.0.2-py_0
  sphinxcontrib-serializinghtml-1.1.3-py_0
  sphinxcontrib-websupport-1.1.2-py_0
  spyder-3.3.4-py37_0
  spyder-kernels-0.5.0-py37_0
  sqlalchemy-1.3.4-py37h1de35cc_0
  statsmodels-0.9.0-py37h1d22016_0
  sympy-1.4-py37_0
  tblib-1.4.0-py_0
  toolz-0.9.0-py37_0
  unicodecsv-0.14.1-py37_0
  unixodbc-2.3.7-h1de35cc_0
  werkzeug-0.15.4-py_0
  wrapt-1.11.1-py37h1de35cc_0
  wurlitzer-1.0.2-py37_0
  xlrd-1.2.0-py37_0
  xlsxwriter-1.1.8-py_0
  xlwings-0.15.8-py37_0
  xlwt-1.3.0-py37_0
  zict-0.1.4-py37_0
  zipp-0.5.1-py_0

The following packages will be UPDATED:

  libtiff                                 4.0.10-hcb84e12_2 --> 4.0.10-hcb84e12_1001


Proceed ([y]/n)? n


CondaSystemExit: Exiting.

Steps to Reproduce

conda update --all

Expected Behavior

I think conda should update whichever packages need updating.

Environment Information

`conda info`

conda info

     active environment : base
    active env location : /anaconda3
            shell level : 1
       user config file : /Users/cgivre/.condarc
 populated config files :
          conda version : 4.7.5
    conda-build version : 3.18.5
         python version : 3.7.3.final.0
       virtual packages :
       base environment : /anaconda3  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /anaconda3/pkgs
                          /Users/cgivre/.conda/pkgs
       envs directories : /anaconda3/envs
                          /Users/cgivre/.conda/envs
               platform : osx-64
             user-agent : conda/4.7.5 requests/2.22.0 CPython/3.7.3 Darwin/18.6.0 OSX/10.14.5
                UID:GID : 501:20
             netrc file : None
           offline mode : False

`conda config --show-sources`

(no output)

`conda list --show-channel-urls`

conda list --show-channel-urls
# packages in environment at /anaconda3:
#
# Name                    Version                   Build  Channel
_ipyw_jlab_nb_ext_conf    0.1.0                    py37_0    defaults
alabaster                 0.7.12                   py37_0    defaults
anaconda                  custom                   py37_0    defaults
anaconda-client           1.7.2                    py37_0    defaults
anaconda-navigator        1.9.7                    py37_0    defaults
anaconda-project          0.8.3                      py_0    defaults
appnope                   0.1.0                    py37_0    defaults
appscript                 1.1.0            py37h1de35cc_0    defaults
asn1crypto                0.24.0                   py37_0    defaults
astroid                   2.2.5                    py37_0    defaults
astropy                   3.2.1            py37h1de35cc_0    defaults
atomicwrites              1.3.0                    py37_1    defaults
attrs                     19.1.0                   py37_1    defaults
babel                     2.7.0                      py_0    defaults
backcall                  0.1.0                    py37_0    defaults
backports                 1.0                        py_2    defaults
backports.functools_lru_cache 1.5                        py_2    defaults
backports.os              0.1.1                    py37_0    defaults
backports.shutil_get_terminal_size 1.0.0                    py37_2    defaults
backports.tempfile        1.0                        py_1    defaults
backports.weakref         1.0.post1                  py_1    defaults
beautifulsoup4            4.7.1                    py37_1    defaults
bitarray                  0.9.3            py37h1de35cc_0    defaults
bkcharts                  0.2                      py37_0    defaults
blas                      1.0                         mkl    defaults
bleach                    3.1.0                    py37_0    defaults
blosc                     1.16.3               hd9629dc_0    defaults
bokeh                     1.2.0                    py37_0    defaults
boto                      2.49.0                   py37_0    defaults
bottleneck                1.2.1            py37h1d22016_1    defaults
bzip2                     1.0.6                h1de35cc_5    defaults
ca-certificates           2019.5.15                     0    defaults
certifi                   2019.6.16                py37_0    defaults
cffi                      1.12.3           py37hb5b8e2f_0    defaults
chardet                   3.0.4                    py37_1    defaults
click                     7.0                      py37_0    defaults
cloudpickle               1.1.1                      py_0    defaults
clyent                    1.2.2                    py37_1    defaults
colorama                  0.4.1                    py37_0    defaults
conda                     4.7.5                    py37_0    defaults
conda-build               3.18.5                   py37_0    defaults
conda-env                 2.6.0                         1    defaults
conda-package-handling    1.3.10                   py37_0    defaults
conda-verify              3.4.2                      py_0    defaults
contextlib2               0.5.5                    py37_0    defaults
cryptography              2.7              py37ha12b0ac_0    defaults
curl                      7.64.1               ha441bb4_0    defaults
cycler                    0.10.0                   py37_0    defaults
cython                    0.29.10          py37h0a44026_0    defaults
cytoolz                   0.9.0.1          py37h1de35cc_1    defaults
dask                      2.0.0                      py_0    defaults
dask-core                 2.0.0                      py_0    defaults
dbus                      1.13.6               h90a0687_0    defaults
decorator                 4.4.0                    py37_1    defaults
defusedxml                0.6.0                      py_0    defaults
distributed               2.0.1                      py_0    defaults
docutils                  0.14                     py37_0    defaults
entrypoints               0.3                      py37_0    defaults
et_xmlfile                1.0.1                    py37_0    defaults
expat                     2.2.6                h0a44026_0    defaults
fastcache                 1.1.0            py37h1de35cc_0    defaults
filelock                  3.0.12                     py_0    defaults
flask                     1.0.3                    py37_0    defaults
freetype                  2.9.1                hb4e5f40_0    defaults
future                    0.17.1                   py37_0    defaults
get_terminal_size         1.0.0                h7520d66_0    defaults
gettext                   0.19.8.1             h15daf44_3    defaults
gevent                    1.4.0            py37h1de35cc_0    defaults
glib                      2.56.2               hd9629dc_0    defaults
glob2                     0.6                      py37_1    defaults
gmp                       6.1.2                hb37e062_1    defaults
gmpy2                     2.0.8            py37h6ef4df4_2    defaults
greenlet                  0.4.15           py37h1de35cc_0    defaults
h5py                      2.9.0            py37h3134771_0    defaults
hdf5                      1.10.4               hfa1e0ec_0    defaults
heapdict                  1.0.0                    py37_2    defaults
html5lib                  1.0.1                    py37_0    defaults
icu                       58.2                 h4b95b61_1    defaults
idna                      2.8                      py37_0    defaults
imageio                   2.5.0                    py37_0    defaults
imagesize                 1.1.0                    py37_0    defaults
importlib_metadata        0.17                     py37_1    defaults
intel-openmp              2019.4                      233    defaults
ipykernel                 5.1.1            py37h39e3cac_0    defaults
ipython                   7.5.0            py37h39e3cac_0    defaults
ipython_genutils          0.2.0                    py37_0    defaults
ipywidgets                7.4.2                    py37_0    defaults
isort                     4.3.20                   py37_0    defaults
itsdangerous              1.1.0                    py37_0    defaults
jbig                      2.1                  h4d881f8_0    defaults
jdcal                     1.4.1                      py_0    defaults
jedi                      0.13.3                   py37_0    defaults
jinja2                    2.10.1                   py37_0    defaults
joblib                    0.13.2                   py37_0    defaults
jpeg                      9b                   he5867d9_2    defaults
jsonschema                3.0.1                    py37_0    defaults
jupyter                   1.0.0                    py37_7    defaults
jupyter_client            5.2.4                    py37_0    defaults
jupyter_console           6.0.0                    py37_0    defaults
jupyter_core              4.4.0                    py37_0    defaults
jupyterlab                0.35.5           py37hf63ae98_0    defaults
jupyterlab_server         0.2.0                    py37_0    defaults
keyring                   18.0.0                   py37_0    defaults
kiwisolver                1.1.0            py37h0a44026_0    defaults
krb5                      1.16.1               hddcf347_7    defaults
lazy-object-proxy         1.4.1            py37h1de35cc_0    defaults
libarchive                3.3.3                h786848e_5    defaults
libcurl                   7.64.1               h051b688_0    defaults
libcxx                    4.0.1                hcfea43d_1    defaults
libcxxabi                 4.0.1                hcfea43d_1    defaults
libedit                   3.1.20181209         hb402a30_0    defaults
libffi                    3.2.1                h475c297_4    defaults
libgfortran               3.0.1                h93005f0_2    defaults
libiconv                  1.15                 hdd342a3_7    defaults
liblief                   0.9.0                h2a1bed3_2    defaults
libpng                    1.6.37               ha441bb4_0    defaults
libsodium                 1.0.16               h3efe00b_0    defaults
libssh2                   1.8.2                ha12b0ac_0    defaults
libtiff                   4.0.10               hcb84e12_2    defaults
libxml2                   2.9.9                hf6e021a_1    defaults
libxslt                   1.1.33               h33a18ac_0    defaults
llvm-openmp               4.0.1                hcfea43d_1    defaults
llvmlite                  0.29.0           py37h98b8051_0    defaults
locket                    0.2.0                    py37_1    defaults
lxml                      4.3.3            py37hef8c89e_0    defaults
lz4-c                     1.8.1.2              h1de35cc_0    defaults
lzo                       2.10                 h362108e_2    defaults
markupsafe                1.1.1            py37h1de35cc_0    defaults
matplotlib                3.1.0            py37h54f8f79_0    defaults
mccabe                    0.6.1                    py37_1    defaults
mistune                   0.8.4            py37h1de35cc_0    defaults
mkl                       2019.4                      233    defaults
mkl-service               2.0.2            py37h1de35cc_0    defaults
mkl_fft                   1.0.12           py37h5e564d8_0    defaults
mkl_random                1.0.2            py37h27c97d8_0    defaults
mock                      3.0.5                    py37_0    defaults
more-itertools            7.0.0                    py37_0    defaults
mpc                       1.1.0                h6ef4df4_1    defaults
mpfr                      4.0.1                h3018a27_3    defaults
mpmath                    1.1.0                    py37_0    defaults
msgpack-python            0.6.1            py37h04f5b5a_1    defaults
multipledispatch          0.6.0                    py37_0    defaults
navigator-updater         0.2.1                    py37_0    defaults
nbconvert                 5.5.0                      py_0    defaults
nbformat                  4.4.0                    py37_0    defaults
ncurses                   6.1                  h0a44026_1    defaults
networkx                  2.3                        py_0    defaults
nltk                      3.4.1                    py37_0    defaults
nose                      1.3.7                    py37_2    defaults
notebook                  5.7.8                    py37_0    defaults
numba                     0.44.1           py37h6440ff4_0    defaults
numexpr                   2.6.9            py37h7413580_0    defaults
numpy                     1.16.4           py37hacdab7b_0    defaults
numpy-base                1.16.4           py37h6575580_0    defaults
numpydoc                  0.9.1                      py_0    defaults
olefile                   0.46                     py37_0    defaults
openpyxl                  2.6.2                      py_0    defaults
openssl                   1.1.1c               h1de35cc_1    defaults
packaging                 19.0                     py37_0    defaults
pandas                    0.24.2           py37h0a44026_0    defaults
pandoc                    2.2.3.2                       0    defaults
pandocfilters             1.4.2                    py37_1    defaults
parso                     0.4.0                      py_0    defaults
partd                     0.3.10                   py37_1    defaults
path.py                   12.0.1                     py_0    defaults
pathlib2                  2.3.3                    py37_0    defaults
patsy                     0.5.1                    py37_0    defaults
pcre                      8.43                 h0a44026_0    defaults
pep8                      1.7.1                    py37_0    defaults
pexpect                   4.7.0                    py37_0    defaults
pickleshare               0.7.5                    py37_0    defaults
pillow                    6.0.0            py37hb68e598_0    defaults
pip                       19.1.1                   py37_0    defaults
pkginfo                   1.5.0.1                  py37_0    defaults
pluggy                    0.12.0                     py_0    defaults
ply                       3.11                     py37_0    defaults
prometheus_client         0.6.0                    py37_0    defaults
prompt_toolkit            2.0.9                    py37_0    defaults
psutil                    5.6.2            py37h1de35cc_0    defaults
ptyprocess                0.6.0                    py37_0    defaults
py                        1.8.0                    py37_0    defaults
py-lief                   0.9.0            py37h1413db1_2    defaults
pycodestyle               2.5.0                    py37_0    defaults
pycosat                   0.6.3            py37h1de35cc_0    defaults
pycparser                 2.19                     py37_0    defaults
pycrypto                  2.6.1            py37h1de35cc_9    defaults
pycurl                    7.43.0.2         py37ha12b0ac_0    defaults
pyflakes                  2.1.1                    py37_0    defaults
pygments                  2.4.2                      py_0    defaults
pylint                    2.3.1                    py37_0    defaults
pyodbc                    4.0.26           py37h0a44026_0    defaults
pyopenssl                 19.0.0                   py37_0    defaults
pyparsing                 2.4.0                      py_0    defaults
pyqt                      5.9.2            py37h655552a_2    defaults
pyrsistent                0.14.11          py37h1de35cc_0    defaults
pysocks                   1.7.0                    py37_0    defaults
pytables                  3.5.2            py37h5bccee9_1    defaults
pytest                    4.6.2                    py37_0    defaults
pytest-arraydiff          0.3              py37h39e3cac_0    defaults
pytest-astropy            0.5.0                    py37_0    defaults
pytest-doctestplus        0.3.0                    py37_0    defaults
pytest-openfiles          0.3.2                    py37_0    defaults
pytest-remotedata         0.3.1                    py37_0    defaults
python                    3.7.3                h359304d_0    defaults
python-dateutil           2.8.0                    py37_0    defaults
python-libarchive-c       2.8                      py37_6    defaults
python.app                2                        py37_9    defaults
pytz                      2019.1                     py_0    defaults
pywavelets                1.0.3            py37h1d22016_1    defaults
pyyaml                    5.1              py37h1de35cc_0    defaults
pyzmq                     18.0.0           py37h0a44026_0    defaults
qt                        5.9.7                h468cd18_1    defaults
qtawesome                 0.5.7                    py37_1    defaults
qtconsole                 4.5.1                      py_0    defaults
qtpy                      1.7.1                      py_0    defaults
readline                  7.0                  h1de35cc_5    defaults
requests                  2.22.0                   py37_0    defaults
rope                      0.14.0                     py_0    defaults
ruamel_yaml               0.15.46          py37h1de35cc_0    defaults
scikit-image              0.15.0           py37h0a44026_0    defaults
scikit-learn              0.21.2           py37h27c97d8_0    defaults
scipy                     1.2.1            py37h1410ff5_0    defaults
seaborn                   0.9.0                    py37_0    defaults
send2trash                1.5.0                    py37_0    defaults
setuptools                41.0.1                   py37_0    defaults
simplegeneric             0.8.1                    py37_2    defaults
singledispatch            3.4.0.3                  py37_0    defaults
sip                       4.19.8           py37h0a44026_0    defaults
six                       1.12.0                   py37_0    defaults
snappy                    1.1.7                he62c110_3    defaults
snowballstemmer           1.2.1                    py37_0    defaults
sortedcollections         1.1.2                    py37_0    defaults
sortedcontainers          2.1.0                    py37_0    defaults
soupsieve                 1.8                      py37_0    defaults
sphinx                    2.1.0                      py_0    defaults
sphinxcontrib             1.0                      py37_1    defaults
sphinxcontrib-applehelp   1.0.1                      py_0    defaults
sphinxcontrib-devhelp     1.0.1                      py_0    defaults
sphinxcontrib-htmlhelp    1.0.2                      py_0    defaults
sphinxcontrib-jsmath      1.0.1                      py_0    defaults
sphinxcontrib-qthelp      1.0.2                      py_0    defaults
sphinxcontrib-serializinghtml 1.1.3                      py_0    defaults
sphinxcontrib-websupport  1.1.2                      py_0    defaults
spyder                    3.3.4                    py37_0    defaults
spyder-kernels            0.5.0                    py37_0    defaults
sqlalchemy                1.3.4            py37h1de35cc_0    defaults
sqlite                    3.28.0               ha441bb4_0    defaults
statsmodels               0.9.0            py37h1d22016_0    defaults
sympy                     1.4                      py37_0    defaults
tblib                     1.4.0                      py_0    defaults
terminado                 0.8.2                    py37_0    defaults
testpath                  0.4.2                    py37_0    defaults
tk                        8.6.8                ha441bb4_0    defaults
toolz                     0.9.0                    py37_0    defaults
tornado                   6.0.2            py37h1de35cc_0    defaults
tqdm                      4.32.1                     py_0    defaults
traitlets                 4.3.2                    py37_0    defaults
unicodecsv                0.14.1                   py37_0    defaults
unixodbc                  2.3.7                h1de35cc_0    defaults
urllib3                   1.24.2                   py37_0    defaults
virtualenv                16.6.1                   pypi_0    pypi
wcwidth                   0.1.7                    py37_0    defaults
webencodings              0.5.1                    py37_1    defaults
werkzeug                  0.15.4                     py_0    defaults
wheel                     0.33.4                   py37_0    defaults
widgetsnbextension        3.4.2                    py37_0    defaults
wrapt                     1.11.1           py37h1de35cc_0    defaults
wurlitzer                 1.0.2                    py37_0    defaults
xlrd                      1.2.0                    py37_0    defaults
xlsxwriter                1.1.8                      py_0    defaults
xlwings                   0.15.8                   py37_0    defaults
xlwt                      1.3.0                    py37_0    defaults
xz                        5.2.4                h1de35cc_4    defaults
yaml                      0.1.7                hc338f04_2    defaults
zeromq                    4.3.1                h0a44026_3    defaults
zict                      0.1.4                    py37_0    defaults
zipp                      0.5.1                      py_0    defaults
zlib                      1.2.11               h1de35cc_3    defaults
zstd                      1.3.7                h5bba6e5_0    defaults

@notemissary

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commented Jun 28, 2019

It's exactly the same on Linux.

@msarahan

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commented Jun 28, 2019

The likely reason for this is that update --all frees up all of your constraints to be optional (as they were not explicitly specs) and they get cleaned up. It's definitely a bug. I'd avoid update --all until we can get to the bottom of this.

@00krishna

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commented Jun 28, 2019

So I get that this is a bug, but I am not clear on where the issue happened. There was a new version of conda-build published in 4.7.5 that was supposed to solve the environment faster. Were users supposed to follow some kind of upgrade instructions to install the new conda-build or other packages? Did we users install something out of order? I found this issue when I did a conda update --all and then the anaconda 4.7.5 got installed. So I can't tell where I as a user was to upgrade in a certain way, didn't do that, and then the bug appeared. Or if there was no defined upgrade path and the bug was somewhere in the conda-build or other package.

@msarahan

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commented Jun 29, 2019

What's happening here is this:

  1. anaconda is a metapackage. Each version consists of a set of versions that have all gone through QA together as a set. If you change any version of any package in that collection, you no longer have that metapackage, because you have strayed from that known set. There is a special version of that metapackage, custom, that is meant to handle this relaxation of constraints. The "custom" version depends only on a particular version of python - it removes the constraints on all other packages.
  2. conda 4.7 builds up its candidates for addition differently from earlier conda versions. It starts with specs from the history, and tries to constrain things where it can, to speed up the solve. When conda finds the anaconda metapackage with the "custom" version, it keeps it, but all of those other dependencies are now orphaned. This is why conda is removing them - they have no spec in the history that tells conda to keep them.

You can restore these by running conda install --only-deps anaconda. From then on, all of those packages are considered part of your explicit history, and you won't have further problems like this.

@cgivre

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commented Jun 30, 2019

Thanks everyone. I'm glad that everything is restorable, though I wish I had known that before re-installing anaconda. I'm still not clear as to the correct procedure for updating my system. I ran the
conda install --only-deps anaconda command. From this point forward, do I periodically run conda update --all?

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commented Jun 30, 2019

Yes, that should be fine going forward. The behavior with the metapackage is very undesirable, and we'll be trying to help other people not have that issue in the future. You should be all set, though.

@eltabbal

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commented Jul 1, 2019

actually , i had the same issue on MacOS mojave , and when i tried to use conda install --only-deps anaconda it still wants to remove lots of packages

Collecting package metadata (current_repodata.json): done
Solving environment: done

Package Plan

environment location: /anaconda3

added / updated specs:
- anaconda

The following packages will be REMOVED:

anaconda-project-0.8.3-py_0
astropy-3.2.1-py37h1de35cc_0
babel-2.7.0-py_0
bitarray-0.9.3-py37h1de35cc_0
blosc-1.16.3-hd9629dc_0
bokeh-1.2.0-py37_0
cloudpickle-1.1.1-py_0
cython-0.29.10-py37h0a44026_0
dask-2.0.0-py_0
dask-core-2.0.0-py_0
distributed-2.0.1-py_0
fastcache-1.1.0-py37h1de35cc_0
flask-1.0.3-py37_0
importlib_metadata-0.17-py37_1
jdcal-1.4.1-py_0
llvmlite-0.29.0-py37h98b8051_0
lxml-4.3.3-py37hef8c89e_0
mkl-service-2.0.2-py37h1de35cc_0
more-itertools-7.0.0-py37_0
networkx-2.3-py_0
nltk-3.4.1-py37_0
numba-0.44.1-py37h6440ff4_0
numpydoc-0.9.1-py_0
openpyxl-2.6.2-py_0
path.py-12.0.1-py_0
pluggy-0.12.0-py_0
pytables-3.5.2-py37h5bccee9_1
pytest-4.6.2-py37_0
pytest-arraydiff-0.3-py37h39e3cac_0
pytest-astropy-0.5.0-py37_0
pytest-doctestplus-0.3.0-py37_0
pytest-openfiles-0.3.2-py37_0
pytest-remotedata-0.3.1-py37_0
pywavelets-1.0.3-py37h1d22016_1
rope-0.14.0-py_0
scikit-image-0.15.0-py37h0a44026_0
scikit-learn-0.21.2-py37h27c97d8_0
sphinx-2.1.0-py_0
sphinxcontrib-websupport-1.1.2-py_0
spyder-3.3.4-py37_0
spyder-kernels-0.5.0-py37_0
sqlalchemy-1.3.4-py37h1de35cc_0
sympy-1.4-py37_0
tblib-1.4.0-py_0
werkzeug-0.15.4-py_0
xlsxwriter-1.1.8-py_0
xlwings-0.15.8-py37_0
zipp-0.5.1-py_0

@pxcandeias

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commented Jul 1, 2019

Apparently I have a related issue, have been recommended to post here what happened.

I work with three different machines, a Linux Mint 19.1 64 bits laptop, a Windows 10 64 bits laptop and a Windows 7 64 bits desktop. I have Anaconda installed on all three machines (base environment only) and I keep them updated. You can find what I did in here (https://groups.google.com/a/continuum.io/forum/#!topic/anaconda/1PxQi3Q_4WQ), I am pasting below just the (partial) error I could retrieve from my console while doing a simple "conda update conda" on the third machine mentioned above (edited username for privacy):

"""
tqdm pkgs/main/win-64::tqdm-4.31.1-py37_1 --> pkgs/main/noarch
::tqdm-4.32.1-py_0
urllib3 1.24.1-py37_0 --> 1.24.2-py37_0
vs2015_runtime 14.15.26706-h3a45250_0 --> 14.15.26706-h3a4
5250_4
wheel 0.33.1-py37_0 --> 0.33.4-py37_0

Proceed ([y]/n)?

Downloading and Extracting Packages
sphinxcontrib-htmlhe | 28 KB | #################################### | 100%
sphinxcontrib-jsmath | 8 KB | #################################### | 100%
psutil-5.6.2 | 350 KB | #################################### | 100%
cffi-1.12.3 | 225 KB | #################################### | 100%
wheel-0.33.4 | 57 KB | #################################### | 100%
babel-2.7.0 | 5.8 MB | #################################### | 100%
tqdm-4.32.1 | 48 KB | #################################### | 100%
jinja2-2.10.1 | 188 KB | #################################### | 100%
pillow-6.0.0 | 689 KB | #################################### | 100%
cryptography-2.7 | 564 KB | #################################### | 100%
sphinxcontrib-qthelp | 26 KB | #################################### | 100%
qtpy-1.7.1 | 35 KB | #################################### | 100%
defusedxml-0.6.0 | 23 KB | #################################### | 100%
vs2015_runtime-14.15 | 2.4 MB | #################################### | 100%
sqlite-3.28.0 | 945 KB | #################################### | 100%
numpydoc-0.9.1 | 31 KB | #################################### | 100%
filelock-3.0.12 | 12 KB | #################################### | 100%
rope-0.14.0 | 113 KB | #################################### | 100%
sphinxcontrib-devhel | 23 KB | #################################### | 100%
lazy-object-proxy-1. | 31 KB | #################################### | 100%
pysocks-1.7.0 | 30 KB | #################################### | 100%
pygments-2.4.2 | 664 KB | #################################### | 100%
sphinxcontrib-serial | 24 KB | #################################### | 100%
terminado-0.8.2 | 22 KB | #################################### | 100%
sphinxcontrib-appleh | 29 KB | #################################### | 100%
urllib3-1.24.2 | 153 KB | #################################### | 100%
ipython-7.5.0 | 1.1 MB | #################################### | 100%
libpng-1.6.37 | 598 KB | #################################### | 100%
setuptools-41.0.1 | 680 KB | #################################### | 100%
pyparsing-2.4.0 | 58 KB | #################################### | 100%
isort-4.3.20 | 86 KB | #################################### | 100%
pip-19.1.1 | 1.8 MB | #################################### | 100%
conda-build-3.18.5 | 550 KB | #################################### | 100%
cloudpickle-1.1.1 | 23 KB | #################################### | 100%
pytz-2019.1 | 236 KB | #################################### | 100%
parso-0.4.0 | 66 KB | #################################### | 100%
sphinx-2.1.0 | 1.4 MB | #################################### | 100%
ipykernel-5.1.1 | 163 KB | #################################### | 100%
nbconvert-5.5.0 | 381 KB | #################################### | 100%
requests-2.22.0 | 90 KB | #################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: | DEBUG menuinst_win32:init(199): Menu: name: 'Anacon
da${PY_VER} ${PLATFORM}', prefix: 'C:\Users---\AppData\Local\Continuum\an
aconda3', env_name: 'None', mode: 'user', used_mode: 'user'
DEBUG menuinst_win32:create(323): Shortcut cmd is %windir%\System32\WindowsPower
Shell\v1.0\powershell.exe, args are ['-ExecutionPolicy', 'ByPass', '-NoExit', '-
Command', '"& 'C:\Users\---\AppData\Local\Continuum\anaconda3\shel
l\condabin\conda-hook.ps1' ; conda activate 'C:\Users\---\AppData\
Local\Continuum\anaconda3' "']
\ DEBUG menuinst_win32:init(199): Menu: name: 'Anaconda${PY_VER} ${PLATFORM}
', prefix: 'C:\Users---\AppData\Local\Continuum\anaconda3', env_name: 'No
ne', mode: 'user', used_mode: 'user'
DEBUG menuinst_win32:create(323): Shortcut cmd is %windir%\System32\cmd.exe, arg
s are ['"/K"', 'C:\Users\---\AppData\Local\Continuum\anaconda3\Scri
pts\activate.bat', 'C:\Users\---\AppData\Local\Continuum\anaconda3'
]
done

(base) C:\Users--->
"""

@msarahan

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commented Jul 1, 2019

And my response from that mailing list post:

You have 2 things coming together to ruin your day. One is definitely the issue that I pointed you to. That is causing removal of the console_shortcut package, which takes away your start menu anaconda prompt shortcut. The next is this: #8835

The simplest way to recover is:

  • open a cmd shell
  • run call "path\to\anaconda\root\Scripts\activate" - this is what the "anaconda prompt" does
    conda install --only-deps anaconda=2019

This should restore everything, including your start menu shortcuts. Future updates will not mess up, because the explicit dependencies will be in the history now.

@msarahan

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commented Jul 1, 2019

We are working on fixing the Anaconda metapackage to account for this change in behavior. The change in behavior is expected and desired, but the side effect here with the anaconda metapackage in particular is not.

@ECon87

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commented Jul 3, 2019

I ran "conda install --only-deps anaconda" but the apps shortcuts are still not displayed on the navigator. I am using a MacOS 10.10.5.

Also, I can only create new environments in python2.7.

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commented Jul 3, 2019

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commented Jul 3, 2019

I also had the same problem: https://github.com/ContinuumIO/anaconda-issues/issues/11073#issuecomment-508009172

conda install --only-deps anaconda gave me an error when I reopened Spyder.

conda install --only-deps anaconda=2019 fixed it for me for now. This changes the version from Spyder 3.5.5 to Spyder 3.3.3.

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commented Jul 3, 2019

There are testing packages that will replace the existing anaconda "custom" metapackages up on the c3i_test2 channel:

conda install -c c3i_test2 anaconda

We are testing these ourselves, and will move them to defaults later today or tomorrow.

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commented Jul 4, 2019

I am kind of newbie still to this (ana)conda world, but... what if you do not have any longer the metapackage installed? I needed to remove it to update python because of ContinuumIO/anaconda-issues#10822 and if I try to update, the process says it will delete all those packages as well.

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commented Jul 5, 2019

The new metapackage is uploaded. Further updates might allow updates of more than you expect, but they should no longer go crazy removing things.

conda update anaconda

if you don't have it installed, you can just install it:

conda install anaconda

Sorry for our clumsiness on this one, and thank you for your patience. We'll be writing up a post-mortem next week. If you continue having issues, please post here.

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commented Jul 6, 2019

@msarahan i still have the same problems, any ideas ?
Collecting package metadata (current_repodata.json): done
Solving environment: done

Package Plan

environment location: /anaconda3

added / updated specs:
- anaconda

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
glob2-0.7                  |             py_0          14 KB
ipython-7.6.0              |   py37h39e3cac_0         1.1 MB
jupyter_core-4.5.0         |             py_0          48 KB
parso-0.5.0                |             py_0          67 KB
prometheus_client-0.7.1    |             py_0          42 KB
psutil-5.6.3               |   py37h1de35cc_0         333 KB
python-libarchive-c-2.8    |           py37_8          22 KB
pyyaml-5.1.1               |   py37h1de35cc_0         170 KB
qtpy-1.8.0                 |             py_0          38 KB
tornado-6.0.3              |   py37h1de35cc_0         644 KB
------------------------------------------------------------
                                       Total:         2.5 MB

The following packages will be REMOVED:

alabaster-0.7.12-py37_0
anaconda-project-0.8.3-py_0
appscript-1.1.0-py37h1de35cc_0
astroid-2.2.5-py37_0
astropy-3.2.1-py37h1de35cc_0
atomicwrites-1.3.0-py37_1
babel-2.7.0-py_0
backports.os-0.1.1-py37_0
backports.shutil_get_terminal_size-1.0.0-py37_2
bitarray-0.9.3-py37h1de35cc_0
bkcharts-0.2-py37_0
blas-1.0-mkl
blosc-1.16.3-hd9629dc_0
bokeh-1.2.0-py37_0
boto-2.49.0-py37_0
bottleneck-1.2.1-py37h1d22016_1
cloudpickle-1.1.1-py_0
colorama-0.4.1-py37_0
contextlib2-0.5.5-py37_0
cycler-0.10.0-py37_0
cython-0.29.10-py37h0a44026_0
cytoolz-0.9.0.1-py37h1de35cc_1
dask-2.0.0-py_0
dask-core-2.0.0-py_0
distributed-2.0.1-py_0
docutils-0.14-py37_0
et_xmlfile-1.0.1-py37_0
fastcache-1.1.0-py37h1de35cc_0
flask-1.0.3-py37_0
get_terminal_size-1.0.0-h7520d66_0
gevent-1.4.0-py37h1de35cc_0
gmp-6.1.2-hb37e062_1
gmpy2-2.0.8-py37h6ef4df4_2
greenlet-0.4.15-py37h1de35cc_0
h5py-2.9.0-py37h3134771_0
hdf5-1.10.4-hfa1e0ec_0
heapdict-1.0.0-py37_2
html5lib-1.0.1-py37_0
imageio-2.5.0-py37_0
imagesize-1.1.0-py37_0
importlib_metadata-0.17-py37_1
intel-openmp-2019.4-233
isort-4.3.20-py37_0
itsdangerous-1.1.0-py37_0
jbig-2.1-h4d881f8_0
jdcal-1.4.1-py_0
joblib-0.13.2-py37_0
jupyter-1.0.0-py37_7
jupyter_console-6.0.0-py37_0
keyring-18.0.0-py37_0
kiwisolver-1.1.0-py37h0a44026_0
lazy-object-proxy-1.4.1-py37h1de35cc_0
libxslt-1.1.33-h33a18ac_0
llvmlite-0.29.0-py37h98b8051_0
locket-0.2.0-py37_1
lxml-4.3.3-py37hef8c89e_0
matplotlib-3.1.0-py37h54f8f79_0
mccabe-0.6.1-py37_1
mkl-2019.4-233
mkl-service-2.0.2-py37h1de35cc_0
mkl_fft-1.0.12-py37h5e564d8_0
mkl_random-1.0.2-py37h27c97d8_0
mock-3.0.5-py37_0
more-itertools-7.0.0-py37_0
mpc-1.1.0-h6ef4df4_1
mpfr-4.0.1-h3018a27_3
mpmath-1.1.0-py37_0
msgpack-python-0.6.1-py37h04f5b5a_1
multipledispatch-0.6.0-py37_0
networkx-2.3-py_0
nltk-3.4.1-py37_0
nose-1.3.7-py37_2
numba-0.44.1-py37h6440ff4_0
numexpr-2.6.9-py37h7413580_0
numpy-1.16.4-py37hacdab7b_0
numpy-base-1.16.4-py37h6575580_0
numpydoc-0.9.1-py_0
openpyxl-2.6.2-py_0
packaging-19.0-py37_0
pandas-0.24.2-py37h0a44026_0
partd-0.3.10-py37_1
path.py-12.0.1-py_0
pathlib2-2.3.3-py37_0
patsy-0.5.1-py37_0
pep8-1.7.1-py37_0
pluggy-0.12.0-py_0
ply-3.11-py37_0
py-1.8.0-py37_0
pycodestyle-2.5.0-py37_0
pycrypto-2.6.1-py37h1de35cc_9
pycurl-7.43.0.2-py37ha12b0ac_0
pyflakes-2.1.1-py37_0
pylint-2.3.1-py37_0
pyodbc-4.0.26-py37h0a44026_0
pyparsing-2.4.0-py_0
pytables-3.5.2-py37h5bccee9_1
pytest-4.6.2-py37_0
pytest-arraydiff-0.3-py37h39e3cac_0
pytest-astropy-0.5.0-py37_0
pytest-doctestplus-0.3.0-py37_0
pytest-openfiles-0.3.2-py37_0
pytest-remotedata-0.3.1-py37_0
pywavelets-1.0.3-py37h1d22016_1
qtawesome-0.5.7-py37_1
qtconsole-4.5.1-py_0
rope-0.14.0-py_0
scikit-image-0.15.0-py37h0a44026_0
scikit-learn-0.21.2-py37h27c97d8_0
scipy-1.2.1-py37h1410ff5_0
seaborn-0.9.0-py37_0
simplegeneric-0.8.1-py37_2
singledispatch-3.4.0.3-py37_0
snappy-1.1.7-he62c110_3
snowballstemmer-1.2.1-py37_0
sortedcollections-1.1.2-py37_0
sortedcontainers-2.1.0-py37_0
sphinx-2.1.0-py_0
sphinxcontrib-1.0-py37_1
sphinxcontrib-applehelp-1.0.1-py_0
sphinxcontrib-devhelp-1.0.1-py_0
sphinxcontrib-htmlhelp-1.0.2-py_0
sphinxcontrib-jsmath-1.0.1-py_0
sphinxcontrib-qthelp-1.0.2-py_0
sphinxcontrib-serializinghtml-1.1.3-py_0
sphinxcontrib-websupport-1.1.2-py_0
spyder-3.3.4-py37_0
spyder-kernels-0.5.0-py37_0
sqlalchemy-1.3.4-py37h1de35cc_0
statsmodels-0.9.0-py37h1d22016_0
sympy-1.4-py37_0
tblib-1.4.0-py_0
toolz-0.9.0-py37_0
unicodecsv-0.14.1-py37_0
werkzeug-0.15.4-py_0
wrapt-1.11.1-py37h1de35cc_0
wurlitzer-1.0.2-py37_0
xlrd-1.2.0-py37_0
xlsxwriter-1.1.8-py_0
xlwings-0.15.8-py37_0
xlwt-1.3.0-py37_0
zict-0.1.4-py37_0
zipp-0.5.1-py_0

The following packages will be UPDATED:

glob2 pkgs/main/osx-64::glob2-0.6-py37_1 --> pkgs/main/noarch::glob2-0.7-py_0
ipython 7.5.0-py37h39e3cac_0 --> 7.6.0-py37h39e3cac_0
jupyter_core pkgs/main/osx-64::jupyter_core-4.4.0-~ --> pkgs/main/noarch::jupyter_core-4.5.0-py_0
parso 0.4.0-py_0 --> 0.5.0-py_0
prometheus_client pkgs/main/osx-64::prometheus_client-0~ --> pkgs/main/noarch::prometheus_client-0.7.1-py_0
psutil 5.6.2-py37h1de35cc_0 --> 5.6.3-py37h1de35cc_0
python-libarchive~ 2.8-py37_6 --> 2.8-py37_8
pyyaml 5.1-py37h1de35cc_0 --> 5.1.1-py37h1de35cc_0
qtpy 1.7.1-py_0 --> 1.8.0-py_0
tornado 6.0.2-py37h1de35cc_0 --> 6.0.3-py37h1de35cc_0

@aakhmetz

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commented Jul 6, 2019

I think I was able to resolve by first doing conda install -c c3i_test2 anaconda and then updating.
@eltabbal, have you tried that?

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commented Jul 6, 2019

@aakhmetz yeah that is working fine now, what is the c3i-test3 metapackage ?. thanks a lot anyhow

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commented Jul 6, 2019

@eltabbal it was a temporary solution proposed in the thread above

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commented Jul 6, 2019

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commented Jul 7, 2019

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commented Jul 7, 2019

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commented Jul 8, 2019

@msarahan I tried the conda update anaconda command, but I am getting some Assertion errors and then the update gets rolled back. Am I doing something wrong? I am running on Ubuntu 18.04 LTS. Is it okay to track this problem under this existing issue, or should this be a new issue?

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
ERROR conda.core.link:_execute(637): An error occurred while installing package 'None'.
AssertionError()
Attempting to roll back.

Rolling back transaction: done

AssertionError()
()
AssertionError()
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commented Jul 8, 2019

Hi. I'm looking for a fix that works for Miniconda also - I don't want to install the full Anaconda.

From a fresh install of Miniconda3 4.6.14 (Python 3.7.3 64-bit) on both Windows 10 and Window 7 machines, then running conda update conda gives the following:

The following NEW packages will be INSTALLED:

  bzip2              pkgs/main/win-64::bzip2-1.0.7-he774522_0
  conda-package-han~ pkgs/main/win-64::conda-package-handling-1.3.10-py37_0
  libarchive         pkgs/main/win-64::libarchive-3.3.3-h0643e63_5
  libiconv           pkgs/main/win-64::libiconv-1.15-h1df5818_7
  libxml2            pkgs/main/win-64::libxml2-2.9.9-h464c3ec_0
  lz4-c              pkgs/main/win-64::lz4-c-1.8.1.2-h2fa13f4_0
  lzo                pkgs/main/win-64::lzo-2.10-h6df0209_2
  python-libarchive~ pkgs/main/win-64::python-libarchive-c-2.8-py37_9
  tqdm               pkgs/main/noarch::tqdm-4.32.1-py_0
  xz                 pkgs/main/win-64::xz-5.2.4-h2fa13f4_4
  zlib               pkgs/main/win-64::zlib-1.2.11-h62dcd97_3
  zstd               pkgs/main/win-64::zstd-1.3.7-h508b16e_0

The following packages will be UPDATED:

  ca-certificates                               2019.1.23-0 --> 2019.5.15-0
  certifi                                   2019.3.9-py37_0 --> 2019.6.16-py37_0
  conda                                       4.6.14-py37_0 --> 4.7.5-py37_0
  openssl                                 1.1.1b-he774522_1 --> 1.1.1c-he774522_1


Proceed ([y]/n)? y

After proceeding, conda update --all gives:

The following packages will be REMOVED:

  console_shortcut-0.1.1-3
  powershell_shortcut-0.0.1-2

The following packages will be UPDATED:

  cffi                                1.12.2-py37h7a1dbc1_1 --> 1.12.3-py37h7a1dbc1_0
  cryptography                         2.6.1-py37h7a1dbc1_0 --> 2.7-py37h7a1dbc1_0
  pip                                         19.0.3-py37_0 --> 19.1.1-py37_0
  pysocks                                      1.6.8-py37_0 --> 1.7.0-py37_0
  python                                   3.7.3-h8c8aaf0_0 --> 3.7.3-h8c8aaf0_1
  requests                                    2.21.0-py37_0 --> 2.22.0-py37_0
  setuptools                                  41.0.0-py37_0 --> 41.0.1-py37_0
  sqlite                                  3.27.2-he774522_0 --> 3.28.0-he774522_0
  urllib3                                     1.24.1-py37_0 --> 1.24.2-py37_0
  vs2015_runtime                     14.15.26706-h3a45250_0 --> 14.15.26706-h3a45250_4
  wheel                                       0.33.1-py37_0 --> 0.33.4-py37_0


Proceed ([y]/n)? n

I don't think I want to remove the console and powershell shortcuts? Or should I not be updating all in Miniconda anyway?

Thanks!

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commented Jul 8, 2019

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commented Jul 8, 2019

Noarch means it can be used on any platform. It's fine.

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commented Jul 8, 2019

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commented Jul 8, 2019

When will it be safe to do a complete reinstall of Anaconda and then do "conda upgrade --all" as usual? In other words, when will the bugs be squashed definitively? Already? Next week? Never?

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commented Jul 10, 2019

The problems with the anaconda metapackage should be gone. The undesired removal of powershell_shortcut and console_shortcut will be fixed in the next conda release, 4.7.6. conda update --all should be fine for most people now. If you are someone who installs packages only to immediately remove them, so that you get that package's dependencies, then you need to adapt to using conda install --only-deps instead of the install-then-remove dance.

@msarahan msarahan referenced this issue Jul 11, 2019

Closed

Conda update --all #8904

0 of 135 tasks complete
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commented Jul 11, 2019

Sorry, msarahan, but this problem is not gone. I did a clean install of 2019.03, then did conda upgrade --all and then did conda upgrade --all again. The following is what happened. This is on an iMac running MacOS Mojave 10.14.5.

108-211-183-124:~ ojohns$ conda upgrade --all
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Collecting package metadata: done
Solving environment: done

Package Plan

environment location: /Users/ojohns/anaconda3
The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
_anaconda_depends-2019.03  |           py37_0           5 KB
anaconda-custom            |           py37_1           3 KB
anaconda-project-0.8.3     |             py_0         212 KB
astropy-3.2.1              |   py37h1de35cc_0         6.9 MB
babel-2.7.0                |             py_0         5.8 MB
backports-1.0              |             py_2         139 KB
backports.functools_lru_cache-1.5|             py_2           9 KB
backports.tempfile-1.0     |             py_1          12 KB
backports.weakref-1.0.post1|             py_1           7 KB
bitarray-0.9.3             |   py37h1de35cc_0          59 KB
blosc-1.16.3               |       hd9629dc_0          64 KB
bokeh-1.2.0                |           py37_0         3.9 MB
bzip2-1.0.7                |       h1de35cc_0         104 KB
ca-certificates-2019.5.15  |                0         133 KB
certifi-2019.6.16          |           py37_0         154 KB
cffi-1.12.3                |   py37hb5b8e2f_0         214 KB
cloudpickle-1.2.1          |             py_0          28 KB
conda-4.7.5                |           py37_0         3.0 MB
conda-build-3.18.7         |           py37_0         528 KB
conda-package-handling-1.3.11|           py37_0         260 KB
conda-verify-3.4.2         |             py_0          25 KB
cryptography-2.7           |   py37ha12b0ac_0         571 KB
curl-7.64.1                |       ha441bb4_0         131 KB
cython-0.29.11             |   py37h0a44026_0         2.0 MB
dask-2.1.0                 |             py_0          11 KB
dask-core-2.1.0            |             py_0         578 KB
defusedxml-0.6.0           |             py_0          23 KB
distributed-2.1.0          |             py_0         369 KB
fastcache-1.1.0            |   py37h1de35cc_0          29 KB
filelock-3.0.12            |             py_0          12 KB
flask-1.0.3                |           py37_0         123 KB
glob2-0.7                  |             py_0          14 KB
importlib_metadata-0.17    |           py37_1          39 KB
intel-openmp-2019.4        |              233         1.1 MB
ipykernel-5.1.1            |   py37h39e3cac_0         162 KB
ipython-7.6.1              |   py37h39e3cac_0         1.1 MB
isort-4.3.21               |           py37_0          68 KB
jdcal-1.4.1                |             py_0          11 KB
jinja2-2.10.1              |           py37_0         188 KB
joblib-0.13.2              |           py37_0         367 KB
jupyter_core-4.5.0         |             py_0          48 KB
jupyterlab-0.35.5          |   py37hf63ae98_0        10.6 MB
kiwisolver-1.1.0           |   py37h0a44026_0          60 KB
lazy-object-proxy-1.4.1    |   py37h1de35cc_0          28 KB
libcurl-7.64.1             |       h051b688_0         546 KB
libpng-1.6.37              |       ha441bb4_0         325 KB
libssh2-1.8.2              |       ha12b0ac_0         221 KB
libxml2-2.9.9              |       hf6e021a_1         1.9 MB
llvm-openmp-4.0.1          |       hcfea43d_1         454 KB
llvmlite-0.29.0            |   py37h98b8051_0        13.7 MB
lxml-4.3.4                 |   py37hef8c89e_0         1.3 MB
matplotlib-3.1.0           |   py37h54f8f79_0         6.6 MB
mkl-2019.4                 |              233       155.2 MB
mkl-service-2.0.2          |   py37h1de35cc_0          51 KB
mkl_fft-1.0.12             |   py37h5e564d8_0         155 KB
mock-3.0.5                 |           py37_0          47 KB
more-itertools-7.0.0       |           py37_0          93 KB
nbconvert-5.5.0            |             py_0         381 KB
networkx-2.3               |             py_0         1.1 MB
nltk-3.4.3                 |           py37_0         2.1 MB
numba-0.44.1               |   py37h6440ff4_0         2.8 MB
numpy-1.16.4               |   py37hacdab7b_0          49 KB
numpy-base-1.16.4          |   py37h6575580_0         4.2 MB
numpydoc-0.9.1             |             py_0          31 KB
openpyxl-2.6.2             |             py_0         157 KB
openssl-1.1.1c             |       h1de35cc_1         3.4 MB
parso-0.5.0                |             py_0          67 KB
partd-1.0.0                |             py_0          19 KB
path.py-12.0.1             |             py_0          23 KB
pathlib2-2.3.4             |           py37_0          36 KB
pexpect-4.7.0              |           py37_0          82 KB
pillow-6.0.0               |   py37hb68e598_0         579 KB
pip-19.1.1                 |           py37_0         1.8 MB
pluggy-0.12.0              |             py_0          20 KB
prometheus_client-0.7.1    |             py_0          42 KB
psutil-5.6.3               |   py37h1de35cc_0         333 KB
pycurl-7.43.0.3            |   py37ha12b0ac_0          71 KB
pygments-2.4.2             |             py_0         664 KB
pyparsing-2.4.0            |             py_0          58 KB
pysocks-1.7.0              |           py37_0          29 KB
pytables-3.5.2             |   py37h5bccee9_1         1.4 MB
pytest-5.0.0               |           py37_0         358 KB
python-libarchive-c-2.8    |          py37_10          22 KB
pytz-2019.1                |             py_0         236 KB
pywavelets-1.0.3           |   py37h1d22016_1         4.2 MB
pyyaml-5.1.1               |   py37h1de35cc_0         170 KB
qtconsole-4.5.1            |             py_0          92 KB
qtpy-1.8.0                 |             py_0          38 KB
requests-2.22.0            |           py37_0          89 KB
rope-0.14.0                |             py_0         113 KB
scikit-image-0.15.0        |   py37h0a44026_0        27.6 MB
scikit-learn-0.21.2        |   py37h27c97d8_0         5.9 MB
setuptools-41.0.1          |           py37_0         635 KB
snowballstemmer-1.9.0      |             py_0          53 KB
sphinx-2.1.2               |             py_0         1.4 MB
sphinxcontrib-applehelp-1.0.1|             py_0          29 KB
sphinxcontrib-devhelp-1.0.1|             py_0          23 KB
sphinxcontrib-htmlhelp-1.0.2|             py_0          28 KB
sphinxcontrib-jsmath-1.0.1 |             py_0           8 KB
sphinxcontrib-qthelp-1.0.2 |             py_0          26 KB
sphinxcontrib-serializinghtml-1.1.3|             py_0          24 KB
sphinxcontrib-websupport-1.1.2|             py_0          35 KB
spyder-3.3.5               |           py37_0         2.5 MB
spyder-kernels-0.5.0       |           py37_0          69 KB
sqlalchemy-1.3.5           |   py37h1de35cc_0         1.7 MB
sqlite-3.28.0              |       ha441bb4_0         2.3 MB
statsmodels-0.10.0         |   py37h1d22016_0         8.8 MB
sympy-1.4                  |           py37_0         9.7 MB
tblib-1.4.0                |             py_0          14 KB
terminado-0.8.2            |           py37_0          22 KB
tornado-6.0.3              |   py37h1de35cc_0         644 KB
tqdm-4.32.1                |             py_0          48 KB
urllib3-1.24.2             |           py37_0         152 KB
werkzeug-0.15.4            |             py_0         262 KB
wheel-0.33.4               |           py37_0          39 KB
wrapt-1.11.2               |   py37h1de35cc_0          44 KB
xlsxwriter-1.1.8           |             py_0         105 KB
xlwings-0.15.8             |           py37_0         464 KB
zict-1.0.0                 |             py_0          12 KB
zipp-0.5.1                 |             py_0           8 KB
------------------------------------------------------------
                                       Total:       307.1 MB

The following NEW packages will be INSTALLED:

_anaconda_depends pkgs/main/osx-64::_anaconda_depends-2019.03-py37_0
backports.functoo~ pkgs/main/noarch::backports.functools_lru_cache-1.5-py_2
backports.tempfile pkgs/main/noarch::backports.tempfile-1.0-py_1
backports.weakref pkgs/main/noarch::backports.weakref-1.0.post1-py_1
conda-package-han~ pkgs/main/osx-64::conda-package-handling-1.3.11-py37_0
joblib pkgs/main/osx-64::joblib-0.13.2-py37_0
llvm-openmp pkgs/main/osx-64::llvm-openmp-4.0.1-hcfea43d_1
mock pkgs/main/osx-64::mock-3.0.5-py37_0
sphinxcontrib-app~ pkgs/main/noarch::sphinxcontrib-applehelp-1.0.1-py_0
sphinxcontrib-dev~ pkgs/main/noarch::sphinxcontrib-devhelp-1.0.1-py_0
sphinxcontrib-htm~ pkgs/main/noarch::sphinxcontrib-htmlhelp-1.0.2-py_0
sphinxcontrib-jsm~ pkgs/main/noarch::sphinxcontrib-jsmath-1.0.1-py_0
sphinxcontrib-qth~ pkgs/main/noarch::sphinxcontrib-qthelp-1.0.2-py_0
sphinxcontrib-ser~ pkgs/main/noarch::sphinxcontrib-serializinghtml-1.1.3-py_0

The following packages will be UPDATED:

anaconda-project pkgs/main/osx-64::anaconda-project-0.~ --> pkgs/main/noarch::anaconda-project-0.8.3-py_0
astropy 3.1.2-py37h1de35cc_0 --> 3.2.1-py37h1de35cc_0
babel pkgs/main/osx-64::babel-2.6.0-py37_0 --> pkgs/main/noarch::babel-2.7.0-py_0
backports pkgs/main/osx-64::backports-1.0-py37_1 --> pkgs/main/noarch::backports-1.0-py_2
bitarray 0.8.3-py37h1de35cc_0 --> 0.9.3-py37h1de35cc_0
blosc 1.15.0-hd9629dc_0 --> 1.16.3-hd9629dc_0
bokeh 1.0.4-py37_0 --> 1.2.0-py37_0
bzip2 1.0.6-h1de35cc_5 --> 1.0.7-h1de35cc_0
ca-certificates 2019.1.23-0 --> 2019.5.15-0
certifi 2019.3.9-py37_0 --> 2019.6.16-py37_0
cffi 1.12.2-py37hb5b8e2f_1 --> 1.12.3-py37hb5b8e2f_0
cloudpickle pkgs/main/osx-64::cloudpickle-0.8.0-p~ --> pkgs/main/noarch::cloudpickle-1.2.1-py_0
conda 4.6.11-py37_0 --> 4.7.5-py37_0
conda-build 3.17.8-py37_0 --> 3.18.7-py37_0
conda-verify pkgs/main/osx-64::conda-verify-3.1.1-~ --> pkgs/main/noarch::conda-verify-3.4.2-py_0
cryptography 2.6.1-py37ha12b0ac_0 --> 2.7-py37ha12b0ac_0
curl 7.64.0-ha441bb4_2 --> 7.64.1-ha441bb4_0
cython 0.29.6-py37h0a44026_0 --> 0.29.11-py37h0a44026_0
dask pkgs/main/osx-64::dask-1.1.4-py37_1 --> pkgs/main/noarch::dask-2.1.0-py_0
dask-core pkgs/main/osx-64::dask-core-1.1.4-py3~ --> pkgs/main/noarch::dask-core-2.1.0-py_0
defusedxml pkgs/main/osx-64::defusedxml-0.5.0-py~ --> pkgs/main/noarch::defusedxml-0.6.0-py_0
distributed pkgs/main/osx-64::distributed-1.26.0-~ --> pkgs/main/noarch::distributed-2.1.0-py_0
fastcache 1.0.2-py37h1de35cc_2 --> 1.1.0-py37h1de35cc_0
filelock pkgs/main/osx-64::filelock-3.0.10-py3~ --> pkgs/main/noarch::filelock-3.0.12-py_0
flask 1.0.2-py37_1 --> 1.0.3-py37_0
glob2 pkgs/main/osx-64::glob2-0.6-py37_1 --> pkgs/main/noarch::glob2-0.7-py_0
importlib_metadata 0.8-py37_0 --> 0.17-py37_1
intel-openmp 2019.3-199 --> 2019.4-233
ipykernel 5.1.0-py37h39e3cac_0 --> 5.1.1-py37h39e3cac_0
ipython 7.4.0-py37h39e3cac_0 --> 7.6.1-py37h39e3cac_0
isort 4.3.16-py37_0 --> 4.3.21-py37_0
jdcal pkgs/main/osx-64::jdcal-1.4-py37_0 --> pkgs/main/noarch::jdcal-1.4.1-py_0
jinja2 2.10-py37_0 --> 2.10.1-py37_0
jupyter_core pkgs/main/osx-64::jupyter_core-4.4.0-~ --> pkgs/main/noarch::jupyter_core-4.5.0-py_0
jupyterlab 0.35.4-py37hf63ae98_0 --> 0.35.5-py37hf63ae98_0
kiwisolver 1.0.1-py37h0a44026_0 --> 1.1.0-py37h0a44026_0
lazy-object-proxy 1.3.1-py37h1de35cc_2 --> 1.4.1-py37h1de35cc_0
libcurl 7.64.0-h051b688_2 --> 7.64.1-h051b688_0
libpng 1.6.36-ha441bb4_0 --> 1.6.37-ha441bb4_0
libssh2 1.8.0-ha12b0ac_4 --> 1.8.2-ha12b0ac_0
libxml2 2.9.9-hab757c2_0 --> 2.9.9-hf6e021a_1
llvmlite 0.28.0-py37h8c7ce04_0 --> 0.29.0-py37h98b8051_0
lxml 4.3.2-py37hef8c89e_0 --> 4.3.4-py37hef8c89e_0
matplotlib 3.0.3-py37h54f8f79_0 --> 3.1.0-py37h54f8f79_0
mkl 2019.3-199 --> 2019.4-233
mkl-service 1.1.2-py37hfbe908c_5 --> 2.0.2-py37h1de35cc_0
mkl_fft 1.0.10-py37h5e564d8_0 --> 1.0.12-py37h5e564d8_0
more-itertools 6.0.0-py37_0 --> 7.0.0-py37_0
nbconvert pkgs/main/osx-64::nbconvert-5.4.1-py3~ --> pkgs/main/noarch::nbconvert-5.5.0-py_0
networkx pkgs/main/osx-64::networkx-2.2-py37_1 --> pkgs/main/noarch::networkx-2.3-py_0
nltk 3.4-py37_1 --> 3.4.3-py37_0
numba 0.43.1-py37h6440ff4_0 --> 0.44.1-py37h6440ff4_0
numpy 1.16.2-py37hacdab7b_0 --> 1.16.4-py37hacdab7b_0
numpy-base 1.16.2-py37h6575580_0 --> 1.16.4-py37h6575580_0
numpydoc pkgs/main/osx-64::numpydoc-0.8.0-py37~ --> pkgs/main/noarch::numpydoc-0.9.1-py_0
openpyxl pkgs/main/osx-64::openpyxl-2.6.1-py37~ --> pkgs/main/noarch::openpyxl-2.6.2-py_0
openssl 1.1.1b-h1de35cc_1 --> 1.1.1c-h1de35cc_1
parso pkgs/main/osx-64::parso-0.3.4-py37_0 --> pkgs/main/noarch::parso-0.5.0-py_0
partd pkgs/main/osx-64::partd-0.3.10-py37_1 --> pkgs/main/noarch::partd-1.0.0-py_0
path.py pkgs/main/osx-64::path.py-11.5.0-py37~ --> pkgs/main/noarch::path.py-12.0.1-py_0
pathlib2 2.3.3-py37_0 --> 2.3.4-py37_0
pexpect 4.6.0-py37_0 --> 4.7.0-py37_0
pillow 5.4.1-py37hb68e598_0 --> 6.0.0-py37hb68e598_0
pip 19.0.3-py37_0 --> 19.1.1-py37_0
pluggy pkgs/main/osx-64::pluggy-0.9.0-py37_0 --> pkgs/main/noarch::pluggy-0.12.0-py_0
prometheus_client pkgs/main/osx-64::prometheus_client-0~ --> pkgs/main/noarch::prometheus_client-0.7.1-py_0
psutil 5.6.1-py37h1de35cc_0 --> 5.6.3-py37h1de35cc_0
pycurl 7.43.0.2-py37ha12b0ac_0 --> 7.43.0.3-py37ha12b0ac_0
pygments pkgs/main/osx-64::pygments-2.3.1-py37~ --> pkgs/main/noarch::pygments-2.4.2-py_0
pyparsing pkgs/main/osx-64::pyparsing-2.3.1-py3~ --> pkgs/main/noarch::pyparsing-2.4.0-py_0
pysocks 1.6.8-py37_0 --> 1.7.0-py37_0
pytables 3.5.1-py37h5bccee9_0 --> 3.5.2-py37h5bccee9_1
pytest 4.3.1-py37_0 --> 5.0.0-py37_0
python-libarchive~ 2.8-py37_6 --> 2.8-py37_10
pytz pkgs/main/osx-64::pytz-2018.9-py37_0 --> pkgs/main/noarch::pytz-2019.1-py_0
pywavelets 1.0.2-py37h1d22016_0 --> 1.0.3-py37h1d22016_1
pyyaml 5.1-py37h1de35cc_0 --> 5.1.1-py37h1de35cc_0
qtconsole pkgs/main/osx-64::qtconsole-4.4.3-py3~ --> pkgs/main/noarch::qtconsole-4.5.1-py_0
qtpy pkgs/main/osx-64::qtpy-1.7.0-py37_1 --> pkgs/main/noarch::qtpy-1.8.0-py_0
requests 2.21.0-py37_0 --> 2.22.0-py37_0
rope pkgs/main/osx-64::rope-0.12.0-py37_0 --> pkgs/main/noarch::rope-0.14.0-py_0
scikit-image 0.14.2-py37h0a44026_0 --> 0.15.0-py37h0a44026_0
scikit-learn 0.20.3-py37h27c97d8_0 --> 0.21.2-py37h27c97d8_0
setuptools 40.8.0-py37_0 --> 41.0.1-py37_0
snowballstemmer pkgs/main/osx-64::snowballstemmer-1.2~ --> pkgs/main/noarch::snowballstemmer-1.9.0-py_0
sphinx pkgs/main/osx-64::sphinx-1.8.5-py37_0 --> pkgs/main/noarch::sphinx-2.1.2-py_0
sphinxcontrib-web~ pkgs/main/osx-64::sphinxcontrib-websu~ --> pkgs/main/noarch::sphinxcontrib-websupport-1.1.2-py_0
spyder 3.3.3-py37_0 --> 3.3.5-py37_0
spyder-kernels 0.4.2-py37_0 --> 0.5.0-py37_0
sqlalchemy 1.3.1-py37h1de35cc_0 --> 1.3.5-py37h1de35cc_0
sqlite 3.27.2-ha441bb4_0 --> 3.28.0-ha441bb4_0
statsmodels 0.9.0-py37h1d22016_0 --> 0.10.0-py37h1d22016_0
sympy 1.3-py37_0 --> 1.4-py37_0
tblib pkgs/main/osx-64::tblib-1.3.2-py37_0 --> pkgs/main/noarch::tblib-1.4.0-py_0
terminado 0.8.1-py37_1 --> 0.8.2-py37_0
tornado 6.0.2-py37h1de35cc_0 --> 6.0.3-py37h1de35cc_0
tqdm pkgs/main/osx-64::tqdm-4.31.1-py37_1 --> pkgs/main/noarch::tqdm-4.32.1-py_0
urllib3 1.24.1-py37_0 --> 1.24.2-py37_0
werkzeug pkgs/main/osx-64::werkzeug-0.14.1-py3~ --> pkgs/main/noarch::werkzeug-0.15.4-py_0
wheel 0.33.1-py37_0 --> 0.33.4-py37_0
wrapt 1.11.1-py37h1de35cc_0 --> 1.11.2-py37h1de35cc_0
xlsxwriter pkgs/main/osx-64::xlsxwriter-1.1.5-py~ --> pkgs/main/noarch::xlsxwriter-1.1.8-py_0
xlwings 0.15.4-py37_0 --> 0.15.8-py37_0
zict pkgs/main/osx-64::zict-0.1.4-py37_0 --> pkgs/main/noarch::zict-1.0.0-py_0
zipp pkgs/main/osx-64::zipp-0.3.3-py37_1 --> pkgs/main/noarch::zipp-0.5.1-py_0

The following packages will be DOWNGRADED:

anaconda 2019.03-py37_0 --> custom-py37_1

Proceed ([y]/n)? y

Downloading and Extracting Packages
conda-verify-3.4.2 | 25 KB | ######################################################################################################################################### | 100%
kiwisolver-1.1.0 | 60 KB | ######################################################################################################################################### | 100%
sphinxcontrib-appleh | 29 KB | ######################################################################################################################################### | 100%
openpyxl-2.6.2 | 157 KB | ######################################################################################################################################### | 100%
libxml2-2.9.9 | 1.9 MB | ######################################################################################################################################### | 100%
flask-1.0.3 | 123 KB | ######################################################################################################################################### | 100%
cython-0.29.11 | 2.0 MB | ######################################################################################################################################### | 100%
libssh2-1.8.2 | 221 KB | ######################################################################################################################################### | 100%
tblib-1.4.0 | 14 KB | ######################################################################################################################################### | 100%
statsmodels-0.10.0 | 8.8 MB | ######################################################################################################################################### | 100%
tornado-6.0.3 | 644 KB | ######################################################################################################################################### | 100%
bitarray-0.9.3 | 59 KB | ######################################################################################################################################### | 100%
sphinxcontrib-htmlhe | 28 KB | ######################################################################################################################################### | 100%
sphinxcontrib-jsmath | 8 KB | ######################################################################################################################################### | 100%
sphinxcontrib-qthelp | 26 KB | ######################################################################################################################################### | 100%
libcurl-7.64.1 | 546 KB | ######################################################################################################################################### | 100%
bzip2-1.0.7 | 104 KB | ######################################################################################################################################### | 100%
pysocks-1.7.0 | 29 KB | ######################################################################################################################################### | 100%
conda-4.7.5 | 3.0 MB | ######################################################################################################################################### | 100%
qtpy-1.8.0 | 38 KB | ######################################################################################################################################### | 100%
isort-4.3.21 | 68 KB | ######################################################################################################################################### | 100%
lazy-object-proxy-1. | 28 KB | ######################################################################################################################################### | 100%
path.py-12.0.1 | 23 KB | ######################################################################################################################################### | 100%
partd-1.0.0 | 19 KB | ######################################################################################################################################### | 100%
pip-19.1.1 | 1.8 MB | ######################################################################################################################################### | 100%
scikit-image-0.15.0 | 27.6 MB | ######################################################################################################################################### | 100%
psutil-5.6.3 | 333 KB | ######################################################################################################################################### | 100%
pathlib2-2.3.4 | 36 KB | ######################################################################################################################################### | 100%
ca-certificates-2019 | 133 KB | ######################################################################################################################################### | 100%
pyparsing-2.4.0 | 58 KB | ######################################################################################################################################### | 100%
pluggy-0.12.0 | 20 KB | ######################################################################################################################################### | 100%
setuptools-41.0.1 | 635 KB | ######################################################################################################################################### | 100%
jinja2-2.10.1 | 188 KB | ######################################################################################################################################### | 100%
babel-2.7.0 | 5.8 MB | ######################################################################################################################################### | 100%
conda-package-handli | 260 KB | ######################################################################################################################################### | 100%
sympy-1.4 | 9.7 MB | ######################################################################################################################################### | 100%
bokeh-1.2.0 | 3.9 MB | ######################################################################################################################################### | 100%
mkl-2019.4 | 155.2 MB | ######################################################################################################################################### | 100%
numpy-1.16.4 | 49 KB | ######################################################################################################################################### | 100%
anaconda-custom | 3 KB | ######################################################################################################################################### | 100%
jdcal-1.4.1 | 11 KB | ######################################################################################################################################### | 100%
distributed-2.1.0 | 369 KB | ######################################################################################################################################### | 100%
xlsxwriter-1.1.8 | 105 KB | ######################################################################################################################################### | 100%
urllib3-1.24.2 | 152 KB | ######################################################################################################################################### | 100%
terminado-0.8.2 | 22 KB | ######################################################################################################################################### | 100%
cloudpickle-1.2.1 | 28 KB | ######################################################################################################################################### | 100%
nltk-3.4.3 | 2.1 MB | ######################################################################################################################################### | 100%
jupyterlab-0.35.5 | 10.6 MB | ######################################################################################################################################### | 100%
openssl-1.1.1c | 3.4 MB | ######################################################################################################################################### | 100%
pexpect-4.7.0 | 82 KB | ######################################################################################################################################### | 100%
matplotlib-3.1.0 | 6.6 MB | ######################################################################################################################################### | 100%
wrapt-1.11.2 | 44 KB | ######################################################################################################################################### | 100%
numpy-base-1.16.4 | 4.2 MB | ######################################################################################################################################### | 100%
parso-0.5.0 | 67 KB | ######################################################################################################################################### | 100%
backports.tempfile-1 | 12 KB | ######################################################################################################################################### | 100%
pillow-6.0.0 | 579 KB | ######################################################################################################################################### | 100%
backports-1.0 | 139 KB | ######################################################################################################################################### | 100%
spyder-kernels-0.5.0 | 69 KB | ######################################################################################################################################### | 100%
numpydoc-0.9.1 | 31 KB | ######################################################################################################################################### | 100%
blosc-1.16.3 | 64 KB | ######################################################################################################################################### | 100%
pyyaml-5.1.1 | 170 KB | ######################################################################################################################################### | 100%
llvm-openmp-4.0.1 | 454 KB | ######################################################################################################################################### | 100%
pytest-5.0.0 | 358 KB | ######################################################################################################################################### | 100%
glob2-0.7 | 14 KB | ######################################################################################################################################### | 100%
joblib-0.13.2 | 367 KB | ######################################################################################################################################### | 100%
sqlalchemy-1.3.5 | 1.7 MB | ######################################################################################################################################### | 100%
wheel-0.33.4 | 39 KB | ######################################################################################################################################### | 100%
cryptography-2.7 | 571 KB | ######################################################################################################################################### | 100%
sphinxcontrib-websup | 35 KB | ######################################################################################################################################### | 100%
ipykernel-5.1.1 | 162 KB | ######################################################################################################################################### | 100%
pycurl-7.43.0.3 | 71 KB | ######################################################################################################################################### | 100%
mkl-service-2.0.2 | 51 KB | ######################################################################################################################################### | 100%
zict-1.0.0 | 12 KB | ######################################################################################################################################### | 100%
backports.weakref-1. | 7 KB | ######################################################################################################################################### | 100%
spyder-3.3.5 | 2.5 MB | ######################################################################################################################################### | 100%
numba-0.44.1 | 2.8 MB | ######################################################################################################################################### | 100%
astropy-3.2.1 | 6.9 MB | ######################################################################################################################################### | 100%
qtconsole-4.5.1 | 92 KB | ######################################################################################################################################### | 100%
anaconda-project-0.8 | 212 KB | ######################################################################################################################################### | 100%
prometheus_client-0. | 42 KB | ######################################################################################################################################### | 100%
mock-3.0.5 | 47 KB | ######################################################################################################################################### | 100%
werkzeug-0.15.4 | 262 KB | ######################################################################################################################################### | 100%
conda-build-3.18.7 | 528 KB | ######################################################################################################################################### | 100%
nbconvert-5.5.0 | 381 KB | ######################################################################################################################################### | 100%
ipython-7.6.1 | 1.1 MB | ######################################################################################################################################### | 100%
sqlite-3.28.0 | 2.3 MB | ######################################################################################################################################### | 100%
dask-core-2.1.0 | 578 KB | ######################################################################################################################################### | 100%
llvmlite-0.29.0 | 13.7 MB | ######################################################################################################################################### | 100%
libpng-1.6.37 | 325 KB | ######################################################################################################################################### | 100%
python-libarchive-c- | 22 KB | ######################################################################################################################################### | 100%
dask-2.1.0 | 11 KB | ######################################################################################################################################### | 100%
xlwings-0.15.8 | 464 KB | ######################################################################################################################################### | 100%
backports.functools_ | 9 KB | ######################################################################################################################################### | 100%
fastcache-1.1.0 | 29 KB | ######################################################################################################################################### | 100%
cffi-1.12.3 | 214 KB | ######################################################################################################################################### | 100%
zipp-0.5.1 | 8 KB | ######################################################################################################################################### | 100%
pytables-3.5.2 | 1.4 MB | ######################################################################################################################################### | 100%
pygments-2.4.2 | 664 KB | ######################################################################################################################################### | 100%
pywavelets-1.0.3 | 4.2 MB | ######################################################################################################################################### | 100%
certifi-2019.6.16 | 154 KB | ######################################################################################################################################### | 100%
networkx-2.3 | 1.1 MB | ######################################################################################################################################### | 100%
defusedxml-0.6.0 | 23 KB | ######################################################################################################################################### | 100%
pytz-2019.1 | 236 KB | ######################################################################################################################################### | 100%
scikit-learn-0.21.2 | 5.9 MB | ######################################################################################################################################### | 100%
rope-0.14.0 | 113 KB | ######################################################################################################################################### | 100%
_anaconda_depends-20 | 5 KB | ######################################################################################################################################### | 100%
requests-2.22.0 | 89 KB | ######################################################################################################################################### | 100%
filelock-3.0.12 | 12 KB | ######################################################################################################################################### | 100%
intel-openmp-2019.4 | 1.1 MB | ######################################################################################################################################### | 100%
tqdm-4.32.1 | 48 KB | ######################################################################################################################################### | 100%
snowballstemmer-1.9. | 53 KB | ######################################################################################################################################### | 100%
importlib_metadata-0 | 39 KB | ######################################################################################################################################### | 100%
jupyter_core-4.5.0 | 48 KB | ######################################################################################################################################### | 100%
sphinxcontrib-devhel | 23 KB | ######################################################################################################################################### | 100%
mkl_fft-1.0.12 | 155 KB | ######################################################################################################################################### | 100%
curl-7.64.1 | 131 KB | ######################################################################################################################################### | 100%
lxml-4.3.4 | 1.3 MB | ######################################################################################################################################### | 100%
more-itertools-7.0.0 | 93 KB | ######################################################################################################################################### | 100%
sphinxcontrib-serial | 24 KB | ######################################################################################################################################### | 100%
sphinx-2.1.2 | 1.4 MB | ######################################################################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

108-211-183-124:~ ojohns$ conda upgrade --all
Collecting package metadata (current_repodata.json): done
Solving environment: done

Package Plan

environment location: /Users/ojohns/anaconda3
The following packages will be REMOVED:
_anaconda_depends-2019.03-py37_0
alabaster-0.7.12-py37_0
anaconda-custom-py37_1
anaconda-project-0.8.3-py_0
appscript-1.1.0-py37h1de35cc_0
astroid-2.2.5-py37_0
astropy-3.2.1-py37h1de35cc_0
atomicwrites-1.3.0-py37_1
babel-2.7.0-py_0
backports.os-0.1.1-py37_0
backports.shutil_get_terminal_size-1.0.0-py37_2
bitarray-0.9.3-py37h1de35cc_0
bkcharts-0.2-py37_0
blas-1.0-mkl
blosc-1.16.3-hd9629dc_0
bokeh-1.2.0-py37_0
boto-2.49.0-py37_0
bottleneck-1.2.1-py37h1d22016_1
cloudpickle-1.2.1-py_0
colorama-0.4.1-py37_0
contextlib2-0.5.5-py37_0
curl-7.64.1-ha441bb4_0
cycler-0.10.0-py37_0
cython-0.29.11-py37h0a44026_0
cytoolz-0.9.0.1-py37h1de35cc_1
dask-2.1.0-py_0
dask-core-2.1.0-py_0
distributed-2.1.0-py_0
docutils-0.14-py37_0
et_xmlfile-1.0.1-py37_0
fastcache-1.1.0-py37h1de35cc_0
flask-1.0.3-py37_0
get_terminal_size-1.0.0-h7520d66_0
gevent-1.4.0-py37h1de35cc_0
gmp-6.1.2-hb37e062_1
gmpy2-2.0.8-py37h6ef4df4_2
greenlet-0.4.15-py37h1de35cc_0
h5py-2.9.0-py37h3134771_0
hdf5-1.10.4-hfa1e0ec_0
heapdict-1.0.0-py37_2
html5lib-1.0.1-py37_0
imageio-2.5.0-py37_0
imagesize-1.1.0-py37_0
importlib_metadata-0.17-py37_1
intel-openmp-2019.4-233
isort-4.3.21-py37_0
itsdangerous-1.1.0-py37_0
jbig-2.1-h4d881f8_0
jdcal-1.4.1-py_0
joblib-0.13.2-py37_0
jupyter-1.0.0-py37_7
jupyter_console-6.0.0-py37_0
keyring-18.0.0-py37_0
kiwisolver-1.1.0-py37h0a44026_0
krb5-1.16.1-hddcf347_7
lazy-object-proxy-1.4.1-py37h1de35cc_0
libcurl-7.64.1-h051b688_0
libgfortran-3.0.1-h93005f0_2
libssh2-1.8.2-ha12b0ac_0
libxslt-1.1.33-h33a18ac_0
llvm-openmp-4.0.1-hcfea43d_1
llvmlite-0.29.0-py37h98b8051_0
locket-0.2.0-py37_1
lxml-4.3.4-py37hef8c89e_0
matplotlib-3.1.0-py37h54f8f79_0
mccabe-0.6.1-py37_1
mkl-2019.4-233
mkl-service-2.0.2-py37h1de35cc_0
mkl_fft-1.0.12-py37h5e564d8_0
mkl_random-1.0.2-py37h27c97d8_0
mock-3.0.5-py37_0
more-itertools-7.0.0-py37_0
mpc-1.1.0-h6ef4df4_1
mpfr-4.0.1-h3018a27_3
mpmath-1.1.0-py37_0
msgpack-python-0.6.1-py37h04f5b5a_1
multipledispatch-0.6.0-py37_0
networkx-2.3-py_0
nltk-3.4.3-py37_0
nose-1.3.7-py37_2
numba-0.44.1-py37h6440ff4_0
numexpr-2.6.9-py37h7413580_0
numpy-1.16.4-py37hacdab7b_0
numpy-base-1.16.4-py37h6575580_0
numpydoc-0.9.1-py_0
openpyxl-2.6.2-py_0
packaging-19.0-py37_0
pandas-0.24.2-py37h0a44026_0
partd-1.0.0-py_0
path.py-12.0.1-py_0
pathlib2-2.3.4-py37_0
patsy-0.5.1-py37_0
pep8-1.7.1-py37_0
pluggy-0.12.0-py_0
ply-3.11-py37_0
py-1.8.0-py37_0
pycodestyle-2.5.0-py37_0
pycrypto-2.6.1-py37h1de35cc_9
pycurl-7.43.0.3-py37ha12b0ac_0
pyflakes-2.1.1-py37_0
pylint-2.3.1-py37_0
pyodbc-4.0.26-py37h0a44026_0
pyparsing-2.4.0-py_0
pytables-3.5.2-py37h5bccee9_1
pytest-5.0.0-py37_0
pytest-arraydiff-0.3-py37h39e3cac_0
pytest-astropy-0.5.0-py37_0
pytest-doctestplus-0.3.0-py37_0
pytest-openfiles-0.3.2-py37_0
pytest-remotedata-0.3.1-py37_0
pywavelets-1.0.3-py37h1d22016_1
qtawesome-0.5.7-py37_1
qtconsole-4.5.1-py_0
rope-0.14.0-py_0
scikit-image-0.15.0-py37h0a44026_0
scikit-learn-0.21.2-py37h27c97d8_0
scipy-1.2.1-py37h1410ff5_0
seaborn-0.9.0-py37_0
simplegeneric-0.8.1-py37_2
singledispatch-3.4.0.3-py37_0
snappy-1.1.7-he62c110_3
snowballstemmer-1.9.0-py_0
sortedcollections-1.1.2-py37_0
sortedcontainers-2.1.0-py37_0
sphinx-2.1.2-py_0
sphinxcontrib-1.0-py37_1
sphinxcontrib-applehelp-1.0.1-py_0
sphinxcontrib-devhelp-1.0.1-py_0
sphinxcontrib-htmlhelp-1.0.2-py_0
sphinxcontrib-jsmath-1.0.1-py_0
sphinxcontrib-qthelp-1.0.2-py_0
sphinxcontrib-serializinghtml-1.1.3-py_0
sphinxcontrib-websupport-1.1.2-py_0
spyder-3.3.5-py37_0
spyder-kernels-0.5.0-py37_0
sqlalchemy-1.3.5-py37h1de35cc_0
statsmodels-0.10.0-py37h1d22016_0
sympy-1.4-py37_0
tblib-1.4.0-py_0
toolz-0.9.0-py37_0
unicodecsv-0.14.1-py37_0
unixodbc-2.3.7-h1de35cc_0
werkzeug-0.15.4-py_0
wrapt-1.11.2-py37h1de35cc_0
wurlitzer-1.0.2-py37_0
xlrd-1.2.0-py37_0
xlsxwriter-1.1.8-py_0
xlwings-0.15.8-py37_0
xlwt-1.3.0-py37_0
zict-1.0.0-py_0
zipp-0.5.1-py_0

Proceed ([y]/n)? n
CondaSystemExit: Exiting.

@msarahan

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commented Jul 11, 2019

@SomeUserName1

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commented Jul 13, 2019

After doing a conda update conda I'm getting the warning as above and am now stuck with a broken installation. nothing installs or removes anymore.
Neither conda update conda-build nor conda update anaconda fixed this.

WARNING conda.base.context:use_only_tar_bz2(632): Conda is constrained to only using the old .tar.bz2 file format because you have conda-build installed, and it is <3.18.3.  Update or remove conda-build to get smaller downloads and faster extractions.
Collecting package metadata (repodata.json): done
Solving environment: | 
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:

  - defaults/linux-64::anaconda==2018.12=py37_0
done

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

    Traceback (most recent call last):
      File "/usr/local/anaconda3/lib/python3.7/site-packages/conda/models/prefix_graph.py", line 252, in _topo_sort_handle_cycles
        value = next(t)
      File "/usr/local/anaconda3/lib/python3.7/site-packages/conda/models/prefix_graph.py", line 230, in _toposort_raise_on_cycles
        raise CyclicalDependencyError(tuple(graph))
    conda.exceptions.CyclicalDependencyError: Cyclic dependencies exist among these items: 
      - defaults::_anaconda_depends-2019.03-py37_0
      - defaults::anaconda-custom-py37_1
      - defaults::astropy-3.2.1-py37h7b6447c_0
      - defaults::bkcharts-0.2-py37_0
      - defaults::bokeh-1.2.0-py37_0
      - defaults::bottleneck-1.2.1-py37h035aef0_1
      - defaults::dask-2.1.0-py_0
      - defaults::h5py-2.9.0-py37h7918eee_0
      - defaults::imageio-2.5.0-py37_0
      - defaults::matplotlib-3.0.2-py37h5429711_0
      - defaults::mkl-service-2.0.2-py37h7b6447c_0
      - defaults::mkl_fft-1.0.12-py37ha843d7b_0
      - defaults::numba-0.44.1-py37h962f231_0
      - defaults::numexpr-2.6.9-py37h9e4a6bb_0
      - defaults::numpy-1.16.4-py37h7e9f1db_0
      - defaults::pandas-0.24.2-py37he6710b0_0
      - defaults::patsy-0.5.1-py37_0
      - defaults::pytables-3.5.2-py37h71ec239_1
      - defaults::pytest-arraydiff-0.3-py37h39e3cac_0
      - defaults::pytest-astropy-0.5.0-py37_0
      - defaults::pytest-doctestplus-0.3.0-py37_0
      - defaults::pywavelets-1.0.3-py37hdd07704_1
      - defaults::scikit-image-0.15.0-py37he6710b0_0
      - defaults::scikit-learn-0.21.2-py37hd81dba3_0
      - defaults::scipy-1.2.1-py37h7c811a0_0
      - defaults::seaborn-0.9.0-py37_0
      - defaults::statsmodels-0.10.0-py37hdd07704_0
      - conda-forge::umap-learn-0.3.8-py37_0
      - defaults::datashape-0.5.4-py37_1
      - defaults::statsmodels-0.9.0-py37h035aef0_0
      - defaults::scipy-1.1.0-py37h7c811a0_2
      - defaults::numexpr-2.6.8-py37h9e4a6bb_0
      - defaults::pywavelets-1.0.1-py37hdd07704_0
      - defaults::blaze-0.11.3-py37_0
      - defaults::scikit-image-0.14.1-py37he6710b0_0
      - defaults::astropy-3.1-py37h7b6447c_0
      - defaults::bokeh-1.0.2-py37_0
      - defaults::odo-0.5.1-py37_0
      - defaults::pytest-doctestplus-0.2.0-py37_0
      - defaults::dask-1.0.0-py37_0
      - defaults::numpy-1.15.4-py37h7e9f1db_0
      - defaults::pytables-3.4.4-py37ha205bf6_0
      - defaults::h5py-2.8.0-py37h989c5e5_3
      - defaults::numba-0.41.0-py37h962f231_0
      - defaults::imageio-2.4.1-py37_0
      - defaults::scikit-learn-0.20.1-py37hd81dba3_0
      - defaults::pandas-0.23.4-py37h04863e7_0
    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "/usr/local/anaconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1043, in __call__
        return func(*args, **kwargs)
      File "/usr/local/anaconda3/lib/python3.7/site-packages/conda/cli/main.py", line 84, in _main
        exit_code = do_call(args, p)
      File "/usr/local/anaconda3/lib/python3.7/site-packages/conda/cli/conda_argparse.py", line 82, in do_call
        exit_code = getattr(module, func_name)(args, parser)
      File "/usr/local/anaconda3/lib/python3.7/site-packages/conda/cli/main_update.py", line 20, in execute
        install(args, parser, 'update')
      File "/usr/local/anaconda3/lib/python3.7/site-packages/conda/cli/install.py", line 280, in install
        force_reinstall=context.force_reinstall or context.force,
      File "/usr/local/anaconda3/lib/python3.7/site-packages/conda/core/solve.py", line 112, in solve_for_transaction
        force_remove, force_reinstall)
      File "/usr/local/anaconda3/lib/python3.7/site-packages/conda/core/solve.py", line 150, in solve_for_diff
        force_remove)
      File "/usr/local/anaconda3/lib/python3.7/site-packages/conda/core/solve.py", line 261, in solve_final_state
        ssc.solution_precs = IndexedSet(PrefixGraph(ssc.solution_precs).graph)
      File "/usr/local/anaconda3/lib/python3.7/site-packages/conda/models/prefix_graph.py", line 47, in __init__
        self._toposort()
      File "/usr/local/anaconda3/lib/python3.7/site-packages/conda/models/prefix_graph.py", line 202, in _toposort
        sorted_nodes = tuple(self._topo_sort_handle_cycles(graph_copy))
      File "/usr/local/anaconda3/lib/python3.7/site-packages/conda/models/prefix_graph.py", line 259, in _topo_sort_handle_cycles
        yield cls._toposort_pop_key(graph)
      File "/usr/local/anaconda3/lib/python3.7/site-packages/conda/models/prefix_graph.py", line 274, in _toposort_pop_key
        (len(parents), node.name, node) for node, parents in iteritems(graph)
    TypeError: '<' not supported between instances of 'PrefixRecord' and 'PackageRecord'

`$ /usr/local/anaconda3/bin/conda update anaconda`

  environment variables:
                 CIO_TEST=<not set>
                CONDA_EXE=/usr/local/anaconda3/bin/conda
         CONDA_PYTHON_EXE=/usr/local/anaconda3/bin/python
               CONDA_ROOT=/usr/local/anaconda3
              CONDA_SHLVL=0
            DEFAULTS_PATH=/usr/share/gconf/plasma.default.path
           MANDATORY_PATH=/usr/share/gconf/plasma.mandatory.path
                     PATH=/usr/local/anaconda3/bin:/usr/local/anaconda3/condabin:/home/fabian/.c
                          argo/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:
                          /usr/games:/usr/local/games:/home/fabian/.fzf/bin:/home/fabian/.cargo/
                          bin:/home/fabian/bin:/usr/local/anaconda3/bin:/usr/local/anaconda3/con
                          dabin:/home/fabian/.cargo/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin
                          :/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/fabian/.fzf/bin
       REQUESTS_CA_BUNDLE=<not set>
             SSH_KEY_PATH=~/.ssh/rsa_id
            SSL_CERT_FILE=<not set>
            XDG_SEAT_PATH=/org/freedesktop/DisplayManager/Seat0
         XDG_SESSION_PATH=/org/freedesktop/DisplayManager/Session1

     active environment : None
            shell level : 0
       user config file : /home/fabian/.condarc
 populated config files : 
          conda version : 4.7.5
    conda-build version : 3.17.6
         python version : 3.7.3.final.0
       virtual packages : 
       base environment : /usr/local/anaconda3  (writable)
           channel URLs : 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 : /usr/local/anaconda3/pkgs
                          /home/fabian/.conda/pkgs
       envs directories : /usr/local/anaconda3/envs
                          /home/fabian/.conda/envs
               platform : linux-64
             user-agent : conda/4.7.5 requests/2.22.0 CPython/3.7.3 Linux/5.0.0-20-generic ubuntu/19.04 glibc/2.29
                UID:GID : 1000:1000
             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.
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by running

    $ conda config --set report_errors true```
@aakhmetz

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commented Jul 14, 2019

@SomeUserName1 I had also a similar error, and the command conda install anaconda helped me to resolve it. Could you try to do it also?

@MHouse

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commented Jul 15, 2019

I could be off-base here, but running a conda update anaconda helped me get back on track.

The other thing that I noticed is that there seem to be dependency solving issues due to the new jupyterlab_server package. It's now up to version 1.0.0, but the build was coded out as py_0. This seems to have caused quite a few problems for whatever reason. I downgraded to the prior version to help with dependency resolution: conda install jupyterlab_server=0.3.4=py36_0

The problem after that is with version priority vs. channel priority, since jupyterlab_server went from the win-64 channel to the noarch channel.

@msarahan

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commented Jul 15, 2019

Anything that works for you is a good thing. @SomeUserName1 other users have had success deleting files in their package cache. conda clean -ay might help, but if it doesn't work, you should try to remove the .tar.bz2 and .conda files in your <anaconda install dir>/pkgs folder.

@MHouse

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commented Jul 16, 2019

Updated version of jupyterlab released today has some updated package dependencies. I was just able to do a full conda update --all and am all good now.

@SomeUserName1

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commented Jul 20, 2019

funnily conda install anaconda-clean got it working again

@mthomp89

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commented Jul 21, 2019

@msarahan I am a very new to anaconda and just now seeing the statement referred to earlier: WARNING conda.base.context:use_only_tar_bz2(632): Conda is constrained to only using the old .tar.bz2 file format because you have conda-build installed, and it is <3.18.3. Update or remove conda-build to get smaller downloads and faster extractions. What is the correct fix? Running Mac OS 10.14.5

@o12johns

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commented Jul 22, 2019

This comment is for new users trying to install and upgrade the anaconda distro. This works currently (2019.07.22) on an iMac running MacOS 10.14.5

The new version of conda does not play well with the meta-package anaconda. The Continuum people seem unable to fix the problem. But here is a work-around that will give you a functioning, up-to-date distro.

(1) Remove all trace of the anaconda distro from your system.

(2) Download and install 2019.03 using the MacOS graphical installer.

(3) Do conda upgrade --all This will upgrade a long list of packages, and also downgrade anaconda from 2019.03 to custom

(4) Do conda upgrade --all again. This will downgrade a long list of packages (presumably the ones you just upgraded in step 3.) It will also upgrade anaconda from custom back to 2019.03 This should not happen, but currently it does.

(5) Do conda upgrade mkl This will update a long list of packages (the same ones we had at the end of step 3?). It will also downgrade anaconda from 2019.03 to custom.

(6) As a test, do conda upgrade --all This should tell you that "All requested packages are already installed." You now should have a functioning, up-to-date anaconda distro.

@msarahan

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commented Jul 22, 2019

The Continuum people seem unable to fix the problem.

No, we just haven't managed to find and close all of the related issues. The answer to this is in #8842

Closing this as a duplicate issue. For specific explanations of the behavior and the fix, see:

The entire reason why your instructions work is encapsulated in those 2 comments. The fix was to make the anaconda-custom metapackage have named dependencies, rather than just python. All of your other steps are just fidgeting with that metapackage - flip-flopping between optimizing its version and the versions of everything else. This happens because of how explicit vs. implicit dependencies get optimized.

@o12johns

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commented Jul 24, 2019

Mr. Sarahan,

I know that my list of steps is a kludge. But it does work. It gets a new user to an up-to-date, functioning system. Maybe you should publish a HOWTO that tells a new user the correct step-by-step process to go from installing a new system to finally getting an up-to-date system that works. If you have already done that, please give me the URL. I mean step-by-step instructions, do this and then do that, etc.

All best,

Oliver (o12johns)

@drevicko

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commented Aug 11, 2019

FWIW, applying @msarahan's second suggestion twice times landed me in what seems a stable state. At least conda update anaconda doesn't do anything now and no inconsistencies are reported.

conda update conda however is trying to downgrade the 'anaconda' package again to 'custom' --- I'm not going to try that for now. :)

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