`conda` executable deleted by `conda update --all`

egentry commented 8 years ago

If I install a clean copy of Anaconda, and run conda update conda -y && conda update --all -y everything runs fine. But if I install a clean copy of Anaconda and add conda-forge to my channels, something deletes my conda executable the first time I run conda update --all. As best as I can tell, this happens when linking new packages. (If I have a seperate window open, I can run conda info fine until it gets to "Unlinking packages" and "Linking packages" of the conda update --all stage.)

This seems separate from this issue, since I don't see any uncaught errors.

To reproduce this on my machine (Mac OS 10.11.5), after installing a fresh copy of Anaconda:

conda config --add channels conda-forge
conda update conda
conda update --all

Which yields no error messages until I try conda info and am told -bash: /Users/egentry/anaconda3/bin/conda: No such file or directory

(I believe I've properly cleared my old config information between installations)

jakirkham commented 8 years ago

Weird. So, I tried to reproduce your issue with Miniconda, which didn't work. Tried to install Anaconda to reproduce the issue, but Anaconda failed to install.

EDIT: Raised this upstream in this issue ( https://github.com/ContinuumIO/anaconda-issues/issues/860 ).

$ curl -L http://repo.continuum.io/archive/Anaconda2-4.1.0-MacOSX-x86_64.sh > anaconda.sh
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  295M  100  295M    0     0  53.2M      0  0:00:05  0:00:05 --:--:-- 59.3M
$ bash anaconda.sh -b -p miniconda-test
PREFIX=/Users/kirkhamj/miniconda-test
installing: python-2.7.11-5 ...
installing: _nb_ext_conf-0.2.0-py27_0 ...
installing: alabaster-0.7.8-py27_0 ...
installing: anaconda-client-1.4.0-py27_0 ...
installing: anaconda-navigator-1.2.1-py27_0 ...
installing: appnope-0.1.0-py27_0 ...
installing: appscript-1.0.1-py27_0 ...
installing: argcomplete-1.0.0-py27_1 ...
installing: astropy-1.2.1-np111py27_0 ...
installing: babel-2.3.3-py27_0 ...
installing: backports-1.0-py27_0 ...
installing: backports_abc-0.4-py27_0 ...
installing: beautifulsoup4-4.4.1-py27_0 ...
installing: bitarray-0.8.1-py27_0 ...
installing: bokeh-0.11.1-py27_0 ...
installing: boto-2.40.0-py27_0 ...
installing: bottleneck-1.0.0-np111py27_1 ...
installing: cdecimal-2.3-py27_2 ...
installing: cffi-1.6.0-py27_0 ...
installing: chest-0.2.3-py27_0 ...
installing: click-6.6-py27_0 ...
installing: cloudpickle-0.2.1-py27_0 ...
installing: clyent-1.2.2-py27_0 ...
installing: colorama-0.3.7-py27_0 ...
installing: configobj-5.0.6-py27_0 ...
installing: configparser-3.5.0b2-py27_1 ...
installing: contextlib2-0.5.3-py27_0 ...
installing: cryptography-1.4-py27_0 ...
installing: curl-7.49.0-0 ...
installing: cycler-0.10.0-py27_0 ...
installing: cython-0.24-py27_0 ...
installing: cytoolz-0.8.0-py27_0 ...
installing: dask-0.10.0-py27_0 ...
installing: datashape-0.5.2-py27_0 ...
installing: decorator-4.0.10-py27_0 ...
installing: dill-0.2.5-py27_0 ...
installing: docutils-0.12-py27_2 ...
installing: dynd-python-0.7.2-py27_0 ...
installing: entrypoints-0.2.2-py27_0 ...
installing: enum34-1.1.6-py27_0 ...
installing: et_xmlfile-1.0.1-py27_0 ...
installing: fastcache-1.0.2-py27_1 ...
installing: flask-0.11.1-py27_0 ...
installing: flask-cors-2.1.2-py27_0 ...
installing: freetype-2.5.5-1 ...
installing: funcsigs-1.0.2-py27_0 ...
installing: functools32-3.2.3.2-py27_0 ...
installing: futures-3.0.5-py27_0 ...
installing: get_terminal_size-1.0.0-py27_0 ...
installing: gevent-1.1.1-py27_0 ...
installing: greenlet-0.4.10-py27_0 ...
installing: grin-1.2.1-py27_3 ...
installing: h5py-2.6.0-np111py27_1 ...
installing: hdf5-1.8.16-0 ...
installing: heapdict-1.0.0-py27_1 ...
installing: idna-2.1-py27_0 ...
installing: imagesize-0.7.1-py27_0 ...
installing: ipaddress-1.0.16-py27_0 ...
installing: ipykernel-4.3.1-py27_0 ...
installing: ipython-4.2.0-py27_1 ...
installing: ipython_genutils-0.1.0-py27_0 ...
installing: ipywidgets-4.1.1-py27_0 ...
installing: itsdangerous-0.24-py27_0 ...
installing: jbig-2.1-0 ...
installing: jdcal-1.2-py27_1 ...
installing: jedi-0.9.0-py27_1 ...
installing: jinja2-2.8-py27_1 ...
installing: jpeg-8d-1 ...
installing: jsonschema-2.5.1-py27_0 ...
installing: jupyter-1.0.0-py27_3 ...
installing: jupyter_client-4.3.0-py27_0 ...
installing: jupyter_console-4.1.1-py27_0 ...
installing: jupyter_core-4.1.0-py27_0 ...
installing: libdynd-0.7.2-0 ...
installing: libpng-1.6.22-0 ...
installing: libtiff-4.0.6-2 ...
installing: libxml2-2.9.2-0 ...
installing: libxslt-1.1.28-2 ...
installing: llvmlite-0.11.0-py27_0 ...
installing: locket-0.2.0-py27_1 ...
installing: lxml-3.6.0-py27_0 ...
installing: markupsafe-0.23-py27_2 ...
installing: matplotlib-1.5.1-np111py27_0 ...
installing: mistune-0.7.2-py27_1 ...
installing: mkl-11.3.3-0 ...
installing: mkl-service-1.1.2-py27_2 ...
installing: mpmath-0.19-py27_1 ...
installing: multipledispatch-0.4.8-py27_0 ...
installing: nb_anacondacloud-1.1.0-py27_0 ...
installing: nb_conda-1.1.0-py27_0 ...
installing: nb_conda_kernels-1.0.3-py27_0 ...
installing: nbconvert-4.2.0-py27_0 ...
installing: nbformat-4.0.1-py27_0 ...
installing: nbpresent-3.0.2-py27_0 ...
installing: networkx-1.11-py27_0 ...
installing: nltk-3.2.1-py27_0 ...
installing: nose-1.3.7-py27_1 ...
installing: notebook-4.2.1-py27_0 ...
installing: numba-0.26.0-np111py27_0 ...
installing: numexpr-2.6.0-np111py27_0 ...
installing: numpy-1.11.0-py27_2 ...
installing: odo-0.5.0-py27_0 ...
installing: openpyxl-2.3.2-py27_0 ...
installing: openssl-1.0.2h-1 ...
installing: pandas-0.18.1-np111py27_0 ...
installing: partd-0.3.4-py27_0 ...
installing: path.py-8.2.1-py27_0 ...
installing: pathlib2-2.1.0-py27_0 ...
installing: patsy-0.4.1-py27_0 ...
installing: pep8-1.7.0-py27_0 ...
installing: pexpect-4.0.1-py27_0 ...
installing: pickleshare-0.7.2-py27_0 ...
installing: pillow-3.2.0-py27_1 ...
installing: pip-8.1.2-py27_0 ...
installing: ply-3.8-py27_0 ...
installing: psutil-4.3.0-py27_0 ...
installing: ptyprocess-0.5.1-py27_0 ...
installing: py-1.4.31-py27_0 ...
installing: pyasn1-0.1.9-py27_0 ...
installing: pyaudio-0.2.7-py27_0 ...
installing: pycosat-0.6.1-py27_1 ...
installing: pycparser-2.14-py27_1 ...
installing: pycrypto-2.6.1-py27_4 ...
installing: pycurl-7.43.0-py27_0 ...
installing: pyflakes-1.2.3-py27_0 ...
installing: pygments-2.1.3-py27_0 ...
installing: pyopenssl-0.16.0-py27_0 ...
installing: pyparsing-2.1.4-py27_0 ...
installing: pyqt-4.11.4-py27_3 ...
installing: pytables-3.2.2-np111py27_4 ...
installing: pytest-2.9.2-py27_0 ...
installing: python-dateutil-2.5.3-py27_0 ...
installing: python.app-1.2-py27_4 ...
installing: pytz-2016.4-py27_0 ...
installing: pyyaml-3.11-py27_4 ...
installing: pyzmq-15.2.0-py27_1 ...
installing: qt-4.8.7-3 ...
installing: qtconsole-4.2.1-py27_0 ...
installing: qtpy-1.0.2-py27_0 ...
installing: readline-6.2-2 ...
installing: redis-3.2.0-0 ...
installing: redis-py-2.10.5-py27_0 ...
installing: requests-2.10.0-py27_0 ...
installing: rope-0.9.4-py27_1 ...
installing: ruamel_yaml-0.11.7-py27_0 ...
installing: scikit-image-0.12.3-np111py27_1 ...
installing: scikit-learn-0.17.1-np111py27_2 ...
installing: scipy-0.17.1-np111py27_1 ...
installing: setuptools-23.0.0-py27_0 ...
installing: simplegeneric-0.8.1-py27_1 ...
installing: singledispatch-3.4.0.3-py27_0 ...
installing: sip-4.16.9-py27_0 ...
installing: six-1.10.0-py27_0 ...
installing: snowballstemmer-1.2.1-py27_0 ...
installing: sockjs-tornado-1.0.3-py27_0 ...
installing: sphinx-1.4.1-py27_0 ...
installing: sphinx_rtd_theme-0.1.9-py27_0 ...
installing: spyder-2.3.9-py27_0 ...
installing: sqlalchemy-1.0.13-py27_0 ...
installing: sqlite-3.13.0-0 ...
installing: ssl_match_hostname-3.4.0.2-py27_1 ...
installing: statsmodels-0.6.1-np111py27_1 ...
installing: sympy-1.0-py27_0 ...
installing: terminado-0.6-py27_0 ...
installing: tk-8.5.18-0 ...
installing: toolz-0.8.0-py27_0 ...
installing: tornado-4.3-py27_1 ...
installing: traitlets-4.2.1-py27_0 ...
installing: unicodecsv-0.14.1-py27_0 ...
installing: werkzeug-0.11.10-py27_0 ...
installing: wheel-0.29.0-py27_0 ...
installing: xlrd-1.0.0-py27_0 ...
installing: xlsxwriter-0.9.2-py27_0 ...
installing: xlwings-0.7.2-py27_0 ...
installing: xlwt-1.1.2-py27_0 ...
installing: xz-5.2.2-0 ...
installing: yaml-0.1.6-0 ...
installing: zlib-1.2.8-3 ...
installing: anaconda-4.1.0-np111py27_0 ...
installing: conda-4.1.4-py27_0 ...
installing: conda-build-1.21.2-py27_0 ...
installing: conda-env-2.5.1-py27_0 ...
Python 2.7.11 :: Continuum Analytics, Inc.
creating default environment...
ERROR:root:code for hash md5 was not found.
Traceback (most recent call last):
  File "/Users/kirkhamj/miniconda-test/pkgs/python-2.7.11-5/lib/python2.7/hashlib.py", line 147, in <module>
    globals()[__func_name] = __get_hash(__func_name)
  File "/Users/kirkhamj/miniconda-test/pkgs/python-2.7.11-5/lib/python2.7/hashlib.py", line 97, in __get_builtin_constructor
    raise ValueError('unsupported hash type ' + name)
ValueError: unsupported hash type md5
ERROR:root:code for hash sha1 was not found.
Traceback (most recent call last):
  File "/Users/kirkhamj/miniconda-test/pkgs/python-2.7.11-5/lib/python2.7/hashlib.py", line 147, in <module>
    globals()[__func_name] = __get_hash(__func_name)
  File "/Users/kirkhamj/miniconda-test/pkgs/python-2.7.11-5/lib/python2.7/hashlib.py", line 97, in __get_builtin_constructor
    raise ValueError('unsupported hash type ' + name)
ValueError: unsupported hash type sha1
ERROR:root:code for hash sha224 was not found.
Traceback (most recent call last):
  File "/Users/kirkhamj/miniconda-test/pkgs/python-2.7.11-5/lib/python2.7/hashlib.py", line 147, in <module>
    globals()[__func_name] = __get_hash(__func_name)
  File "/Users/kirkhamj/miniconda-test/pkgs/python-2.7.11-5/lib/python2.7/hashlib.py", line 97, in __get_builtin_constructor
    raise ValueError('unsupported hash type ' + name)
ValueError: unsupported hash type sha224
ERROR:root:code for hash sha256 was not found.
Traceback (most recent call last):
  File "/Users/kirkhamj/miniconda-test/pkgs/python-2.7.11-5/lib/python2.7/hashlib.py", line 147, in <module>
    globals()[__func_name] = __get_hash(__func_name)
  File "/Users/kirkhamj/miniconda-test/pkgs/python-2.7.11-5/lib/python2.7/hashlib.py", line 97, in __get_builtin_constructor
    raise ValueError('unsupported hash type ' + name)
ValueError: unsupported hash type sha256
ERROR:root:code for hash sha384 was not found.
Traceback (most recent call last):
  File "/Users/kirkhamj/miniconda-test/pkgs/python-2.7.11-5/lib/python2.7/hashlib.py", line 147, in <module>
    globals()[__func_name] = __get_hash(__func_name)
  File "/Users/kirkhamj/miniconda-test/pkgs/python-2.7.11-5/lib/python2.7/hashlib.py", line 97, in __get_builtin_constructor
    raise ValueError('unsupported hash type ' + name)
ValueError: unsupported hash type sha384
ERROR:root:code for hash sha512 was not found.
Traceback (most recent call last):
  File "/Users/kirkhamj/miniconda-test/pkgs/python-2.7.11-5/lib/python2.7/hashlib.py", line 147, in <module>
    globals()[__func_name] = __get_hash(__func_name)
  File "/Users/kirkhamj/miniconda-test/pkgs/python-2.7.11-5/lib/python2.7/hashlib.py", line 97, in __get_builtin_constructor
    raise ValueError('unsupported hash type ' + name)
ValueError: unsupported hash type sha512
installation finished.

jjhelmus commented 8 years ago

First off, conda update --all is nearly always a bad idea. You probably should not be doing that.

That said, I'm not able to reproduce this exactly but when I do a conda update --all. I do get an error which leaves conda unusable (requests gets uninstalled and the replacement is not installed before the error). If

The error I'm getting is comes when either simplegeneric or python-simplegeneric is installed as the files for it already exist. I think we need to remove the python- prefixed one from conda-forge.

jakirkham commented 8 years ago

cc @pelson

jjhelmus commented 8 years ago

@jakirkham Try Anaconda3, that where I'm seeing the issue and my guess from the path is what the OP was using.

jjhelmus commented 8 years ago

Here is the error I'm getting:

~$ bash ~/Downloads/Anaconda3-4.1.0-MacOSX-x86_64.sh -b -p anaconda_test
PREFIX=/Users/jhelmus/anaconda_test
installing: python-3.5.1-5 ...
... more installing ...
installing: conda-env-2.5.1-py35_0 ...
Python 3.5.1 :: Continuum Analytics, Inc.
creating default environment...
ln: /Applications//Navigator.app: Permission denied
installation finished.
~$ export PATH=/Users/jhelmus/anaconda_test/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/texbin
 ~$ conda config --add channels conda-forge
 ~$ conda update conda
Using Anaconda Cloud api site https://api.anaconda.org
Fetching package metadata .........
# All requested packages already installed.
# packages in environment at /Users/jhelmus/anaconda_test:
#
conda                     4.1.4                    py35_0    defaults
~$ conda update --all
Using Anaconda Cloud api site https://api.anaconda.org
Fetching package metadata .........
Solving package specifications: ..........

Package plan for installation in environment /Users/jhelmus/anaconda_test:

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2016.2.28  |                1         158 KB  conda-forge
    icu-56.1                   |                2        22.0 MB  conda-forge
    jpeg-9b                    |                0         243 KB  conda-forge
    libgcc-4.8.5               |                1         785 KB  defaults
    libiconv-1.14              |                2         685 KB  conda-forge
    libsodium-1.0.10           |                0         494 KB  conda-forge
    ncurses-5.9                |                7         976 KB  conda-forge
    sqlite-3.13.0              |                1         1.4 MB  conda-forge
    tk-8.5.19                  |                0         2.0 MB  conda-forge
    xz-5.0.5                   |                1         245 KB  conda-forge
    yaml-0.1.6                 |                0          82 KB  conda-forge
    zlib-1.2.8                 |                3          90 KB  conda-forge
    hdf5-1.8.16                |                3         2.9 MB  conda-forge
    libpng-1.6.21              |                1         287 KB  conda-forge
    libtiff-4.0.6              |                5         556 KB  conda-forge
    libxml2-2.9.3              |                8         1.9 MB  conda-forge
    openblas-0.2.18            |                2        15.9 MB  conda-forge
    openssl-1.0.2h             |                0         3.2 MB  conda-forge
    readline-6.2               |                0         311 KB  conda-forge
    zeromq-4.1.5               |                0         603 KB  conda-forge
    blas-1.1                   |         openblas           1 KB  conda-forge
    curl-7.49.1                |                0         507 KB  conda-forge
    freetype-2.6.3             |                1         782 KB  conda-forge
    python-3.5.1               |                0        12.7 MB  defaults
    anaconda-custom            |           py35_0           3 KB  defaults
    backports.shutil_get_terminal_size-1.0.0|           py35_0           5 KB  conda-forge
    cloudpickle-0.2.1          |           py35_2          18 KB  conda-forge
    colorama-0.3.7             |           py35_0          19 KB  conda-forge
    contextlib2-0.5.1          |           py35_0           9 KB  conda-forge
    cython-0.24                |           py35_0         2.6 MB  conda-forge
    dill-0.2.5                 |           py35_0          75 KB  conda-forge
    entrypoints-0.2.1          |           py35_0           3 KB  conda-forge
    jmespath-0.9.0             |           py35_0          28 KB  defaults
    jsonschema-2.5.1           |           py35_0          58 KB  conda-forge
    locket-0.2.0               |           py35_0           5 KB  conda-forge
    markupsafe-0.23            |           py35_0          23 KB  conda-forge
    mistune-0.7.2              |           py35_0          22 KB  conda-forge
    mpmath-0.19                |           py35_0         899 KB  conda-forge
    msgpack-python-0.4.6       |           py35_0          67 KB  defaults
    nose-1.3.7                 |           py35_0         196 KB  conda-forge
    numpy-1.11.0               |py35_blas_openblas_201         2.8 MB  conda-forge
    pep8-1.7.0                 |           py35_0          49 KB  conda-forge
    pickleshare-0.7.2          |           py35_0           9 KB  conda-forge
    pillow-3.2.0               |           py35_2         514 KB  conda-forge
    psutil-4.1.0               |           py35_0         207 KB  conda-forge
    ptyprocess-0.5.1           |           py35_0          19 KB  conda-forge
    pycosat-0.6.1              |           py35_0          58 KB  conda-forge
    pycrypto-2.6.1             |           py35_0         450 KB  conda-forge
    pyflakes-1.2.3             |           py35_0          73 KB  conda-forge
    pyparsing-2.1.1            |           py35_0          69 KB  conda-forge
    python-decorator-4.0.10    |           py35_0          12 KB  conda-forge
    python-simplegeneric-0.8.1 |           py35_0           7 KB  conda-forge
    pytz-2016.3                |           py35_0         182 KB  conda-forge
    pyyaml-3.11                |           py35_0         140 KB  conda-forge
    pyzmq-14.7.0               |           py35_1         315 KB  conda-forge
    requests-2.9.2             |           py35_0         646 KB  conda-forge
    sip-4.18                   |           py35_0         221 KB  conda-forge
    six-1.10.0                 |           py35_0          18 KB  conda-forge
    tblib-1.3.0                |           py35_0          12 KB  defaults
    toolz-0.8.0                |           py35_0          79 KB  conda-forge
    babel-2.3.4                |           py35_0         4.8 MB  conda-forge
    bottleneck-1.0.0           |      np111py35_0         170 KB  conda-forge
    cycler-0.10.0              |           py35_0          13 KB  conda-forge
    cytoolz-0.8.0              |           py35_0         308 KB  conda-forge
    jinja2-2.8                 |           py35_0         302 KB  conda-forge
    partd-0.3.4                |           py35_0          26 KB  conda-forge
    pexpect-4.1.0              |           py35_0          67 KB  conda-forge
    python-dateutil-2.5.2      |           py35_0         238 KB  conda-forge
    scipy-0.17.1               |np111py35_blas_openblas_200        12.0 MB  conda-forge
    sympy-1.0                  |           py35_0         6.0 MB  conda-forge
    terminado-0.6              |           py35_0          18 KB  conda-forge
    traitlets-4.2.1            |           py35_0         112 KB  conda-forge
    bokeh-0.12.0               |           py35_0         3.2 MB  defaults
    botocore-1.4.28            |           py35_0         1.8 MB  defaults
    conda-build-1.21.3         |           py35_0         238 KB  defaults
    ipython-4.2.0              |           py35_2        1002 KB  conda-forge
    jupyter_core-4.1.0         |           py35_0          51 KB  conda-forge
    matplotlib-1.5.1           |      np111py35_3         3.9 MB  conda-forge
    pandas-0.18.1              |      np111py35_0         7.4 MB  conda-forge
    scikit-learn-0.17.1        |np111py35_blas_openblas_200         3.8 MB  conda-forge
    boto3-1.3.1                |           py35_0          97 KB  defaults
    jupyter_client-4.2.2       |           py35_0          99 KB  conda-forge
    nbformat-4.0.1             |           py35_0         114 KB  conda-forge
    scikit-image-0.12.3        |      np111py35_0        18.0 MB  conda-forge
    statsmodels-0.6.1          |      np111py35_0         4.8 MB  conda-forge
    nbconvert-4.2.0            |           py35_0         315 KB  conda-forge
    s3fs-0.0.6                 |           py35_0          22 KB  conda-forge
    jupyter_console-4.1.1      |           py35_0          25 KB  conda-forge
    notebook-4.2.1             |           py35_0         5.1 MB  conda-forge
    qtconsole-4.2.1            |           py35_0         136 KB  conda-forge
    nb_anacondacloud-1.1.0     |           py35_1          21 KB  conda-forge
    nb_conda_kernels-1.0.3     |           py35_0          28 KB  conda-forge
    nbpresent-3.0.2            |           py35_1         466 KB  conda-forge
    spyder-2.3.9               |           py35_0         2.0 MB  conda-forge
    widgetsnbextension-1.2.3   |           py35_1         1.1 MB  conda-forge
    ipywidgets-5.1.5           |           py35_0          61 KB  conda-forge
    dask-0.10.0                |           py35_1         551 KB  conda-forge
    distributed-1.11.0         |           py35_0         162 KB  conda-forge
    ------------------------------------------------------------
                                           Total:       157.0 MB

The following NEW packages will be INSTALLED:

    backports.shutil_get_terminal_size: 1.0.0-py35_0       conda-forge
    blas:                               1.1-openblas       conda-forge
    boto3:                              1.3.1-py35_0       defaults
    botocore:                           1.4.28-py35_0      defaults
    ca-certificates:                    2016.2.28-1        conda-forge
    distributed:                        1.11.0-py35_0      conda-forge
    icu:                                56.1-2             conda-forge
    jmespath:                           0.9.0-py35_0       defaults
    libgcc:                             4.8.5-1            defaults
    libiconv:                           1.14-2             conda-forge
    libsodium:                          1.0.10-0           conda-forge
    msgpack-python:                     0.4.6-py35_0       defaults
    ncurses:                            5.9-7              conda-forge
    openblas:                           0.2.18-2           conda-forge
    python-decorator:                   4.0.10-py35_0      conda-forge
    python-simplegeneric:               0.8.1-py35_0       conda-forge
    s3fs:                               0.0.6-py35_0       conda-forge
    tblib:                              1.3.0-py35_0       defaults
    widgetsnbextension:                 1.2.3-py35_1       conda-forge
    zeromq:                             4.1.5-0            conda-forge

The following packages will be UPDATED:

    anaconda:                           4.1.0-np111py35_0  defaults    --> custom-py35_0                      defaults
    babel:                              2.3.3-py35_0       defaults    --> 2.3.4-py35_0                       conda-forge
    bokeh:                              0.11.1-py35_0      defaults    --> 0.12.0-py35_0                      defaults
    cloudpickle:                        0.2.1-py35_0       defaults    --> 0.2.1-py35_2                       conda-forge
    conda-build:                        1.21.2-py35_0      defaults    --> 1.21.3-py35_0                      defaults
    curl:                               7.49.0-0           defaults    --> 7.49.1-0                           conda-forge
    dask:                               0.10.0-py35_0      defaults    --> 0.10.0-py35_1                      conda-forge
    freetype:                           2.5.5-1            defaults    --> 2.6.3-1                            conda-forge
    hdf5:                               1.8.16-0           defaults    --> 1.8.16-3                           conda-forge
    ipython:                            4.2.0-py35_1       defaults    --> 4.2.0-py35_2                       conda-forge
    ipywidgets:                         4.1.1-py35_0       defaults    --> 5.1.5-py35_0                       conda-forge
    jpeg:                               8d-1               defaults    --> 9b-0                               conda-forge
    libtiff:                            4.0.6-2            defaults    --> 4.0.6-5                            conda-forge
    libxml2:                            2.9.2-0            defaults    --> 2.9.3-8                            conda-forge
    matplotlib:                         1.5.1-np111py35_0  defaults    --> 1.5.1-np111py35_3                  conda-forge
    nb_anacondacloud:                   1.1.0-py35_0       defaults    --> 1.1.0-py35_1                       conda-forge
    nbpresent:                          3.0.2-py35_0       defaults    --> 3.0.2-py35_1                       conda-forge
    numpy:                              1.11.0-py35_2      defaults    --> 1.11.0-py35_blas_openblas_201      conda-forge [blas_openblas]
    pexpect:                            4.0.1-py35_0       defaults    --> 4.1.0-py35_0                       conda-forge
    pillow:                             3.2.0-py35_1       defaults    --> 3.2.0-py35_2                       conda-forge
    scikit-learn:                       0.17.1-np111py35_2 defaults    --> 0.17.1-np111py35_blas_openblas_200 conda-forge [blas_openblas]
    scipy:                              0.17.1-np111py35_1 defaults    --> 0.17.1-np111py35_blas_openblas_200 conda-forge [blas_openblas]
    sip:                                4.16.9-py35_0      defaults    --> 4.18-py35_0                        conda-forge
    sqlite:                             3.13.0-0           defaults    --> 3.13.0-1                           conda-forge
    tk:                                 8.5.18-0           defaults    --> 8.5.19-0                           conda-forge

The following packages will be SUPERCEDED by a higher-priority channel:

    bottleneck:                         1.0.0-np111py35_1  defaults    --> 1.0.0-np111py35_0                  conda-forge
    colorama:                           0.3.7-py35_0       defaults    --> 0.3.7-py35_0                       conda-forge
    contextlib2:                        0.5.3-py35_0       defaults    --> 0.5.1-py35_0                       conda-forge
    cycler:                             0.10.0-py35_0      defaults    --> 0.10.0-py35_0                      conda-forge
    cython:                             0.24-py35_0        defaults    --> 0.24-py35_0                        conda-forge
    cytoolz:                            0.8.0-py35_0       defaults    --> 0.8.0-py35_0                       conda-forge
    dill:                               0.2.5-py35_0       defaults    --> 0.2.5-py35_0                       conda-forge
    entrypoints:                        0.2.2-py35_0       defaults    --> 0.2.1-py35_0                       conda-forge
    jinja2:                             2.8-py35_1         defaults    --> 2.8-py35_0                         conda-forge
    jsonschema:                         2.5.1-py35_0       defaults    --> 2.5.1-py35_0                       conda-forge
    jupyter_client:                     4.3.0-py35_0       defaults    --> 4.2.2-py35_0                       conda-forge
    jupyter_console:                    4.1.1-py35_0       defaults    --> 4.1.1-py35_0                       conda-forge
    jupyter_core:                       4.1.0-py35_0       defaults    --> 4.1.0-py35_0                       conda-forge
    libpng:                             1.6.22-0           defaults    --> 1.6.21-1                           conda-forge
    locket:                             0.2.0-py35_1       defaults    --> 0.2.0-py35_0                       conda-forge
    markupsafe:                         0.23-py35_2        defaults    --> 0.23-py35_0                        conda-forge
    mistune:                            0.7.2-py35_1       defaults    --> 0.7.2-py35_0                       conda-forge
    mpmath:                             0.19-py35_1        defaults    --> 0.19-py35_0                        conda-forge
    nb_conda_kernels:                   1.0.3-py35_0       defaults    --> 1.0.3-py35_0                       conda-forge
    nbconvert:                          4.2.0-py35_0       defaults    --> 4.2.0-py35_0                       conda-forge
    nbformat:                           4.0.1-py35_0       defaults    --> 4.0.1-py35_0                       conda-forge
    nose:                               1.3.7-py35_1       defaults    --> 1.3.7-py35_0                       conda-forge
    notebook:                           4.2.1-py35_0       defaults    --> 4.2.1-py35_0                       conda-forge
    openssl:                            1.0.2h-1           defaults    --> 1.0.2h-0                           conda-forge
    pandas:                             0.18.1-np111py35_0 defaults    --> 0.18.1-np111py35_0                 conda-forge
    partd:                              0.3.4-py35_0       defaults    --> 0.3.4-py35_0                       conda-forge
    pep8:                               1.7.0-py35_0       defaults    --> 1.7.0-py35_0                       conda-forge
    pickleshare:                        0.7.2-py35_0       defaults    --> 0.7.2-py35_0                       conda-forge
    psutil:                             4.3.0-py35_0       defaults    --> 4.1.0-py35_0                       conda-forge
    ptyprocess:                         0.5.1-py35_0       defaults    --> 0.5.1-py35_0                       conda-forge
    pycosat:                            0.6.1-py35_1       defaults    --> 0.6.1-py35_0                       conda-forge
    pycrypto:                           2.6.1-py35_4       defaults    --> 2.6.1-py35_0                       conda-forge
    pyflakes:                           1.2.3-py35_0       defaults    --> 1.2.3-py35_0                       conda-forge
    pyparsing:                          2.1.4-py35_0       defaults    --> 2.1.1-py35_0                       conda-forge
    python-dateutil:                    2.5.3-py35_0       defaults    --> 2.5.2-py35_0                       conda-forge
    pytz:                               2016.4-py35_0      defaults    --> 2016.3-py35_0                      conda-forge
    pyyaml:                             3.11-py35_4        defaults    --> 3.11-py35_0                        conda-forge
    pyzmq:                              15.2.0-py35_1      defaults    --> 14.7.0-py35_1                      conda-forge
    qtconsole:                          4.2.1-py35_0       defaults    --> 4.2.1-py35_0                       conda-forge
    readline:                           6.2-2              defaults    --> 6.2-0                              conda-forge
    requests:                           2.10.0-py35_0      defaults    --> 2.9.2-py35_0                       conda-forge
    scikit-image:                       0.12.3-np111py35_1 defaults    --> 0.12.3-np111py35_0                 conda-forge
    six:                                1.10.0-py35_0      defaults    --> 1.10.0-py35_0                      conda-forge
    spyder:                             2.3.9-py35_0       defaults    --> 2.3.9-py35_0                       conda-forge
    statsmodels:                        0.6.1-np111py35_1  defaults    --> 0.6.1-np111py35_0                  conda-forge
    sympy:                              1.0-py35_0         defaults    --> 1.0-py35_0                         conda-forge
    terminado:                          0.6-py35_0         defaults    --> 0.6-py35_0                         conda-forge
    toolz:                              0.8.0-py35_0       defaults    --> 0.8.0-py35_0                       conda-forge
    traitlets:                          4.2.1-py35_0       defaults    --> 4.2.1-py35_0                       conda-forge
    xz:                                 5.2.2-0            defaults    --> 5.0.5-1                            conda-forge
    yaml:                               0.1.6-0            defaults    --> 0.1.6-0                            conda-forge
    zlib:                               1.2.8-3            defaults    --> 1.2.8-3                            conda-forge

The following packages will be DOWNGRADED due to dependency conflicts:

    python:                             3.5.1-5            defaults    --> 3.5.1-0                            defaults

Proceed ([y]/n)? y

Pruning fetched packages from the cache ...
Fetching packages ...
ca-certificate 100% |################################| Time: 0:00:00 764.07 kB/s
... more downloads ...

Extracting packages ...
[      COMPLETE      ]|####################################################################################| 100%
Unlinking packages ...
[      COMPLETE      ]|####################################################################################| 100%
Linking packages ...
An unexpected error has occurred, please consider sending the#####                                         |  52%
following traceback to the conda GitHub issue tracker at:

    https://github.com/conda/conda/issues

Include the output of the command 'conda info' in your report.

Traceback (most recent call last):
  File "/Users/jhelmus/anaconda_test/bin/conda", line 6, in <module>
    sys.exit(main())
  File "/Users/jhelmus/anaconda_test/lib/python3.5/site-packages/conda/cli/main.py", line 120, in main
    exit_code = args_func(args, p)
  File "/Users/jhelmus/anaconda_test/lib/python3.5/site-packages/conda/cli/main.py", line 130, in args_func
    exit_code = args.func(args, p)
  File "/Users/jhelmus/anaconda_test/lib/python3.5/site-packages/conda/cli/main_update.py", line 64, in execute
    install(args, parser, 'update')
  File "/Users/jhelmus/anaconda_test/lib/python3.5/site-packages/conda/cli/install.py", line 407, in install
    execute_actions(actions, index, verbose=not args.quiet)
  File "/Users/jhelmus/anaconda_test/lib/python3.5/site-packages/conda/plan.py", line 595, in execute_actions
    inst.execute_instructions(plan, index, verbose)
  File "/Users/jhelmus/anaconda_test/lib/python3.5/site-packages/conda/instructions.py", line 136, in execute_instructions
    cmd(state, arg)
  File "/Users/jhelmus/anaconda_test/lib/python3.5/site-packages/conda/instructions.py", line 79, in LINK_CMD
    link(state['prefix'], dist, lt, index=state['index'], shortcuts=shortcuts)
  File "/Users/jhelmus/anaconda_test/lib/python3.5/site-packages/conda/install.py", line 1048, in link
    os.makedirs(dst_dir)
  File "/Users/jhelmus/anaconda_test/lib/python3.5/os.py", line 241, in makedirs
    mkdir(name, mode)
FileExistsError: [Errno 17] File exists: '/Users/jhelmus/anaconda_test/lib/python3.5/site-packages/simplegeneric-0.8.1-py3.5.egg-info'

~$ conda --version
Traceback (most recent call last):
  File "/Users/jhelmus/anaconda_test/bin/conda", line 6, in <module>
    sys.exit(main())
  File "/Users/jhelmus/anaconda_test/lib/python3.5/site-packages/conda/cli/main.py", line 94, in main
    imported = importlib.import_module(module)
  File "/Users/jhelmus/anaconda_test/lib/python3.5/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 986, in _gcd_import
  File "<frozen importlib._bootstrap>", line 969, in _find_and_load
  File "<frozen importlib._bootstrap>", line 958, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 673, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 662, in exec_module
  File "<frozen importlib._bootstrap>", line 222, in _call_with_frames_removed
  File "/Users/jhelmus/anaconda_test/lib/python3.5/site-packages/conda/cli/main_list.py", line 18, in <module>
    from ..egg_info import get_egg_info
  File "/Users/jhelmus/anaconda_test/lib/python3.5/site-packages/conda/egg_info.py", line 15, in <module>
    from .misc import rel_path
  File "/Users/jhelmus/anaconda_test/lib/python3.5/site-packages/conda/misc.py", line 18, in <module>
    from .fetch import fetch_index
  File "/Users/jhelmus/anaconda_test/lib/python3.5/site-packages/conda/fetch.py", line 13, in <module>
    import requests
ImportError: No module named 'requests'

jjhelmus commented 8 years ago

conda install -c conda-forge python-simplegeneric will result in the same issue.

astrofrog commented 8 years ago

Any chance this could be related to https://github.com/conda/conda/issues/2897? (maybe not, but just wanted to check)

kalefranz commented 8 years ago

@jjhelmus

First off, conda update --all is nearly always a bad idea. You probably should not be doing that.

It used to be. I thought we had greatly improved it as of 4.0.

I do get an error which leaves conda unusable (requests gets uninstalled and the replacement is not installed before the error)

😤😡

Until we can get conda into it's own private env and out of the root or "default" env--probably in 5.0--I might just start to vendor all of conda's dependencies to avoid problems just like this.

We're also doing structural work within the conda code base to enable us to make things more atomic and roll back on errors.

The error I'm getting is comes when either simplegeneric or python-simplegeneric is installed as the files for it already exist. I think we need to remove the python- prefixed one from conda-forge.

https://github.com/conda-forge/python-simplegeneric-feedstock/issues/1

jankatins commented 8 years ago

First off, conda update --all is nearly always a bad idea. You probably should not be doing that.

Sorry, but this can't be the idea about a rolling distribution (no "big release ever few month/years" -> even anaconda AFAIK installs the default channel and not a "security for the xx release"). I guess that for a lot of scenarios the "install a specific set of packages" is the way to go, but at least my root env is "get me the latest and greatest" and I expect that I can install it in one go. So this has to work and IMO conda itself should be designed to do it well!

egentry commented 8 years ago

Yeah, this was originally for Anaconda3, version 4.0.0.

Now if I start with Anaconda3, version 4.1.0, I get the same issue, but at least this time I see the python-simplegeneric error message. So I think the problem's been identified (conda-forge/python-simplegeneric-feedstock#1), and the conda update process is no longer silently catching (but not resolving) the error.

jjhelmus commented 8 years ago

Sorry for the commend about conda update --all. I know in the past this command has not recommended but with the recent improvements to conda it does seem to work quite well!

jakirkham commented 8 years ago

@pelson, looks like we are going to need rename python-simplegeneric. It's having some pretty rough consequences for end-users.

jjhelmus commented 8 years ago

What package is pulling in python-simplegeneric? Changing that requirement may be sufficient.

jakirkham commented 8 years ago

I think your heart is in the right place, @jjhelmus. Unfortunately, we have made changes in conda-forge AFAICT. The problem is that defaults hasn't. As a result, users can end up going back and forth between simplegeneric and python-simplegeneric depending on which one is more recent or which one comes bundled. As versions may be more recent here or there, I think we will sadly find ourselves being affected by this repeatedly. While I loved the idea of prefixing, I think it is time to be practical and drop the ones that conflict with defaults and are likely to (or already do) cause problems.

jjhelmus commented 8 years ago

@jakirkham I agree, I think we need to follow defaults to provide a better user experience even if prefixing is the more forward thinking solution.

I was just trying to figure out what package upgrade was pulling in python-simplegeneric in the example above.

jakirkham commented 8 years ago

IIRC it is ipython.

jjhelmus commented 8 years ago

Yes, ipython. I opened an issue in the feedstock suggesting a name change for the requirement, conda-forge/ipython-feedstock#9.

pelson commented 8 years ago

While I loved the idea of prefixing, I think it is time to be practical and drop the ones that conflict with defaults

Unfortunately I do agree with your conclusion. The only other option is that we introduce an Obsoletes concept, analogous to the RPM meaning.

jjhelmus commented 8 years ago

we introduce an Obsoletes concept, analogous to the RPM meaning.

That would need to be added to conda correct? :+1: for suggesting this as a feature to add to conda. A conflicts option would be nice also for cases where two packages cannot (or should not) be installed in the same environment.

robmarkcole commented 8 years ago

I just experienced this issue, and worst of all when I try a fresh install I get the error

Couldn't open "Anaconda3-4.2.0-MacOSX-x86_64.pkg".

conda-forge / conda-forge.github.io

`conda` executable deleted by `conda update --all` #180