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Navigator Error: Updatable packages won't update #9591

Open odebroqueville opened 6 years ago

odebroqueville commented 6 years ago

Actual Behavior

A popup window appeared, but it remained blank. Nothing seemed to be happening and the packages weren't updated. (screenshot)

Expected Behavior

Instead of a blank popup, I should have seen which packages were being updated and, once updated, the packages should have been removed from the Updatable packages list.

Steps to Reproduce

I first installed the latest version of Anaconda (Python 3.6 version, 64-Bit Graphical Installer 613 MB) for macOS. In the Navigator, I filtered the list of packages to view only updatable packages. 2 packages were shown:

  1. freetype (2.8)
  2. xlwt (1.2.0) I clicked on both blue arrows just before the version numbers and then clicked on the Apply button. A popup window appeared, but it remained blank. Nothing seemed to be happening and the packages weren't updated.
Anaconda or Miniconda version:

Anaconda Navigator 1.8.7 anaconda Command line client (version 1.6.14)

Operating System:

macOS 10.13.5 High Sierra

conda info
     active environment : None
       user config file : /Users/odebroqueville/.condarc
 populated config files : /Users/odebroqueville/.condarc
          conda version : 4.5.4
    conda-build version : 3.10.5
         python version : 3.6.5.final.0
       base environment : /Users/odebroqueville/anaconda3  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/osx-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/osx-64
                          https://repo.anaconda.com/pkgs/pro/noarch
          package cache : /Users/odebroqueville/anaconda3/pkgs
                          /Users/odebroqueville/.conda/pkgs
       envs directories : /Users/odebroqueville/anaconda3/envs
                          /Users/odebroqueville/.conda/envs
               platform : osx-64
             user-agent : conda/4.5.4 requests/2.18.4 CPython/3.6.5 Darwin/17.6.0 OSX/10.13.5
                UID:GID : 501:20
             netrc file : /Users/odebroqueville/.netrc
           offline mode : False
conda list --show-channel-urls
# packages in environment at /Users/odebroqueville/anaconda3:
#
# Name                    Version                   Build  Channel
_ipyw_jlab_nb_ext_conf    0.1.0            py36h2fc01ae_0    defaults
alabaster                 0.7.10           py36h174008c_0    defaults
anaconda                  5.2.0                    py36_3    defaults
anaconda-client           1.6.14                   py36_0    defaults
anaconda-navigator        1.8.7                    py36_0    defaults
anaconda-project          0.8.2            py36h9ee5d53_0    defaults
appnope                   0.1.0            py36hf537a9a_0    defaults
appscript                 1.0.1            py36h9e71e49_1    defaults
asn1crypto                0.24.0                   py36_0    defaults
astroid                   1.6.3                    py36_0    defaults
astropy                   3.0.2            py36h917ab60_1    defaults
attrs                     18.1.0                   py36_0    defaults
babel                     2.5.3                    py36_0    defaults
backcall                  0.1.0                    py36_0    defaults
backports                 1.0              py36ha3c1827_1    defaults
backports.shutil_get_terminal_size 1.0.0            py36hd7a2ee4_2    defaults
beautifulsoup4            4.6.0            py36h72d3c9f_1    defaults
bitarray                  0.8.1            py36h1de35cc_1    defaults
bkcharts                  0.2              py36h073222e_0    defaults
blas                      1.0                         mkl    defaults
blaze                     0.11.3           py36h02e7a37_0    defaults
bleach                    2.1.3                    py36_0    defaults
blosc                     1.14.3               hd9629dc_0    defaults
bokeh                     0.12.16                  py36_0    defaults
boto                      2.48.0           py36hdbc59ac_1    defaults
bottleneck                1.2.1            py36hbd380ad_0    defaults
bzip2                     1.0.6                h1de35cc_5    defaults
ca-certificates           2018.03.07                    0    defaults
certifi                   2018.4.16                py36_0    defaults
cffi                      1.11.5           py36h342bebf_0    defaults
chardet                   3.0.4            py36h96c241c_1    defaults
click                     6.7              py36hec950be_0    defaults
cloudpickle               0.5.3                    py36_0    defaults
clyent                    1.2.2            py36hae3ad88_0    defaults
colorama                  0.3.9            py36hd29a30c_0    defaults
conda                     4.5.4                    py36_0    defaults
conda-build               3.10.5                   py36_0    defaults
conda-env                 2.6.0                h36134e3_0    defaults
conda-verify              2.0.0            py36he837df3_0    defaults
contextlib2               0.5.5            py36hd66e5e7_0    defaults
cryptography              2.2.2            py36h1de35cc_0    defaults
curl                      7.60.0               ha441bb4_0    defaults
cycler                    0.10.0           py36hfc81398_0    defaults
cython                    0.28.2           py36h1de35cc_0    defaults
cytoolz                   0.9.0.1          py36h1de35cc_0    defaults
dask                      0.17.5                   py36_0    defaults
dask-core                 0.17.5                   py36_0    defaults
datashape                 0.5.4            py36hfb22df8_0    defaults
dbus                      1.13.2               h760590f_1    defaults
decorator                 4.3.0                    py36_0    defaults
distributed               1.21.8                   py36_0    defaults
docutils                  0.14             py36hbfde631_0    defaults
entrypoints               0.2.3            py36hd81d71f_2    defaults
et_xmlfile                1.0.1            py36h1315bdc_0    defaults
expat                     2.2.5                hb8e80ba_0    defaults
fastcache                 1.0.2            py36h1de35cc_2    defaults
filelock                  3.0.4                    py36_0    defaults
flask                     1.0.2                    py36_1    defaults
flask-cors                3.0.4                    py36_0    defaults
freetype                  2.8                  h12048fb_1    defaults
get_terminal_size         1.0.0                h7520d66_0    defaults
gettext                   0.19.8.1             h15daf44_3    defaults
gevent                    1.3.0            py36h1de35cc_0    defaults
glib                      2.56.1               h35bc53a_0    defaults
glob2                     0.6              py36h94c9186_0    defaults
gmp                       6.1.2                hb37e062_1    defaults
gmpy2                     2.0.8            py36hf9c35bd_2    defaults
greenlet                  0.4.13           py36h1de35cc_0    defaults
h5py                      2.7.1            py36ha8ecd60_2    defaults
hdf5                      1.10.2               hfa1e0ec_1    defaults
heapdict                  1.0.0                    py36_2    defaults
html5lib                  1.0.1            py36h2f9c1c0_0    defaults
icu                       58.2                 h4b95b61_1    defaults
idna                      2.6              py36h8628d0a_1    defaults
imageio                   2.3.0                    py36_0    defaults
imagesize                 1.0.0                    py36_0    defaults
intel-openmp              2018.0.0                      8    defaults
ipykernel                 4.8.2                    py36_0    defaults
ipython                   6.4.0                    py36_0    defaults
ipython_genutils          0.2.0            py36h241746c_0    defaults
ipywidgets                7.2.1                    py36_0    defaults
isort                     4.3.4                    py36_0    defaults
itsdangerous              0.24             py36h49fbb8d_1    defaults
jbig                      2.1                  h4d881f8_0    defaults
jdcal                     1.4                      py36_0    defaults
jedi                      0.12.0                   py36_1    defaults
jinja2                    2.10             py36hd36f9c5_0    defaults
jpeg                      9b                   he5867d9_2    defaults
jsonschema                2.6.0            py36hb385e00_0    defaults
jupyter                   1.0.0                    py36_4    defaults
jupyter_client            5.2.3                    py36_0    defaults
jupyter_console           5.2.0            py36hccf5b1c_1    defaults
jupyter_core              4.4.0            py36h79cf704_0    defaults
jupyterlab                0.32.1                   py36_0    defaults
jupyterlab_launcher       0.10.5                   py36_0    defaults
kiwisolver                1.0.1            py36h792292d_0    defaults
lazy-object-proxy         1.3.1            py36h2fbbe47_0    defaults
libcurl                   7.60.0               hf30b1f0_0    defaults
libcxx                    4.0.1                h579ed51_0    defaults
libcxxabi                 4.0.1                hebd6815_0    defaults
libedit                   3.1.20170329         hb402a30_2    defaults
libffi                    3.2.1                h475c297_4    defaults
libgfortran               3.0.1                h93005f0_2    defaults
libiconv                  1.15                 hdd342a3_7    defaults
libpng                    1.6.34               he12f830_0    defaults
libsodium                 1.0.16               h3efe00b_0    defaults
libssh2                   1.8.0                h322a93b_4    defaults
libtiff                   4.0.9                hcb84e12_1    defaults
libxml2                   2.9.8                hab757c2_1    defaults
libxslt                   1.1.32               hb819dd2_0    defaults
llvmlite                  0.23.1           py36hc454e04_0    defaults
locket                    0.2.0            py36hca03003_1    defaults
lxml                      4.2.1            py36h7166777_0    defaults
lzo                       2.10                 h362108e_2    defaults
markupsafe                1.0              py36h3a1e703_1    defaults
matplotlib                2.2.2            py36ha7267d0_0    defaults
mccabe                    0.6.1            py36hdaeb55d_0    defaults
mistune                   0.8.3            py36h1de35cc_1    defaults
mkl                       2018.0.2                      1    defaults
mkl-service               1.1.2            py36h7ea6df4_4    defaults
mkl_fft                   1.0.1            py36h917ab60_0    defaults
mkl_random                1.0.1            py36h78cc56f_0    defaults
more-itertools            4.1.0                    py36_0    defaults
mpc                       1.0.3                h7a72875_5    defaults
mpfr                      3.1.5                h711e7fd_2    defaults
mpmath                    1.0.0            py36hf1b8295_2    defaults
msgpack-python            0.5.6            py36h04f5b5a_0    defaults
multipledispatch          0.5.0                    py36_0    defaults
navigator-updater         0.2.1                    py36_0    defaults
nbconvert                 5.3.1            py36h810822e_0    defaults
nbformat                  4.4.0            py36h827af21_0    defaults
ncurses                   6.1                  h0a44026_0    defaults
networkx                  2.1                      py36_0    defaults
nltk                      3.3.0                    py36_0    defaults
nose                      1.3.7            py36h73fae2b_2    defaults
notebook                  5.5.0                    py36_0    defaults
numba                     0.38.0           py36h1702cab_0    defaults
numexpr                   2.6.5            py36h057f876_0    defaults
numpy                     1.14.3           py36h9bb19eb_1    defaults
numpy-base                1.14.3           py36h479e554_1    defaults
numpydoc                  0.8.0                    py36_0    defaults
odo                       0.5.1            py36hc1af34a_0    defaults
olefile                   0.45.1                   py36_0    defaults
openpyxl                  2.5.3                    py36_0    defaults
openssl                   1.0.2o               h26aff7b_0    defaults
packaging                 17.1                     py36_0    defaults
pandas                    0.23.0           py36h1702cab_0    defaults
pandoc                    1.19.2.1             ha5e8f32_1    defaults
pandocfilters             1.4.2            py36h3b0b094_1    defaults
parso                     0.2.0                    py36_0    defaults
partd                     0.3.8            py36hf5c4cb8_0    defaults
path.py                   11.0.1                   py36_0    defaults
pathlib2                  2.3.2                    py36_0    defaults
patsy                     0.5.0                    py36_0    defaults
pcre                      8.42                 h378b8a2_0    defaults
pep8                      1.7.1                    py36_0    defaults
pexpect                   4.5.0                    py36_0    defaults
pickleshare               0.7.4            py36hf512f8e_0    defaults
pillow                    5.1.0            py36hfcce615_0    defaults
pip                       10.0.1                   py36_0    defaults
pkginfo                   1.4.2                    py36_1    defaults
pluggy                    0.6.0            py36hb1d0581_0    defaults
ply                       3.11                     py36_0    defaults
prompt_toolkit            1.0.15           py36haeda067_0    defaults
psutil                    5.4.5            py36h1de35cc_0    defaults
ptyprocess                0.5.2            py36he6521c3_0    defaults
py                        1.5.3                    py36_0    defaults
pycodestyle               2.4.0                    py36_0    defaults
pycosat                   0.6.3            py36hee92d8f_0    defaults
pycparser                 2.18             py36h724b2fc_1    defaults
pycrypto                  2.6.1            py36h1de35cc_8    defaults
pycurl                    7.43.0.1         py36hdbc3d79_0    defaults
pyflakes                  1.6.0            py36hea45e83_0    defaults
pygments                  2.2.0            py36h240cd3f_0    defaults
pylint                    1.8.4                    py36_0    defaults
pyodbc                    4.0.23           py36h0a44026_0    defaults
pyopenssl                 18.0.0                   py36_0    defaults
pyparsing                 2.2.0            py36hb281f35_0    defaults
pyqt                      5.9.2            py36h11d3b92_0    defaults
pysocks                   1.6.8                    py36_0    defaults
pytables                  3.4.3            py36h5ca999c_2    defaults
pytest                    3.5.1                    py36_0    defaults
pytest-arraydiff          0.2                      py36_0    defaults
pytest-astropy            0.3.0                    py36_0    defaults
pytest-doctestplus        0.1.3                    py36_0    defaults
pytest-openfiles          0.3.0                    py36_0    defaults
pytest-remotedata         0.2.1                    py36_0    defaults
python                    3.6.5                hc167b69_1    defaults
python-dateutil           2.7.3                    py36_0    defaults
python.app                2                        py36_8    defaults
pytz                      2018.4                   py36_0    defaults
pywavelets                0.5.2            py36h2710a04_0    defaults
pyyaml                    3.12             py36h2ba1e63_1    defaults
pyzmq                     17.0.0           py36h1de35cc_1    defaults
qt                        5.9.5                h02808f3_0    defaults
qtawesome                 0.4.4            py36h468c6fb_0    defaults
qtconsole                 4.3.1            py36hd96c0ff_0    defaults
qtpy                      1.4.1                    py36_0    defaults
readline                  7.0                  hc1231fa_4    defaults
requests                  2.18.4           py36h4516966_1    defaults
rope                      0.10.7           py36h68959ac_0    defaults
ruamel_yaml               0.15.35          py36h1de35cc_1    defaults
scikit-image              0.13.1           py36h1de35cc_1    defaults
scikit-learn              0.19.1           py36hffbff8c_0    defaults
scipy                     1.1.0            py36hcaad992_0    defaults
seaborn                   0.8.1            py36h595ecd9_0    defaults
send2trash                1.5.0                    py36_0    defaults
setuptools                39.1.0                   py36_0    defaults
simplegeneric             0.8.1                    py36_2    defaults
singledispatch            3.4.0.3          py36hf20db9d_0    defaults
sip                       4.19.8           py36h0a44026_0    defaults
six                       1.11.0           py36h0e22d5e_1    defaults
snappy                    1.1.7                he62c110_3    defaults
snowballstemmer           1.2.1            py36h6c7b616_0    defaults
sortedcollections         0.6.1                    py36_0    defaults
sortedcontainers          1.5.10                   py36_0    defaults
sphinx                    1.7.4                    py36_0    defaults
sphinxcontrib             1.0              py36h9364dc8_1    defaults
sphinxcontrib-websupport  1.0.1            py36h92f4a7a_1    defaults
spyder                    3.2.8                    py36_0    defaults
sqlalchemy                1.2.7            py36hb402a30_0    defaults
sqlite                    3.23.1               hf1716c9_0    defaults
statsmodels               0.9.0            py36h917ab60_0    defaults
sympy                     1.1.1            py36h7f3cf04_0    defaults
tblib                     1.3.2            py36hda67792_0    defaults
terminado                 0.8.1                    py36_1    defaults
testpath                  0.3.1            py36h625a49b_0    defaults
tk                        8.6.7                h35a86e2_3    defaults
toolz                     0.9.0                    py36_0    defaults
tornado                   5.0.2                    py36_0    defaults
traitlets                 4.3.2            py36h65bd3ce_0    defaults
typing                    3.6.4                    py36_0    defaults
unicodecsv                0.14.1           py36he531d66_0    defaults
unixodbc                  2.3.6                h3efe00b_0    defaults
urllib3                   1.22             py36h68b9469_0    defaults
wcwidth                   0.1.7            py36h8c6ec74_0    defaults
webencodings              0.5.1            py36h3b9701d_1    defaults
werkzeug                  0.14.1                   py36_0    defaults
wheel                     0.31.1                   py36_0    defaults
widgetsnbextension        3.2.1                    py36_0    defaults
wrapt                     1.10.11          py36hc29e774_0    defaults
xlrd                      1.1.0            py36h336f4a2_1    defaults
xlsxwriter                1.0.4                    py36_0    defaults
xlwings                   0.11.8                   py36_0    defaults
xlwt                      1.2.0            py36h5ad1178_0    defaults
xz                        5.2.4                h1de35cc_4    defaults
yaml                      0.1.7                hc338f04_2    defaults
zeromq                    4.2.5                h378b8a2_0    defaults
zict                      0.1.3            py36h71da714_0    defaults
zlib                      1.2.11               hf3cbc9b_2    defaults
goanpeca commented 6 years ago

@odebroqueville will check the issue. In the meantime could you select the specifc version of the package you want installed instead of clicking the blu arrow?

odebroqueville commented 6 years ago

If you mean the green checkboxes to the left, they were already checked. I am able to click on the green checkboxes to mark the packages for update or I can click on the blue arrow or version number for the "Apply" button to appear. But clicking on the "Apply" button still isn't working. No updates are performed. (screenshot)

goanpeca commented 6 years ago

@odebroqueville what I meant is that in the meantime you could do right click on the check mark and select the specific version and that should probably work? While we get this fixed that is what you can do.

screen shot 2018-06-14 at 09 51 33
odebroqueville commented 6 years ago

I tried to update just the freetype package. I had some difficulties (i.e. the context menu would disappear as I moved the mouse pointer) selecting "Mark for specific version installation" after right-clicking but eventually managed to select version 2.9.1. This screenshot shows what happened next and this screenshot shows the final results. No install progress was displayed and finally the package wasn't updated.

conda info freetype namely displays:

freetype 2.9.1 hb4e5f40_0
-------------------------
file name   : freetype-2.9.1-hb4e5f40_0.tar.bz2
name        : freetype
version     : 2.9.1
build string: hb4e5f40_0
build number: 0
channel     : https://repo.anaconda.com/pkgs/main/osx-64
size        : 864 KB
arch        : None
constrains  : ()
license     : GPL-2.0 and FreeType
md5         : 621858a6df6e0b41955d13fb9d4af5f9
platform    : None
subdir      : osx-64
timestamp   : 1527165146829
url         : https://repo.anaconda.com/pkgs/main/osx-64/freetype-2.9.1-hb4e5f40_0.tar.bz2
dependencies:
    libpng >=1.6.34,<1.7.0a0
    zlib >=1.2.11,<1.3.0a0

I checked with the Navigator and dependencies libpng 1.6.34 and zlib 1.2.11 are already installed on my system. I then typed the following:

conda info pillow and the latest version of pillow shown is pillow 4.2.1 whilst version 5.1.0 is installed on my system, so it would appear that conda isn't up to date:

pillow 4.2.1 py36_0
-------------------
file name   : pillow-4.2.1-py36_0.tar.bz2
name        : pillow
version     : 4.2.1
build string: py36_0
build number: 0
channel     : https://repo.anaconda.com/pkgs/free/osx-64
size        : 505 KB
arch        : x86_64
constrains  : ()
date        : 2017-07-08
license     : PIL license
license_family: Other
md5         : 1c57b908ca7ea5c5a9ea16a785c82ea2
platform    : darwin
subdir      : osx-64
url         : https://repo.anaconda.com/pkgs/free/osx-64/pillow-4.2.1-py36_0.tar.bz2
dependencies:
    freetype 2.5.*
    jpeg 9*
    libtiff 4.0.*
    olefile
    python 3.6*
    zlib 1.2.*

It would appear that pillow requires freetype version 2.5.x so perhaps that explains why updates are not being carried out.

goanpeca commented 6 years ago

@odebroqueville I checked with version 1.8.7 and nothing seems out of place. Do you have more than one version of anaconda navigator on your system?

If you click on about navigator do you see 1.8.7. If you open the terminal, activate the base environment, what do you see?

anaconda-navigator
odebroqueville commented 6 years ago

Yes, I have version Anaconda Navigator 1.8.7 and have only installed anaconda once on my macbook. I have the following files in /bin:

-rwxrwxr-x    1 odebroqueville  staff        255 13 Jun 15:15 anaconda
-rwxrwxr-x    1 odebroqueville  staff        256 13 Jun 15:15 anaconda-navigator
-rwxrwxr-x    1 odebroqueville  staff        249 13 Jun 15:15 anaconda-project
conda info --envs
# conda environments:
#
base                  *  /Users/odebroqueville/anaconda3
goanpeca commented 6 years ago

@odebroqueville I am really not sure what is going on :-|

Please try force reinstalling navigator

conda install anaconda-navigator=1.8.7 --force
odebroqueville commented 6 years ago

I performed the following:

conda install anaconda-navigator=1.8.7 --force
Solving environment: done

## Package Plan ##

  environment location: /Users/odebroqueville/anaconda3

  added / updated specs: 
    - anaconda-navigator=1.8.7

The following packages will be UPDATED:

    anaconda-navigator: 1.8.7-py36_0 --> 1.8.7-py36_0

Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

and launched the Navigator. Learning and Community tabs are empty again and I'm getting the same error message when I try to update freetype.

Why is the latest version of pillow in conda only pillow 4.2.1 py36_0 and not 5.1.0 ?

odebroqueville commented 6 years ago

Sorry! I found pillow 5.1.0 after doing conda info pillow:

pillow 5.1.0 py36hfcce615_0
---------------------------
file name   : pillow-5.1.0-py36hfcce615_0.tar.bz2
name        : pillow
version     : 5.1.0
build string: py36hfcce615_0
build number: 0
channel     : https://repo.anaconda.com/pkgs/main/osx-64
size        : 542 KB
arch        : None
constrains  : ()
license     : PIL
md5         : 8f20e17c3f5f4c716400d90713d927ca
platform    : None
subdir      : osx-64
timestamp   : 1523904057734
url         : https://repo.anaconda.com/pkgs/main/osx-64/pillow-5.1.0-py36hfcce615_0.tar.bz2
dependencies:
    freetype >=2.8,<2.9.0a0
    jpeg >=9b,<10a
    libtiff >=4.0.9,<5.0a0
    olefile
    python >=3.6,<3.7.0a0
    tk >=8.6.7,<8.7.0a0
    zlib >=1.2.11,<1.3.0a0

I hadn't found it before because I thought the list was sorted alphabetically, but 5.1.0 appears before 2.1.0!

I'm wondering if "freetype >=2.8,<2.9.0a0" means that pillow 5.1.0 requires freetype 2.8 and not above, i.e. 2.9, and if that condition may block updates.

I tried updating other packages (babel, xlwt), but nothing gets updated.

goanpeca commented 6 years ago

@odebroqueville I have issued a "fix" which will provide the user with more information of what is going on, to be released this week. Basically conda cannot update because the latest verison that does not yield conflicts is the one you already have as you saw when attempting to install the specific version screenshot

I filed https://github.com/conda/conda/issues/7551 to provide a better message that the current:

All requested packages already installed.

This is not an error on Navigator side per se, (except for also displaying the same message which is not happening) BUT conda will behave the same on the CLI so that is why I opened the new issue.

Thanks for the feedback.

I will close this as soon as the new version is released which inlcudes the extra info from conda.

hovikgas commented 5 years ago

Are there any updates to this, because I seem to have the same issue, in addition to 3 other packages. So in total, whenever I try to update jupyterlab to 0.34.12, llvmlite to 0.27.0, sip to 4.19.8, and spyder-kernels to 0.4.2, I have the issue the OP had: either the update packages notification screen pops up and the blue progress bar just keeps scrolling to no end, or it finally resolves, shows the following prompt that 4 packages will be installed, but still nothing happens once it is "installed," (i.e. it shows "installing packages" on the bottom, then says, "4 packages installed," but the same packages are left still there as "updatable." Screen Shot 2019-03-18 at 6 37 55 AM

Except, I now noticed that there might be an incompatibility with jupyterlab-server 0.3.0 and 0.2.0 as updating this drops JupyterLab back to the previous version, and vice versa. Regardless, when I don't touch JupyterLab, the other 3 packages don't do anything in terms of installation. And I too definitely only have 1 version of navigator, because I went and uninstalled everything and reinstalled the latest version.