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ContinuumIO / anaconda-issues

Anaconda issue tracking
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Anaconda/conda issues #8029

Closed connorfreeberg closed 6 years ago

connorfreeberg commented 6 years ago

Hello,

So I was having issues downloading some packages in RStudio and so I went through some of the threads on here trying to figure out why the packages were not installing. It was showing the response that I could not make a connection to the Cran site.

screen shot 2018-01-05 at 12 50 39 pm

While trying some of the bash commands to update conda and Rstudio to see if that would help the process it appears I may made the problem worse. Now when I open Anaconda my channel went from root to anaconda and when open Jupyter (which I was not having problems with before) I can no longer see any of my past notebooks. It appears I have completely installed a new Anaconda, or at least overrode it. See a couple of the screen shots below. I'm hoping I didn't lose all those files. Does anyone know what I did wrong and how I can fix it? R studio is also not even opening now. I know that was a bad explanation so let me know if you have any questions.

image

Last login: Sat Nov 11 09:57:24 on ttys001
Connors-MacBook-Pro:~ connorfreeberg$ pip install plotly
Collecting plotly
  Downloading plotly-2.2.2.tar.gz (1.1MB)
    100% |████████████████████████████████| 1.1MB 718kB/s 
Requirement already satisfied: decorator>=4.0.6 in ./anaconda/lib/python3.6/site-packages (from plotly)
Requirement already satisfied: nbformat>=4.2 in ./anaconda/lib/python3.6/site-packages (from plotly)
Requirement already satisfied: pytz in ./anaconda/lib/python3.6/site-packages (from plotly)
Requirement already satisfied: requests in ./anaconda/lib/python3.6/site-packages (from plotly)
Requirement already satisfied: six in ./anaconda/lib/python3.6/site-packages (from plotly)
Building wheels for collected packages: plotly
  Running setup.py bdist_wheel for plotly ... done
  Stored in directory: /Users/connorfreeberg/Library/Caches/pip/wheels/43/3c/d9/7bb55474a73f126f3c52b2591850df6480f4f55138ea819d84
Successfully built plotly
Installing collected packages: plotly
Successfully installed plotly-2.2.2
Connors-MacBook-Pro:~ connorfreeberg$ pip install textblob
Collecting textblob
  Downloading textblob-0.15.0-py2.py3-none-any.whl (631kB)
    100% |████████████████████████████████| 634kB 1.0MB/s 
Requirement already satisfied: nltk>=3.1 in ./anaconda/lib/python3.6/site-packages (from textblob)
Requirement already satisfied: six in ./anaconda/lib/python3.6/site-packages (from nltk>=3.1->textblob)
Installing collected packages: textblob
Successfully installed textblob-0.15.0
Connors-MacBook-Pro:~ connorfreeberg$ python -m textblob.download_corpora
[nltk_data] Downloading package brown to
[nltk_data]     /Users/connorfreeberg/nltk_data...
[nltk_data]   Unzipping corpora/brown.zip.
[nltk_data] Downloading package punkt to
[nltk_data]     /Users/connorfreeberg/nltk_data...
[nltk_data]   Unzipping tokenizers/punkt.zip.
[nltk_data] Downloading package wordnet to
[nltk_data]     /Users/connorfreeberg/nltk_data...
[nltk_data]   Unzipping corpora/wordnet.zip.
[nltk_data] Downloading package averaged_perceptron_tagger to
[nltk_data]     /Users/connorfreeberg/nltk_data...
[nltk_data]   Unzipping taggers/averaged_perceptron_tagger.zip.
[nltk_data] Downloading package conll2000 to
[nltk_data]     /Users/connorfreeberg/nltk_data...
[nltk_data]   Unzipping corpora/conll2000.zip.
[nltk_data] Downloading package movie_reviews to
[nltk_data]     /Users/connorfreeberg/nltk_data...
[nltk_data]   Unzipping corpora/movie_reviews.zip.
Finished.
Connors-MacBook-Pro:~ connorfreeberg$ conda install krb5
Fetching package metadata .........
Solving package specifications: .

Package plan for installation in environment /Users/connorfreeberg/anaconda:

The following NEW packages will be INSTALLED:

    bkcharts:                 0.2-py35_0        
    certifi:                  2016.2.28-py35_0  
    krb5:                     1.13.2-0          
    pycodestyle:              2.3.1-py35_0      
    sphinxcontrib:            1.0-py35_0        
    sphinxcontrib-websupport: 1.0.1-py35_0      

The following packages will be UPDATED:

    _license:                 1.1-py36_1         --> 1.1-py35_1           
    alabaster:                0.7.10-py36_0      --> 0.7.10-py35_0        
    anaconda:                 4.4.0-np112py36_0  --> custom-py35_0        
    anaconda-client:          1.6.3-py36_0       --> 1.6.3-py35_0         
    anaconda-navigator:       1.6.2-py36_0       --> 1.6.4-py35_0         
    anaconda-project:         0.6.0-py36_0       --> 0.6.0-py35_0         
    appnope:                  0.1.0-py36_0       --> 0.1.0-py35_0         
    appscript:                1.0.1-py36_0       --> 1.0.1-py35_0         
    asn1crypto:               0.22.0-py36_0      --> 0.22.0-py35_0        
    astroid:                  1.4.9-py36_0       --> 1.5.3-py35_0         
    astropy:                  1.3.2-np112py36_0  --> 2.0.2-py35hcd6dafc_4 
    babel:                    2.4.0-py36_0       --> 2.5.0-py35_0         
    backports:                1.0-py36_0         --> 1.0-py35_0           
    beautifulsoup4:           4.6.0-py36_0       --> 4.6.0-py35_0         
    bitarray:                 0.8.1-py36_0       --> 0.8.1-py35_0         
    blaze:                    0.10.1-py36_0      --> 0.10.1-py35_0        
    bleach:                   1.5.0-py36_0       --> 1.5.0-py35_0         
    bokeh:                    0.12.5-py36_1      --> 0.12.7-py35_0        
    boto:                     2.46.1-py36_0      --> 2.48.0-py35_0        
    bottleneck:               1.2.1-np112py36_0  --> 1.2.1-np113py35_0    
    cffi:                     1.10.0-py36_0      --> 1.10.0-py35_0        
    chardet:                  3.0.3-py36_0       --> 3.0.4-py35_0         
    click:                    6.7-py36_0         --> 6.7-py35_0           
    cloudpickle:              0.2.2-py36_0       --> 0.4.0-py35_0         
    clyent:                   1.2.2-py36_0       --> 1.2.2-py35_0         
    colorama:                 0.3.9-py36_0       --> 0.3.9-py35_0         
    conda:                    4.3.24-py36_0      --> 4.3.30-py35hd530ce9_0
    contextlib2:              0.5.5-py36_0       --> 0.5.5-py35_0         
    cryptography:             1.8.1-py36_0       --> 1.8.1-py35_0         
    cycler:                   0.10.0-py36_0      --> 0.10.0-py35_0        
    cython:                   0.25.2-py36_0      --> 0.26-py35_0          
    cytoolz:                  0.8.2-py36_0       --> 0.8.2-py35_0         
    dask:                     0.14.3-py36_1      --> 0.15.2-py35_0        
    datashape:                0.5.4-py36_0       --> 0.5.4-py35_0         
    decorator:                4.0.11-py36_0      --> 4.1.2-py35_0         
    distributed:              1.16.3-py36_0      --> 1.18.1-py35_0        
    docutils:                 0.13.1-py36_0      --> 0.14-py35_0          
    entrypoints:              0.2.2-py36_1       --> 0.2.3-py35_0         
    et_xmlfile:               1.0.1-py36_0       --> 1.0.1-py35_0         
    fastcache:                1.0.2-py36_1       --> 1.0.2-py35_1         
    flask:                    0.12.2-py36_0      --> 0.12.2-py35_0        
    flask-cors:               3.0.2-py36_0       --> 3.0.3-py35_0         
    get_terminal_size:        1.0.0-py36_0       --> 1.0.0-py35_0         
    gevent:                   1.2.1-py36_0       --> 1.2.2-py35_0         
    greenlet:                 0.4.12-py36_0      --> 0.4.12-py35_0        
    h5py:                     2.7.0-np112py36_0  --> 2.7.0-np113py35_0    
    heapdict:                 1.0.0-py36_1       --> 1.0.0-py35_1         
    html5lib:                 0.999-py36_0       --> 0.9999999-py35_0     
    idna:                     2.5-py36_0         --> 2.6-py35_0           
    imagesize:                0.7.1-py36_0       --> 0.7.1-py35_0         
    ipykernel:                4.6.1-py36_0       --> 4.6.1-py35_0         
    ipython:                  5.3.0-py36_0       --> 6.1.0-py35_0         
    ipython_genutils:         0.2.0-py36_0       --> 0.2.0-py35_0         
    ipywidgets:               6.0.0-py36_0       --> 6.0.0-py35_0         
    isort:                    4.2.5-py36_0       --> 4.2.15-py35_0        
    itsdangerous:             0.24-py36_0        --> 0.24-py35_0          
    jdcal:                    1.3-py36_0         --> 1.3-py35_0           
    jedi:                     0.10.2-py36_2      --> 0.10.2-py35_2        
    jinja2:                   2.9.6-py36_0       --> 2.9.6-py35_0         
    jsonschema:               2.6.0-py36_0       --> 2.6.0-py35_0         
    jupyter:                  1.0.0-py36_3       --> 1.0.0-py35_3         
    jupyter_client:           5.0.1-py36_0       --> 5.1.0-py35_0         
    jupyter_console:          5.1.0-py36_0       --> 5.2.0-py35_0         
    jupyter_core:             4.3.0-py36_0       --> 4.3.0-py35_0         
    lazy-object-proxy:        1.2.2-py36_0       --> 1.3.1-py35_0         
    llvmlite:                 0.18.0-py36_0      --> 0.20.0-py35_0        
    locket:                   0.2.0-py36_1       --> 0.2.0-py35_1         
    lxml:                     3.7.3-py36_0       --> 3.8.0-py35_0         
    markupsafe:               0.23-py36_2        --> 1.0-py35_0           
    matplotlib:               2.0.2-np112py36_0  --> 2.0.2-np113py35_0    
    mistune:                  0.7.4-py36_0       --> 0.7.4-py35_0         
    mkl-service:              1.1.2-py36_3       --> 1.1.2-py35_3         
    mpmath:                   0.19-py36_1        --> 0.19-py35_1          
    msgpack-python:           0.4.8-py36_0       --> 0.4.8-py35_0         
    multipledispatch:         0.4.9-py36_0       --> 0.4.9-py35_0         
    navigator-updater:        0.1.0-py36_0       --> 0.1.0-py35_0         
    nbconvert:                5.1.1-py36_0       --> 5.2.1-py35_0         
    nbformat:                 4.3.0-py36_0       --> 4.4.0-py35_0         
    networkx:                 1.11-py36_0        --> 1.11-py35_0          
    nltk:                     3.2.3-py36_0       --> 3.2.4-py35_0         
    nose:                     1.3.7-py36_1       --> 1.3.7-py35_1         
    notebook:                 5.0.0-py36_0       --> 5.0.0-py35_0         
    numba:                    0.33.0-np112py36_0 --> 0.35.0-np113py35_0   
    numexpr:                  2.6.2-np112py36_0  --> 2.6.2-np113py35_0    
    numpy:                    1.12.1-py36_0      --> 1.13.1-py35_0        
    numpydoc:                 0.6.0-py36_0       --> 0.7.0-py35_0         
    odo:                      0.5.0-py36_1       --> 0.5.1-py35_0         
    olefile:                  0.44-py36_0        --> 0.44-py35_0          
    openpyxl:                 2.4.7-py36_0       --> 2.4.8-py35_0         
    packaging:                16.8-py36_0        --> 16.8-py35_0          
    pandas:                   0.20.1-np112py36_0 --> 0.20.3-py35_0        
    pandocfilters:            1.4.1-py36_0       --> 1.4.2-py35_0         
    partd:                    0.3.8-py36_0       --> 0.3.8-py35_0         
    path.py:                  10.3.1-py36_0      --> 10.3.1-py35_0        
    pathlib2:                 2.2.1-py36_0       --> 2.3.0-py35_0         
    patsy:                    0.4.1-py36_0       --> 0.4.1-py35_0         
    pep8:                     1.7.0-py36_0       --> 1.7.0-py35_0         
    pexpect:                  4.2.1-py36_0       --> 4.2.1-py35_0         
    pickleshare:              0.7.4-py36_0       --> 0.7.4-py35_0         
    pillow:                   4.1.1-py36_0       --> 4.2.1-py35_0         
    pip:                      9.0.1-py36_1       --> 9.0.1-py35_1         
    ply:                      3.10-py36_0        --> 3.10-py35_0          
    prompt_toolkit:           1.0.14-py36_0      --> 1.0.15-py35_0        
    psutil:                   5.2.2-py36_0       --> 5.2.2-py35_0         
    ptyprocess:               0.5.1-py36_0       --> 0.5.2-py35_0         
    py:                       1.4.33-py36_0      --> 1.4.34-py35_0        
    pycosat:                  0.6.2-py36_0       --> 0.6.2-py35_0         
    pycparser:                2.17-py36_0        --> 2.18-py35_0          
    pycrypto:                 2.6.1-py36_6       --> 2.6.1-py35_6         
    pycurl:                   7.43.0-py36_2      --> 7.43.0-py35_2        
    pyflakes:                 1.5.0-py36_0       --> 1.6.0-py35_0         
    pygments:                 2.2.0-py36_0       --> 2.2.0-py35_0         
    pylint:                   1.6.4-py36_1       --> 1.7.2-py35_0         
    pyodbc:                   4.0.16-py36_0      --> 4.0.17-py35_0        
    pyopenssl:                17.0.0-py36_0      --> 17.0.0-py35_0        
    pyparsing:                2.1.4-py36_0       --> 2.2.0-py35_0         
    pyqt:                     5.6.0-py36_1       --> 5.6.0-py35_2         
    pytables:                 3.3.0-np112py36_0  --> 3.4.2-np113py35_0    
    pytest:                   3.0.7-py36_0       --> 3.2.1-py35_0         
    python-dateutil:          2.6.0-py36_0       --> 2.6.1-py35_0         
    python.app:               1.2-py36_4         --> 1.2-py35_4           
    pytz:                     2017.2-py36_0      --> 2017.2-py35_0        
    pywavelets:               0.5.2-np112py36_0  --> 0.5.2-np113py35_0    
    pyyaml:                   3.12-py36_0        --> 3.12-py35_0          
    pyzmq:                    16.0.2-py36_0      --> 16.0.2-py35_0        
    qtawesome:                0.4.4-py36_0       --> 0.4.4-py35_0         
    qtconsole:                4.3.0-py36_0       --> 4.3.1-py35_0         
    qtpy:                     1.2.1-py36_0       --> 1.3.1-py35_0         
    requests:                 2.14.2-py36_0      --> 2.14.2-py35_0        
    rope:                     0.9.4-py36_1       --> 0.9.4-py35_1         
    ruamel_yaml:              0.11.14-py36_1     --> 0.11.14-py35_1       
    scikit-image:             0.13.0-np112py36_0 --> 0.13.0-np113py35_0   
    scikit-learn:             0.18.1-np112py36_1 --> 0.19.0-np113py35_0   
    scipy:                    0.19.0-np112py36_0 --> 0.19.1-np113py35_0   
    seaborn:                  0.7.1-py36_0       --> 0.8-py35_0           
    setuptools:               27.2.0-py36_0      --> 36.4.0-py35_1        
    simplegeneric:            0.8.1-py36_1       --> 0.8.1-py35_1         
    singledispatch:           3.4.0.3-py36_0     --> 3.4.0.3-py35_0       
    sip:                      4.18-py36_0        --> 4.18-py35_0          
    six:                      1.10.0-py36_0      --> 1.10.0-py35_0        
    snowballstemmer:          1.2.1-py36_0       --> 1.2.1-py35_0         
    sortedcollections:        0.5.3-py36_0       --> 0.5.3-py35_0         
    sortedcontainers:         1.5.7-py36_0       --> 1.5.7-py35_0         
    sphinx:                   1.5.6-py36_0       --> 1.6.3-py35_0         
    spyder:                   3.1.4-py36_0       --> 3.2.3-py35_0         
    sqlalchemy:               1.1.9-py36_0       --> 1.1.13-py35_0        
    statsmodels:              0.8.0-np112py36_0  --> 0.8.0-np113py35_0    
    sympy:                    1.0-py36_0         --> 1.1.1-py35_0         
    tblib:                    1.3.2-py36_0       --> 1.3.2-py35_0         
    terminado:                0.6-py36_0         --> 0.6-py35_0           
    testpath:                 0.3-py36_0         --> 0.3.1-py35_0         
    toolz:                    0.8.2-py36_0       --> 0.8.2-py35_0         
    tornado:                  4.5.1-py36_0       --> 4.5.2-py35_0         
    traitlets:                4.3.2-py36_0       --> 4.3.2-py35_0         
    unicodecsv:               0.14.1-py36_0      --> 0.14.1-py35_0        
    wcwidth:                  0.1.7-py36_0       --> 0.1.7-py35_0         
    werkzeug:                 0.12.2-py36_0      --> 0.12.2-py35_0        
    wheel:                    0.29.0-py36_0      --> 0.29.0-py35_0        
    widgetsnbextension:       2.0.0-py36_0       --> 3.0.2-py35_0         
    wrapt:                    1.10.10-py36_0     --> 1.10.11-py35_0       
    xlrd:                     1.0.0-py36_0       --> 1.1.0-py35_0         
    xlsxwriter:               0.9.6-py36_0       --> 0.9.8-py35_0         
    xlwings:                  0.10.4-py36_0      --> 0.11.4-py35_0        
    xlwt:                     1.2.0-py36_0       --> 1.3.0-py35_0         
    zict:                     0.1.2-py36_0       --> 0.1.2-py35_0         

The following packages will be DOWNGRADED:

    python:                   3.6.1-2            --> 3.5.4-0              

Proceed ([y]/n)? n

Exiting

Connors-MacBook-Pro:~ connorfreeberg$ conda install install libssh2 python=3.6
Fetching package metadata .........

PackageNotFoundError: Packages missing in current channels:

  - install

We have searched for the packages in the following channels:

  - https://repo.continuum.io/pkgs/free/osx-64
  - https://repo.continuum.io/pkgs/free/noarch
  - https://repo.continuum.io/pkgs/r/osx-64
  - https://repo.continuum.io/pkgs/r/noarch
  - https://repo.continuum.io/pkgs/pro/osx-64
  - https://repo.continuum.io/pkgs/pro/noarch

Connors-MacBook-Pro:~ connorfreeberg$ conda install libssh2 python=3.6
Fetching package metadata .........
Solving package specifications: .

Package plan for installation in environment /Users/connorfreeberg/anaconda:

The following NEW packages will be INSTALLED:

    libssh2:  1.8.0-0          

The following packages will be UPDATED:

    anaconda: 4.4.0-np112py36_0 --> custom-py36_0        
    conda:    4.3.24-py36_0     --> 4.3.30-py36h173c244_0
    python:   3.6.1-2           --> 3.6.2-0              

Proceed ([y]/n)? y

libssh2-1.8.0- 100% |################################| Time: 0:00:00   4.00 MB/s
python-3.6.2-0 100% |################################| Time: 0:00:00  15.78 MB/s
anaconda-custo 100% |################################| Time: 0:00:00   2.82 MB/s
conda-4.3.30-p 100% |################################| Time: 0:00:00  14.05 MB/s
Connors-MacBook-Pro:~ connorfreeberg$ conda install krb5
Fetching package metadata ...........
Solving package specifications: .

Package plan for installation in environment /Users/connorfreeberg/anaconda:

The following NEW packages will be INSTALLED:

    ca-certificates: 2017.08.26-ha1e5d58_0  
    krb5:            1.14.2-h9a779f2_6      
    libcxx:          4.0.1-h579ed51_0       
    libcxxabi:       4.0.1-hebd6815_0       
    libedit:         3.1-hb4e282d_0         
    libgfortran:     3.0.1-h93005f0_2       
    llvm-openmp:     4.0.1-hda82c8b_0       
    r-cvst:          0.2_1-r342hce93a4b_0   
    r-ddalpha:       1.3.1-r342h4276367_0   
    r-deoptimr:      1.0_8-r342h88b17ca_0   
    r-dimred:        0.1.0-r342hcdfbb48_0   
    r-drr:           0.0.2-r342h1687f97_0   
    r-gower:         0.1.2-r342h52ab46c_0   
    r-ipred:         0.9_6-r342hca986ca_0   
    r-kernlab:       0.9_25-r342h16d16b8_0  
    r-lava:          1.5.1-r342h38a1d13_0   
    r-numderiv:      2016.8_1-r342ha7fd6f4_0
    r-prodlim:       1.6.1-r342h1e7dc4e_0   
    r-rcpproll:      0.2.2-r342h72fe326_0   
    r-recipes:       0.1.0-r342h9fa1523_0   
    r-robustbase:    0.92_7-r342h0705e89_0  
    r-sfsmisc:       1.1_1-r342hd831c0a_0   
    r-tidyselect:    0.2.2-r342h4fcf255_0   
    r-timedate:      3012.100-r342h8f8ad6e_4
    r-viridislite:   0.2.0-r342h93fb38b_0   
    r-withr:         2.0.0-r342hd7b5462_0   

The following packages will be UPDATED:

    conda:           4.3.30-py36h173c244_0   --> 4.4.6-py36_0            
    icu:             54.1-0                  --> 58.2-h4b95b61_1         
    libpng:          1.6.27-0                --> 1.6.32-hd1e8b91_4       
    libtiff:         4.0.6-3                 --> 4.0.9-h0dac147_0        
    ncurses:         5.9-10                  --> 6.0-hd04f020_2          
    openssl:         1.0.2l-0                --> 1.0.2n-hdbc3d79_0       
    pycosat:         0.6.2-py36_0            --> 0.6.3-py36hee92d8f_0    
    python:          3.6.2-0                 --> 3.6.4-hc167b69_0        
    qt:              5.6.2-2                 --> 5.6.2-h9975529_14       
    r-assertthat:    0.2.0-r3.4.1_0          --> 0.2.0-r342hacfac53_0    
    r-backports:     1.1.0-r3.4.1_0          --> 1.1.1-r342h894203a_0    
    r-base:          3.4.1-0                 --> 3.4.2-hc151561_0        
    r-base64enc:     0.1_3-r3.4.1_0          --> 0.1_3-r342h0880998_4    
    r-bh:            1.62.0_1-r3.4.1_0       --> 1.65.0_1-r342hc3f23d0_0 
    r-bindr:         0.1-r3.4.1_0            --> 0.1-r342hb4d41c9_0      
    r-bindrcpp:      0.2-r3.4.1_0            --> 0.2-r342h94b3c25_0      
    r-bitops:        1.0_6-r3.4.1_2          --> 1.0_6-r342he7499e7_4    
    r-boot:          1.3_19-r3.4.1_0         --> 1.3_20-r342hfe7f006_0   
    r-broom:         0.4.2-r3.4.1_0          --> 0.4.2-r342hfe0d134_0    
    r-car:           2.1_4-r3.4.1_0          --> 2.1_5-r342hdd1e3e0_0    
    r-caret:         6.0_76-r3.4.1_0         --> 6.0_77-r342h513a81f_0   
    r-catools:       1.17.1-r3.4.1_2         --> 1.17.1-r342hb039934_4   
    r-cellranger:    1.1.0-r3.4.1_0          --> 1.1.0-r342h50a9fb7_0    
    r-class:         7.3_14-r3.4.1_0         --> 7.3_14-r342h43a4a0f_4   
    r-cluster:       2.0.6-r3.4.1_0          --> 2.0.6-r342h26ab8c6_0    
    r-codetools:     0.2_15-r3.4.1_0         --> 0.2_15-r342h7db7eef_0   
    r-colorspace:    1.3_2-r3.4.1_0          --> 1.3_2-r342h18bddb6_0    
    r-crayon:        1.3.2-r3.4.1_0          --> 1.3.4-r342hdefe7e4_0    
    r-curl:          2.6-r3.4.1_0            --> 3.0-r342ha80850a_0      
    r-data.table:    1.10.4-r3.4.1_0         --> 1.10.4_1-r342he1ac18a_0 
    r-dbi:           0.6_1-r3.4.1_0          --> 0.7-r342h6aefa47_0      
    r-dichromat:     2.0_0-r3.4.1_2          --> 2.0_0-r342hcb53b06_4    
    r-digest:        0.6.12-r3.4.1_0         --> 0.6.12-r342h7ffa501_0   
    r-dplyr:         0.7.0-r3.4.1_0          --> 0.7.4-r342hd462e57_0    
    r-essentials:    1.6.0-r3.4.1_0          --> 1.7.0-r342h8f48fb2_0    
    r-evaluate:      0.10-r3.4.1_0           --> 0.10.1-r342h084298f_0   
    r-forcats:       0.2.0-r3.4.1_0          --> 0.2.0-r342hfffa16c_0    
    r-foreach:       1.4.3-r3.4.1_0          --> 1.4.3-r342he26c63b_4    
    r-foreign:       0.8_68-r3.4.1_0         --> 0.8_69-r342hd19c61e_0   
    r-formatr:       1.5-r3.4.1_0            --> 1.5-r342h8f6a739_0      
    r-ggplot2:       2.2.1-r3.4.1_0          --> 2.2.1-r342hab9d682_0    
    r-gistr:         0.4.0-r3.4.1_0          --> 0.4.0-r342h701b2b4_0    
    r-glmnet:        2.0_10-r3.4.1_0         --> 2.0_13-r342h4f2bcf4_0   
    r-glue:          1.1.1-r3.4.1_0          --> 1.1.1-r342hfa53b3f_0    
    r-gtable:        0.2.0-r3.4.1_0          --> 0.2.0-r342h50414d9_0    
    r-haven:         1.0.0-r3.4.1_0          --> 1.1.0-r342h706d249_0    
    r-hexbin:        1.27.1-r3.4.1_0         --> 1.27.1-r342h5ebf162_4   
    r-highr:         0.6-r3.4.1_0            --> 0.6-r342h042980c_0      
    r-hms:           0.3-r3.4.1_0            --> 0.3-r342hdcc9ba2_0      
    r-htmltools:     0.3.6-r3.4.1_0          --> 0.3.6-r342h6918481_0    
    r-htmlwidgets:   0.8-r3.4.1_1            --> 0.9-r342h3fbdbc0_0      
    r-httpuv:        1.3.3-r3.4.1_0          --> 1.3.5-r342hf739786_0    
    r-httr:          1.2.1-r3.4.1_0          --> 1.3.1-r342h7338272_0    
    r-irdisplay:     0.4.4-r3.4.1_0          --> 0.4.4-r342h7974c32_0    
    r-irkernel:      0.7.1-r3.4.1_0          --> 0.8.9-r342hb51cc2a_0    
    r-iterators:     1.0.8-r3.4.1_0          --> 1.0.8-r342h797f5cf_4    
    r-jsonlite:      1.5-r3.4.1_0            --> 1.5-r342h0df1ae0_0      
    r-kernsmooth:    2.23_15-r3.4.1_0        --> 2.23_15-r342hf8f9fa8_4  
    r-knitr:         1.16-r3.4.1_0           --> 1.17-r342h398035c_0     
    r-labeling:      0.3-r3.4.1_2            --> 0.3-r342h3f609a7_4      
    r-lattice:       0.20_35-r3.4.1_0        --> 0.20_35-r342he33934a_0  
    r-lazyeval:      0.2.0-r3.4.1_0          --> 0.2.0-r342hda2787d_0    
    r-lme4:          1.1_13-r3.4.1_0         --> 1.1_14-r342h0f4512c_0   
    r-lubridate:     1.6.0-r3.4.1_0          --> 1.6.0-r342h21d6fc3_0    
    r-magrittr:      1.5-r3.4.1_2            --> 1.5-r342hc800aed_4      
    r-maps:          3.2.0-r3.4.1_0          --> 3.2.0-r342hfd4408e_0    
    r-markdown:      0.8-r3.4.1_0            --> 0.8-r342hfbdeedd_0      
    r-mass:          7.3_47-r3.4.1_0         --> 7.3_47-r342h998d679_0   
    r-matrix:        1.2_10-r3.4.1_0         --> 1.2_11-r342hb831790_0   
    r-matrixmodels:  0.4_1-r3.4.1_0          --> 0.4_1-r342h36cb0dc_4    
    r-mgcv:          1.8_17-r3.4.1_0         --> 1.8_22-r342hf92f93b_0   
    r-mime:          0.5-r3.4.1_0            --> 0.5-r342h0f88ab8_0      
    r-minqa:         1.2.4-r3.4.1_2          --> 1.2.4-r342h0106cc3_4    
    r-mnormt:        1.5_5-r3.4.1_0          --> 1.5_5-r342h42fb15d_0    
    r-modelmetrics:  1.1.0-r3.4.1_0          --> 1.1.0-r342hab8440a_0    
    r-modelr:        0.1.0-r3.4.1_0          --> 0.1.1-r342h8b7c8fd_0    
    r-munsell:       0.4.3-r3.4.1_0          --> 0.4.3-r342h51b9f01_0    
    r-nlme:          3.1_131-r3.4.1_0        --> 3.1_131-r342hbc0088b_0  
    r-nloptr:        1.0.4-r3.4.1_2          --> 1.0.4-r342hfa8e0b4_4    
    r-nnet:          7.3_12-r3.4.1_0         --> 7.3_12-r342hf39805f_0   
    r-openssl:       0.9.6-r3.4.1_0          --> 0.9.7-r342hf1585dd_0    
    r-packrat:       0.4.8_1-r3.4.1_0        --> 0.4.8_1-r342h0db0e49_0  
    r-pbdzmq:        0.2_6-r3.4.1_0          --> 0.2_6-r342h9ee0924_0    
    r-pbkrtest:      0.4_7-r3.4.1_0          --> 0.4_7-r342h8b3686e_0    
    r-pkgconfig:     2.0.1-r3.4.1_0          --> 2.0.1-r342h037cecb_0    
    r-pki:           0.1_3-r3.4.1_0          --> 0.1_5.1-r342hcf715fe_0  
    r-plogr:         0.1_1-r3.4.1_0          --> 0.1_1-r342he1be899_0    
    r-plyr:          1.8.4-r3.4.1_0          --> 1.8.4-r342h66d2667_0    
    r-pryr:          0.1.2-r3.4.1_0          --> 0.1.2-r342ha062742_0    
    r-psych:         1.7.5-r3.4.1_0          --> 1.7.8-r342he3dbd94_0    
    r-purrr:         0.2.2.2-r3.4.1_0        --> 0.2.3-r342h7646bf1_0    
    r-quantmod:      0.4_9-r3.4.1_0          --> 0.4_11-r342ha084b29_0   
    r-quantreg:      5.33-r3.4.1_0           --> 5.33-r342h3078735_0     
    r-r6:            2.2.1-r3.4.1_0          --> 2.2.2-r342hd083555_0    
    r-randomforest:  4.6_12-r3.4.1_0         --> 4.6_12-r342h0f92a3f_4   
    r-rbokeh:        0.5.0-r3.4.1_0          --> 0.5.0-r342h999a230_0    
    r-rcpp:          0.12.11-r3.4.1_0        --> 0.12.13-r342hd23d99a_0  
    r-rcppeigen:     0.3.3.3.0-r3.4.1_0      --> 0.3.3.3.0-r342h43294b0_0
    r-rcurl:         1.95_4.8-r3.4.1_0       --> 1.95_4.8-r342h15ade9d_0 
    r-readr:         1.1.1-r3.4.1_0          --> 1.1.1-r342h26b7cb6_0    
    r-readxl:        1.0.0-r3.4.1_0          --> 1.0.0-r342h7fee92c_0    
    r-recommended:   3.4.1-r3.4.1_0          --> 3.4.2-h1751db4_0        
    r-rematch:       1.0.1-r3.4.1_0          --> 1.0.1-r342he4866fc_0    
    r-repr:          0.10-r3.4.1_0           --> 0.12.0-r342hbf08d7a_0   
    r-reshape2:      1.4.2-r3.4.1_0          --> 1.4.2-r342h4e0c23c_0    
    r-rjsonio:       1.3_0-r3.4.1_2          --> 1.3_0-r342h3e65b66_4    
    r-rlang:         0.1.1-r3.4.1_0          --> 0.1.2-r342h6f7de11_0    
    r-rmarkdown:     1.5-r3.4.1_0            --> 1.6-r342hccf1f8e_2      
    r-rpart:         4.1_11-r3.4.1_0         --> 4.1_11-r342h056d3ea_0   
    r-rprojroot:     1.2-r3.4.1_0            --> 1.2-r342h961df13_0      
    r-rsconnect:     0.8-r3.4.1_0            --> 0.8.5-r342hdc95913_0    
    r-rstudioapi:    0.6-r3.4.1_0            --> 0.7-r342hf20c2a2_0      
    r-rvest:         0.3.2-r3.4.1_0          --> 0.3.2-r342h498b3d2_0    
    r-scales:        0.4.1-r3.4.1_0          --> 0.5.0-r342h4ec2787_0    
    r-selectr:       0.3_1-r3.4.1_0          --> 0.3_1-r342h1005dde_0    
    r-shiny:         1.0.3-r3.4.1_0          --> 1.0.5-r342hb27b129_0    
    r-sourcetools:   0.1.6-r3.4.1_0          --> 0.1.6-r342h35ff172_0    
    r-sparsem:       1.77-r3.4.1_0           --> 1.77-r342h74fc79b_0     
    r-spatial:       7.3_11-r3.4.1_0         --> 7.3_11-r342h4b9b681_4   
    r-stringi:       1.1.5-r3.4.1_0          --> 1.1.5-r342ha83ea67_0    
    r-stringr:       1.2.0-r3.4.1_0          --> 1.2.0-r342h61359ef_0    
    r-survival:      2.41_3-r3.4.1_0         --> 2.41_3-r342h7e0d132_0   
    r-tibble:        1.3.3-r3.4.1_0          --> 1.3.4-r342h9aabc0a_0    
    r-tidyr:         0.6.3-r3.4.1_0          --> 0.7.1-r342h953b3d9_0    
    r-tidyverse:     1.1.1-r3.4.1_0          --> 1.1.1-r342hf375f76_0    
    r-ttr:           0.23_1-r3.4.1_0         --> 0.23_2-r342h9ffbca2_0   
    r-uuid:          0.1_2-r3.4.1_0          --> 0.1_2-r342h22fb745_4    
    r-xml2:          1.1.1-r3.4.1_0          --> 1.1.1-r342h289a617_0    
    r-xtable:        1.8_2-r3.4.1_0          --> 1.8_2-r342hb9d8108_0    
    r-xts:           0.9_7-r3.4.1_2          --> 0.10_0-r342h37a3a43_4   
    r-yaml:          2.1.14-r3.4.1_0         --> 2.1.14-r342he3890bd_0   
    r-zoo:           1.8_0-r3.4.1_0          --> 1.8_0-r342hf4683db_0    
    readline:        6.2-2                   --> 7.0-hc1231fa_4          
    sqlite:          3.13.0-0                --> 3.20.1-h7e4c145_2       
    tk:              8.5.18-0                --> 8.6.7-h35a86e2_3        
    xz:              5.2.2-1                 --> 5.2.3-h0278029_2        
    zlib:            1.2.8-3                 --> 1.2.11-hf3cbc9b_2       

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

    conda-env:       2.6.0-0                 --> 2.6.0-h36134e3_0        

The following packages will be DOWNGRADED:

    r-rcolorbrewer:  1.1_2-r3.4.1_3          --> 1.1_2-r342h009296c_0    

Proceed ([y]/n)? y

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Connors-MacBook-Pro:~ connorfreeberg$ 
Connors-MacBook-Pro:~ connorfreeberg$ conda update r-essentials rstudio
Solving environment: done

## Package Plan ##

  environment location: /Users/connorfreeberg/anaconda

  added / updated specs: 
    - r-essentials
    - rstudio

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    r-blob-1.1.0               |   r342h4b1ee69_0          18 KB
    libntlm-1.4                |       hb1fe7e8_1          31 KB
    r-rjdbc-0.2_5              |   r342hbfbe204_0          77 KB
    cyrus-sasl-2.1.26          |       ha054001_1         238 KB
    r-rjava-0.9_9              |   r342h988b9d2_0         556 KB
    r-mongolite-1.2            |   r342hfcc6d1d_0         253 KB
    r-profvis-0.3.3            |   r342hccd696e_0         146 KB
    r-dbplyr-1.1.0             |   r342h9881601_0         299 KB
    fonts-anaconda-1           |       h8fa9717_0           2 KB
    r-miniui-0.1.1             |   r342hdb62d8b_0          32 KB
    r-odbc-1.1.2               |   r342h198ff3f_0         403 KB
    rstudio-1.1.383            |       h4814094_2        30.0 MB
    r-rappdirs-0.3.1           |   r342hb97dc51_0          83 KB
    r-bit-1.1_12               |   r342hf8cc2cf_0         229 KB
    r-sparklyr-0.6.3           |   r342h4912c76_0         1.4 MB
    r-config-0.2               |   r342ha2bb319_0          25 KB
    r-bit64-0.9_7              |   r342h1cba8d6_0         472 KB
    ------------------------------------------------------------
                                           Total:        34.2 MB

The following NEW packages will be INSTALLED:

    cyrus-sasl:     2.1.26-ha054001_1    
    fonts-anaconda: 1-h8fa9717_0         
    libntlm:        1.4-hb1fe7e8_1       
    r-bit:          1.1_12-r342hf8cc2cf_0
    r-bit64:        0.9_7-r342h1cba8d6_0 
    r-blob:         1.1.0-r342h4b1ee69_0 
    r-config:       0.2-r342ha2bb319_0   
    r-dbplyr:       1.1.0-r342h9881601_0 
    r-miniui:       0.1.1-r342hdb62d8b_0 
    r-mongolite:    1.2-r342hfcc6d1d_0   
    r-odbc:         1.1.2-r342h198ff3f_0 
    r-profvis:      0.3.3-r342hccd696e_0 
    r-rappdirs:     0.3.1-r342hb97dc51_0 
    r-rjava:        0.9_9-r342h988b9d2_0 
    r-rjdbc:        0.2_5-r342hbfbe204_0 
    r-sparklyr:     0.6.3-r342h4912c76_0 

The following packages will be UPDATED:

    rstudio:        1.0.136-1             --> 1.1.383-h4814094_2

Proceed ([y]/n)? y

Downloading and Extracting Packages
r-blob 1.1.0: ########################################################## | 100% 
libntlm 1.4: ########################################################### | 100% 
r-rjdbc 0.2_5: ######################################################### | 100% 
cyrus-sasl 2.1.26: ##################################################### | 100% 
r-rjava 0.9_9: ######################################################### | 100% 
r-mongolite 1.2: ####################################################### | 100% 
r-profvis 0.3.3: ####################################################### | 100% 
r-dbplyr 1.1.0: ######################################################## | 100% 
fonts-anaconda 1: ###################################################### | 100% 
r-miniui 0.1.1: ######################################################## | 100% 
r-odbc 1.1.2: ########################################################## | 100% 
rstudio 1.1.383: ####################################################### | 100% 
r-rappdirs 0.3.1: ###################################################### | 100% 
r-bit 1.1_12: ########################################################## | 100% 
r-sparklyr 0.6.3: ###################################################### | 100% 
r-config 0.2: ########################################################## | 100% 
r-bit64 0.9_7: ######################################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Connors-MacBook-Pro:~ connorfreeberg$ install.packages(igraph)
-bash: syntax error near unexpected token `igraph'
Connors-MacBook-Pro:~ connorfreeberg$ install.packages('igraph')
-bash: syntax error near unexpected token `'igraph''
Connors-MacBook-Pro:~ connorfreeberg$ install.package('igraph')
-bash: syntax error near unexpected token `'igraph''
Connors-MacBook-Pro:~ connorfreeberg$ conda update conda
Solving environment: done

# All requested packages already installed.

Connors-MacBook-Pro:~ connorfreeberg$ conda
usage: conda [-h] [-V] command ...

conda is a tool for managing and deploying applications, environments and packages.

Options:

positional arguments:
  command
    clean        Remove unused packages and caches.
    config       Modify configuration values in .condarc. This is modeled
                 after the git config command. Writes to the user .condarc
                 file (/Users/connorfreeberg/.condarc) by default.
    create       Create a new conda environment from a list of specified
                 packages.
    help         Displays a list of available conda commands and their help
                 strings.
    info         Display information about current conda install.
    install      Installs a list of packages into a specified conda
                 environment.
    list         List linked packages in a conda environment.
    package      Low-level conda package utility. (EXPERIMENTAL)
    remove       Remove a list of packages from a specified conda environment.
    uninstall    Alias for conda remove. See conda remove --help.
    search       Search for packages and display associated information. The
                 input is a MatchSpec, a query language for conda packages.
                 See examples below.
    update       Updates conda packages to the latest compatible version. This
                 command accepts a list of package names and updates them to
                 the latest versions that are compatible with all other
                 packages in the environment. Conda attempts to install the
                 newest versions of the requested packages. To accomplish
                 this, it may update some packages that are already installed,
                 or install additional packages. To prevent existing packages
                 from updating, use the --no-update-deps option. This may
                 force conda to install older versions of the requested
                 packages, and it does not prevent additional dependency
                 packages from being installed. If you wish to skip dependency
                 checking altogether, use the '--force' option. This may
                 result in an environment with incompatible packages, so this
                 option must be used with great caution.
    upgrade      Alias for conda update. See conda update --help.

optional arguments:
  -h, --help     Show this help message and exit.
  -V, --version  Show the conda version number and exit.

conda commands available from other packages:
  env
  server
Connors-MacBook-Pro:~ connorfreeberg$ rstudio version

Connors-MacBook-Pro:~ connorfreeberg$
mingwandroid commented 6 years ago

There are a few distinct problems here.

  1. Your dialog from Anaconda Navigator is a new bug since conda 4.4 what I believe will be fixed very soon (ping @goanpeca).

  2. You used conda install install, there's no package called install, I think you did not mean to type install twice.

  3. You have entered a command meant for the R interpreter into your bash prompt: install.packages(igraph). Here you should prefer to install conda R packages when available; from the bash prompt: conda install r-igraph. For R packages not available as conda packages you should launch R before entering install.packages(package). You should install various development tools from conda before trying to use install.packages though, in particular clangxx_osx-64.

goanpeca commented 6 years ago

Your dialog from Anaconda Navigator is a new bug since conda 4.4 what I believe will be fixed very soon (ping @goanpeca).

Yes, 1.6.12 version which fixes this will be released soon!

goanpeca commented 6 years ago

Please remember to update to the latest version of Navigator to include the latest fixes.

Open a terminal (on Linux or Mac) or the Anaconda Command Prompt (on windows) and type:

conda update conda
conda update anaconda-navigator
conda update navigator-updater