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Unable to install RStudio #10368

Open knzudgt opened 5 years ago

knzudgt commented 5 years ago

Actual Behavior

I am on a Ubuntu 14.04 LTS 64 bit machine. I tried to install RStudio from anaconda navigator but failed. The first time I received error messages and the installation process stopped. The second time the installation process got stuck and I had to close the navigator. However there was a python process that was still running in the background that was taking 100% of cpu. I had to restart the machine. I updated anaconda from 1.8.7 to 1.9.2 and retried to install RStudio but failed again: still the installation process gets stuck and after one hour I had to quit anaconda navigator.

Expected Behavior

anaconda should install RStudio

Steps to Reproduce

# I run the following script to add anaconda to PATH
#!/bin/bash

export PATH="/home/marco/anaconda3/bin:$PATH"
echo "Conda is activated"

# Then I launch anacona navigator from terminal
$ anaconda-navigator

# Finally from the navigator I click on 'install' below the RStudio icon
Anaconda or Miniconda version:

1.9.2

Operating System:

Ubuntu 14.04 LTS 64 bit

conda info
marco@SATELLITE-L50-A-161:~ $ conda info

     active environment : None
       user config file : /home/marco/.condarc
 populated config files : /home/marco/.condarc
          conda version : 4.5.11
    conda-build version : 3.10.5
         python version : 3.6.5.final.0
       base environment : /home/marco/anaconda3  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/linux-64
                          https://repo.anaconda.com/pkgs/pro/noarch
          package cache : /home/marco/anaconda3/pkgs
                          /home/marco/.conda/pkgs
       envs directories : /home/marco/anaconda3/envs
                          /home/marco/.conda/envs
               platform : linux-64
             user-agent : conda/4.5.11 requests/2.18.4 CPython/3.6.5 Linux/4.4.0-139-generic ubuntu/14.04 glibc/2.19
                UID:GID : 1000:1000
             netrc file : /home/marco/.netrc
           offline mode : False
conda list --show-channel-urls
marco@SATELLITE-L50-A-161:~ $ conda list --show-channel-urls
# packages in environment at /home/marco/anaconda3:
#
# Name                    Version                   Build  Channel
_ipyw_jlab_nb_ext_conf    0.1.0            py36he11e457_0    defaults
alabaster                 0.7.10           py36h306e16b_0    defaults
anaconda                  5.2.0                    py36_3    defaults
anaconda-client           1.6.14                   py36_0    defaults
anaconda-navigator        1.9.2                    py36_0    defaults
anaconda-project          0.8.2            py36h44fb852_0    defaults
asn1crypto                0.24.0                   py36_0    defaults
astroid                   1.6.3                    py36_0    defaults
astropy                   3.0.2            py36h3010b51_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              py36hfa02d7e_1    defaults
backports.shutil_get_terminal_size 1.0.0            py36hfea85ff_2    defaults
beautifulsoup4            4.6.0            py36h49b8c8c_1    defaults
bitarray                  0.8.1            py36h14c3975_1    defaults
bkcharts                  0.2              py36h735825a_0    defaults
blas                      1.0                         mkl    defaults
blaze                     0.11.3           py36h4e06776_0    defaults
bleach                    2.1.3                    py36_0    defaults
blosc                     1.14.3               hdbcaa40_0    defaults
bokeh                     0.12.16                  py36_0    defaults
boto                      2.48.0           py36h6e4cd66_1    defaults
bottleneck                1.2.1            py36haac1ea0_0    defaults
bzip2                     1.0.6                h14c3975_5    defaults
ca-certificates           2018.03.07                    0    defaults
cairo                     1.14.12              h7636065_2    defaults
certifi                   2018.4.16                py36_0    defaults
cffi                      1.11.5           py36h9745a5d_0    defaults
chardet                   3.0.4            py36h0f667ec_1    defaults
click                     6.7              py36h5253387_0    defaults
cloudpickle               0.5.3                    py36_0    defaults
clyent                    1.2.2            py36h7e57e65_1    defaults
colorama                  0.3.9            py36h489cec4_0    defaults
conda                     4.5.11                   py36_0    defaults
conda-build               3.10.5                   py36_0    defaults
conda-env                 2.6.0                h36134e3_1    defaults
conda-verify              2.0.0            py36h98955d8_0    defaults
contextlib2               0.5.5            py36h6c84a62_0    defaults
cryptography              2.2.2            py36h14c3975_0    defaults
curl                      7.60.0               h84994c4_0    defaults
cycler                    0.10.0           py36h93f1223_0    defaults
cython                    0.28.2           py36h14c3975_0    defaults
cytoolz                   0.9.0.1          py36h14c3975_0    defaults
dask                      0.17.5                   py36_0    defaults
dask-core                 0.17.5                   py36_0    defaults
datashape                 0.5.4            py36h3ad6b5c_0    defaults
dbus                      1.13.2               h714fa37_1    defaults
decorator                 4.3.0                    py36_0    defaults
distributed               1.21.8                   py36_0    defaults
docutils                  0.14             py36hb0f60f5_0    defaults
entrypoints               0.2.3            py36h1aec115_2    defaults
et_xmlfile                1.0.1            py36hd6bccc3_0    defaults
expat                     2.2.5                he0dffb1_0    defaults
fastcache                 1.0.2            py36h14c3975_2    defaults
filelock                  3.0.4                    py36_0    defaults
flask                     1.0.2                    py36_1    defaults
flask-cors                3.0.4                    py36_0    defaults
fontconfig                2.12.6               h49f89f6_0    defaults
freetype                  2.8                  hab7d2ae_1    defaults
get_terminal_size         1.0.0                haa9412d_0    defaults
gevent                    1.3.0            py36h14c3975_0    defaults
glib                      2.56.1               h000015b_0    defaults
glob2                     0.6              py36he249c77_0    defaults
gmp                       6.1.2                h6c8ec71_1    defaults
gmpy2                     2.0.8            py36hc8893dd_2    defaults
graphite2                 1.3.11               h16798f4_2    defaults
greenlet                  0.4.13           py36h14c3975_0    defaults
gst-plugins-base          1.14.0               hbbd80ab_1    defaults
gstreamer                 1.14.0               hb453b48_1    defaults
h5py                      2.7.1            py36ha1f6525_2    defaults
harfbuzz                  1.7.6                h5f0a787_1    defaults
hdf5                      1.10.2               hba1933b_1    defaults
heapdict                  1.0.0                    py36_2    defaults
html5lib                  1.0.1            py36h2f9c1c0_0    defaults
icu                       58.2                 h9c2bf20_1    defaults
idna                      2.6              py36h82fb2a8_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            py36hb52b0d5_0    defaults
ipywidgets                7.2.1                    py36_0    defaults
isort                     4.3.4                    py36_0    defaults
itsdangerous              0.24             py36h93cc618_1    defaults
jbig                      2.1                  hdba287a_0    defaults
jdcal                     1.4                      py36_0    defaults
jedi                      0.12.0                   py36_1    defaults
jinja2                    2.10             py36ha16c418_0    defaults
jpeg                      9b                   h024ee3a_2    defaults
jsonschema                2.6.0            py36h006f8b5_0    defaults
jupyter                   1.0.0                    py36_4    defaults
jupyter_client            5.2.3                    py36_0    defaults
jupyter_console           5.2.0            py36he59e554_1    defaults
jupyter_core              4.4.0            py36h7c827e3_0    defaults
jupyterlab                0.32.1                   py36_0    defaults
jupyterlab_launcher       0.10.5                   py36_0    defaults
kiwisolver                1.0.1            py36h764f252_0    defaults
lazy-object-proxy         1.3.1            py36h10fcdad_0    defaults
libcurl                   7.60.0               h1ad7b7a_0    defaults
libedit                   3.1.20170329         h6b74fdf_2    defaults
libffi                    3.2.1                hd88cf55_4    defaults
libgcc-ng                 7.2.0                hdf63c60_3    defaults
libgfortran-ng            7.2.0                hdf63c60_3    defaults
libpng                    1.6.34               hb9fc6fc_0    defaults
libsodium                 1.0.16               h1bed415_0    defaults
libssh2                   1.8.0                h9cfc8f7_4    defaults
libstdcxx-ng              7.2.0                hdf63c60_3    defaults
libtiff                   4.0.9                he85c1e1_1    defaults
libtool                   2.4.6                h544aabb_3    defaults
libxcb                    1.13                 h1bed415_1    defaults
libxml2                   2.9.8                h26e45fe_1    defaults
libxslt                   1.1.32               h1312cb7_0    defaults
llvmlite                  0.23.1           py36hdbcaa40_0    defaults
locket                    0.2.0            py36h787c0ad_1    defaults
lxml                      4.2.1            py36h23eabaa_0    defaults
lzo                       2.10                 h49e0be7_2    defaults
markupsafe                1.0              py36hd9260cd_1    defaults
matplotlib                2.2.2            py36h0e671d2_1    defaults
mccabe                    0.6.1            py36h5ad9710_1    defaults
mistune                   0.8.3            py36h14c3975_1    defaults
mkl                       2018.0.2                      1    defaults
mkl-service               1.1.2            py36h17a0993_4    defaults
mkl_fft                   1.0.1            py36h3010b51_0    defaults
mkl_random                1.0.1            py36h629b387_0    defaults
more-itertools            4.1.0                    py36_0    defaults
mpc                       1.0.3                hec55b23_5    defaults
mpfr                      3.1.5                h11a74b3_2    defaults
mpmath                    1.0.0            py36hfeacd6b_2    defaults
msgpack-python            0.5.6            py36h6bb024c_0    defaults
multipledispatch          0.5.0                    py36_0    defaults
navigator-updater         0.2.1                    py36_0    defaults
nbconvert                 5.3.1            py36hb41ffb7_0    defaults
nbformat                  4.4.0            py36h31c9010_0    defaults
ncurses                   6.1                  hf484d3e_0    defaults
networkx                  2.1                      py36_0    defaults
nltk                      3.3.0                    py36_0    defaults
nose                      1.3.7            py36hcdf7029_2    defaults
notebook                  5.5.0                    py36_0    defaults
numba                     0.38.0           py36h637b7d7_0    defaults
numexpr                   2.6.5            py36h7bf3b9c_0    defaults
numpy                     1.14.3           py36hcd700cb_1    defaults
numpy-base                1.14.3           py36h9be14a7_1    defaults
numpydoc                  0.8.0                    py36_0    defaults
odo                       0.5.1            py36h90ed295_0    defaults
olefile                   0.45.1                   py36_0    defaults
openpyxl                  2.5.3                    py36_0    defaults
openssl                   1.0.2o               h20670df_0    defaults
packaging                 17.1                     py36_0    defaults
pandas                    0.23.0           py36h637b7d7_0    defaults
pandoc                    1.19.2.1             hea2e7c5_1    defaults
pandocfilters             1.4.2            py36ha6701b7_1    defaults
pango                     1.41.0               hd475d92_0    defaults
parso                     0.2.0                    py36_0    defaults
partd                     0.3.8            py36h36fd896_0    defaults
patchelf                  0.9                  hf79760b_2    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                 h439df22_0    defaults
pep8                      1.7.1                    py36_0    defaults
pexpect                   4.5.0                    py36_0    defaults
pickleshare               0.7.4            py36h63277f8_0    defaults
pillow                    5.1.0            py36h3deb7b8_0    defaults
pip                       10.0.1                   py36_0    defaults
pixman                    0.34.0               hceecf20_3    defaults
pkginfo                   1.4.2                    py36_1    defaults
pluggy                    0.6.0            py36hb689045_0    defaults
ply                       3.11                     py36_0    defaults
prompt_toolkit            1.0.15           py36h17d85b1_0    defaults
psutil                    5.4.5            py36h14c3975_0    defaults
ptyprocess                0.5.2            py36h69acd42_0    defaults
py                        1.5.3                    py36_0    defaults
pycodestyle               2.4.0                    py36_0    defaults
pycosat                   0.6.3            py36h0a5515d_0    defaults
pycparser                 2.18             py36hf9f622e_1    defaults
pycrypto                  2.6.1            py36h14c3975_8    defaults
pycurl                    7.43.0.1         py36hb7f436b_0    defaults
pyflakes                  1.6.0            py36h7bd6a15_0    defaults
pygments                  2.2.0            py36h0d3125c_0    defaults
pylint                    1.8.4                    py36_0    defaults
pyodbc                    4.0.23           py36hf484d3e_0    defaults
pyopenssl                 18.0.0                   py36_0    defaults
pyparsing                 2.2.0            py36hee85983_1    defaults
pyqt                      5.9.2            py36h751905a_0    defaults
pysocks                   1.6.8                    py36_0    defaults
pytables                  3.4.3            py36h02b9ad4_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                hc3d631a_2    defaults
python-dateutil           2.7.3                    py36_0    defaults
pytz                      2018.4                   py36_0    defaults
pywavelets                0.5.2            py36he602eb0_0    defaults
pyyaml                    3.12             py36hafb9ca4_1    defaults
pyzmq                     17.0.0           py36h14c3975_0    defaults
qt                        5.9.5                h7e424d6_0    defaults
qtawesome                 0.4.4            py36h609ed8c_0    defaults
qtconsole                 4.3.1            py36h8f73b5b_0    defaults
qtpy                      1.4.1                    py36_0    defaults
readline                  7.0                  ha6073c6_4    defaults
requests                  2.18.4           py36he2e5f8d_1    defaults
rope                      0.10.7           py36h147e2ec_0    defaults
ruamel_yaml               0.15.35          py36h14c3975_1    defaults
scikit-image              0.13.1           py36h14c3975_1    defaults
scikit-learn              0.19.1           py36h7aa7ec6_0    defaults
scipy                     1.1.0            py36hfc37229_0    defaults
seaborn                   0.8.1            py36hfad7ec4_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          py36h7a266c3_0    defaults
sip                       4.19.8           py36hf484d3e_0    defaults
six                       1.11.0           py36h372c433_1    defaults
snappy                    1.1.7                hbae5bb6_3    defaults
snowballstemmer           1.2.1            py36h6febd40_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              py36h6d0f590_1    defaults
sphinxcontrib-websupport  1.0.1            py36hb5cb234_1    defaults
spyder                    3.2.8                    py36_0    defaults
sqlalchemy                1.2.7            py36h6b74fdf_0    defaults
sqlite                    3.23.1               he433501_0    defaults
statsmodels               0.9.0            py36h3010b51_0    defaults
sympy                     1.1.1            py36hc6d1c1c_0    defaults
tblib                     1.3.2            py36h34cf8b6_0    defaults
terminado                 0.8.1                    py36_1    defaults
testpath                  0.3.1            py36h8cadb63_0    defaults
tk                        8.6.7                hc745277_3    defaults
toolz                     0.9.0                    py36_0    defaults
tornado                   5.0.2                    py36_0    defaults
traitlets                 4.3.2            py36h674d592_0    defaults
typing                    3.6.4                    py36_0    defaults
unicodecsv                0.14.1           py36ha668878_0    defaults
unixodbc                  2.3.6                h1bed415_0    defaults
urllib3                   1.22             py36hbe7ace6_0    defaults
wcwidth                   0.1.7            py36hdf4376a_0    defaults
webencodings              0.5.1            py36h800622e_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          py36h28b7045_0    defaults
xlrd                      1.1.0            py36h1db9f0c_1    defaults
xlsxwriter                1.0.4                    py36_0    defaults
xlwt                      1.3.0            py36h7b00a1f_0    defaults
xz                        5.2.4                h14c3975_4    defaults
yaml                      0.1.7                had09818_2    defaults
zeromq                    4.2.5                h439df22_0    defaults
zict                      0.1.3            py36h3a3bf81_0    defaults
zlib                      1.2.11               ha838bed_2    defaults
mingwandroid commented 5 years ago 
# I run the following script to add anaconda to PATH
export PATH="/home/marco/anaconda3/bin:$PATH"

This isn't how the Anaconda Distribution is activated, instead, please use . /home/marco/anaconda3/bin/activate.

You should be able to get more information by using conda from the terminal/shell instead of from anaconda-navigator. Please try that and report back with any issues.

knzudgt commented 5 years ago

@mingwandroid Is there any chance to install RStudio from terminal?

mingwandroid commented 5 years ago

Please follow the instructions above (activating), then run conda install rstudio.

If you prefer Ananconda's own R over MRO then add r-base to that line.

knzudgt commented 5 years ago

@mingwandroid During anacoda installation I did not prepend the Anaconda install location to PATH in my /home/marco/.bashrc to avoid conflicts with the Ruby version manager rvm, that is why I use my own script to prepend the Anaconda install location to PATH during a terminal session. So I can use at the same time rvm in another terminal session, avoiding conflicts.

What exactly does the activate script . /home/marco/anaconda3/bin/activate do?

I am successfully using anaconda navigator to launch jupyter notebook and spider, so it works, except when it comes to installing RStudio.