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Anaconda issue tracking
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RSAtudioo and R #1472

Closed spmolnar closed 7 years ago

spmolnar commented 7 years ago

I have just installed anaconda3 v-4.3.0 and installed R and RStudio via anaconda-navigator.

If I try to open RStudio outside of anaconda-navigator I get and error message:

;Unable to find an installation of R on the system (which R didn't return valid output); Unable to locate R binary by scanning standard locations'

I would prefer not to have to open anaconda-navigator each time I want to run RStudio, an navigator is very slooow opening and occupies quite a bite of screen.

Is there a solution to this problem?

Thanks in advance.

comp@AbNormal:~/Apps/anaconda3$ conda info Current conda install:

           platform : linux-64
      conda version : 4.3.13
   conda is private : False
  conda-env version : 4.3.13
conda-build version : not installed
     python version : 3.6.0.final.0
   requests version : 2.13.0
   root environment : /home/comp/Apps/anaconda3  (writable)
default environment : /home/comp/Apps/anaconda3
   envs directories : /home/comp/Apps/anaconda3/envs
                      /home/comp/.conda/envs
      package cache : /home/comp/Apps/anaconda3/pkgs
                      /home/comp/.conda/pkgs
       channel URLs : https://conda.anaconda.org/anaconda-fusion/linux-64
                      https://conda.anaconda.org/anaconda-fusion/noarch
                      https://repo.continuum.io/pkgs/free/linux-64
                      https://repo.continuum.io/pkgs/free/noarch
                      https://repo.continuum.io/pkgs/r/linux-64
                      https://repo.continuum.io/pkgs/r/noarch
                      https://repo.continuum.io/pkgs/pro/linux-64
                      https://repo.continuum.io/pkgs/pro/noarch
        config file : /home/comp/.condarc
       offline mode : False
         user-agent : conda/4.3.13 requests/2.13.0 CPython/3.6.0 Linux/3.16.0-4-amd64 debian/8.7 glibc/2.19
            UID:GID : 1000:1000

comp@AbNormal:~/Apps/anaconda3$ conda list --show-channel-urls

packages in environment at /home/comp/Apps/anaconda3:

# _license 1.1 py36_1 defaults alabaster 0.7.9 py36_0 defaults anaconda 4.3.0 np111py36_0 defaults anaconda-client 1.6.0 py36_0 defaults anaconda-navigator 1.4.3 py36_0 defaults astroid 1.4.9 py36_0 defaults astropy 1.3 np111py36_0 defaults babel 2.3.4 py36_0 defaults backports 1.0 py36_0 defaults beautifulsoup4 4.5.3 py36_0 defaults bitarray 0.8.1 py36_0 defaults blaze 0.10.1 py36_0 defaults bleach 1.5.0 bokeh 0.12.4 py36_0 defaults boto 2.45.0 py36_0 defaults bottleneck 1.2.0 np111py36_0 defaults bzip2 1.0.6 3 defaults cairo 1.14.8 0 defaults cffi 1.9.1 py36_0 defaults chardet 2.3.0 py36_0 defaults chest 0.2.3 py36_0 defaults click 6.7 py36_0 defaults cloudpickle 0.2.2 py36_0 defaults clyent 1.2.2 py36_0 defaults colorama 0.3.7 py36_0 defaults conda 4.3.13 py36_0 defaults conda-env 2.6.0 0 defaults configobj 5.0.6 py36_0 defaults contextlib2 0.5.4 py36_0 defaults cryptography 1.7.1 py36_0 defaults curl 7.52.1 0 defaults cycler 0.10.0 py36_0 defaults cython 0.25.2 py36_0 defaults cytoolz 0.8.2 py36_0 defaults dask 0.13.0 py36_0 defaults datashape 0.5.4 py36_0 defaults dbus 1.10.10 0 defaults decorator 4.0.11 py36_0 defaults dill 0.2.5 py36_0 defaults docutils 0.13.1 py36_0 defaults entrypoints 0.2.2 entrypoints 0.2.2 py36_0 defaults et_xmlfile 1.0.1 py36_0 defaults expat 2.1.0 0 defaults fastcache 1.0.2 py36_1 defaults flask 0.12 py36_0 defaults flask-cors 3.0.2 py36_0 defaults font-ttf-dejavu-sans-mono 2.37 0 defaults font-ttf-inconsolata 2.000 0 defaults font-ttf-source-code-pro 2.030 0 defaults font-ttf-ubuntu 0.83 0 defaults fontconfig 2.12.1 2 defaults fonts-continuum 1 0 defaults freetype 2.5.5 2 defaults get_terminal_size 1.0.0 py36_0 defaults gevent 1.2.1 py36_0 defaults glib 2.50.2 1 defaults glueviz 0.9.1 py36_0 defaults gmp 6.1.0 0 defaults greenlet 0.4.11 py36_0 defaults gsl 2.2.1 0 defaults gst-plugins-base 1.8.0 0 defaults gstreamer 1.8.0 0 defaults h5py 2.6.0 np111py36_2 defaults harfbuzz 0.9.39 2 defaults hdf5 1.8.17 1 defaults heapdict 1.0.0 py36_1 defaults html5lib 0.9999999 icu 54.1 0 defaults idna 2.2 py36_0 defaults imagesize 0.7.1 py36_0 defaults ipykernel 4.5.2 py36_0 defaults ipython 5.1.0 py36_0 defaults ipython_genutils 0.1.0 py36_0 defaults ipywidgets 5.2.2 py36_1 defaults isort 4.2.5 py36_0 defaults itsdangerous 0.24 py36_0 defaults jbig 2.1 0 defaults jdcal 1.3 py36_0 defaults jedi 0.9.0 py36_1 defaults jinja2 2.9.4 py36_0 defaults Jinja2 2.9.5 jpeg 9b 0 defaults jsonschema 2.5.1 py36_0 defaults jupyter 1.0.0 py36_3 defaults jupyter-core 4.3.0 jupyter_client 4.4.0 py36_0 defaults jupyter_console 5.0.0 py36_0 defaults jupyter_core 4.2.1 py36_0 defaults lazy-object-proxy 1.2.2 py36_0 defaults libffi 3.2.1 1 defaults libgcc 4.8.5 2 defaults libgfortran 3.0.0 1 defaults libiconv 1.14 0 defaults libpng 1.6.27 0 defaults libsodium 1.0.10 0 defaults libtiff 4.0.6 3 defaults libuuid 1.0.3 0 defaults libxcb 1.12 1 defaults libxml2 2.9.4 0 defaults libxslt 1.1.29 0 defaults llvmlite 0.15.0 py36_0 defaults locket 0.2.0 py36_1 defaults lxml 3.7.2 py36_0 defaults markupsafe 0.23 py36_2 defaults matplotlib 2.0.0 np111py36_0 defaults mccabe 0.6.1 mistune 0.7.3 py36_0 defaults mkl 2017.0.1 0 defaults mkl-rt 11.1 p0 defaults mkl-service 1.1.2 py36_3 defaults mpmath 0.19 py36_1 defaults multipledispatch 0.4.9 py36_0 defaults nbconvert 5.1.1 nbconvert 4.2.0 py36_0 defaults nbformat 4.2.0 py36_0 defaults ncurses 5.9 10 defaults networkx 1.11 py36_0 defaults nltk 3.2.2 py36_0 defaults nose 1.3.7 py36_1 defaults notebook 4.3.1 py36_0 defaults numba 0.30.1 np111py36_0 defaults numexpr 2.6.1 np111py36_2 defaults numpy 1.11.3 py36_0 defaults numpydoc 0.6.0 py36_0 defaults odo 0.5.0 py36_1 defaults openpyxl 2.4.1 py36_0 defaults openssl 1.0.2k 0 defaults pandas 0.19.2 np111py36_1 defaults pandoc 1.15.0.6 0 defaults pandocfilters 1.4.1 pango 1.40.3 1 defaults partd 0.3.7 py36_0 defaults path.py 10.0 py36_0 defaults pathlib2 2.2.0 py36_0 defaults patsy 0.4.1 py36_0 defaults pcre 8.39 1 defaults pep8 1.7.0 py36_0 defaults pexpect 4.2.1 py36_0 defaults pickleshare 0.7.4 py36_0 defaults pillow 4.0.0 py36_0 defaults pip 9.0.1 py36_1 defaults pixman 0.34.0 0 defaults ply 3.9 py36_0 defaults prompt_toolkit 1.0.9 py36_0 defaults psi4 1.0.54 py36_8 acellera psutil 5.1.3 psutil 5.0.1 py36_0 defaults ptyprocess 0.5.1 py36_0 defaults py 1.4.32 py36_0 defaults pyasn1 0.1.9 py36_0 defaults pycosat 0.6.1 py36_1 defaults pycparser 2.17 py36_0 defaults pycrypto 2.6.1 py36_4 defaults pycurl 7.43.0 py36_2 defaults pyflakes 1.5.0 py36_0 defaults pygments 2.1.3 py36_0 defaults Pygments 2.2.0 pylint 1.6.4 py36_1 defaults pylint 1.6.5 pyopenssl 16.2.0 py36_0 defaults pyparsing 2.1.4 py36_0 defaults pyqt 5.6.0 py36_2 defaults pytables 3.3.0 np111py36_0 defaults pytest 3.0.5 py36_0 defaults python 3.6.0 0 defaults python-dateutil 2.6.0 py36_0 defaults pytz 2016.10 py36_0 defaults pyyaml 3.12 py36_0 defaults pyzmq 16.0.2 py36_0 defaults qt 5.6.2 3 defaults QtAwesome 0.4.4 qtawesome 0.4.3 py36_0 defaults qtconsole 4.2.1 py36_1 defaults qtpy 1.2.1 py36_0 defaults r-assertthat 0.1 r3.3.2_4 defaults r-backports 1.0.4 r3.3.2_0 defaults r-base 3.3.2 1 defaults r-base64enc 0.1_3 r3.3.2_0 defaults r-bh 1.62.0_1 r3.3.2_0 defaults r-bitops 1.0_6 r3.3.2_2 defaults r-boot 1.3_18 r3.3.2_0 defaults r-broom 0.4.1 r3.3.2_0 defaults r-car 2.1_4 r3.3.2_0 defaults r-caret 6.0_73 r3.3.2_0 defaults r-catools 1.17.1 r3.3.2_2 defaults r-class 7.3_14 r3.3.2_0 defaults r-cluster 2.0.5 r3.3.2_0 defaults r-codetools 0.2_15 r3.3.2_0 defaults r-colorspace 1.3_1 r3.3.2_0 defaults r-crayon 1.3.2 r3.3.2_0 defaults r-curl 2.3 r3.3.2_0 defaults r-data.table 1.10.0 r3.3.2_0 defaults r-dbi 0.5_1 r3.3.2_0 defaults r-dichromat 2.0_0 r3.3.2_2 defaults r-digest 0.6.10 r3.3.2_0 defaults r-dplyr 0.5.0 r3.3.2_0 defaults r-essentials 1.5.2 r3.3.2_0 defaults r-evaluate 0.10 r3.3.2_0 defaults r-forcats 0.1.1 r3.3.2_0 defaults r-foreach 1.4.3 r3.3.2_0 defaults r-foreign 0.8_67 r3.3.2_0 defaults r-formatr 1.4 r3.3.2_0 defaults r-ggplot2 2.2.0 r3.3.2_0 defaults r-gistr 0.3.6 r3.3.2_0 defaults r-glmnet 2.0_5 r3.3.2_0 defaults r-gtable 0.2.0 r3.3.2_0 defaults r-haven 1.0.0 r3.3.2_0 defaults r-hexbin 1.27.1 r3.3.2_0 defaults r-highr 0.6 r3.3.2_0 defaults r-hms 0.3 r3.3.2_0 defaults r-htmltools 0.3.5 r3.3.2_0 defaults r-htmlwidgets 0.8 r3.3.2_0 defaults r-httpuv 1.3.3 r3.3.2_0 defaults r-httr 1.2.1 r3.3.2_0 defaults r-irdisplay 0.4.4 r3.3.2_0 defaults r-irkernel 0.7.1 r3.3.2_0 defaults r-iterators 1.0.8 r3.3.2_0 defaults r-jsonlite 1.1 r3.3.2_0 defaults r-kernsmooth 2.23_15 r3.3.2_0 defaults r-knitr 1.15.1 r3.3.2_0 defaults r-labeling 0.3 r3.3.2_2 defaults r-lattice 0.20_34 r3.3.2_0 defaults r-lazyeval 0.2.0 r3.3.2_0 defaults r-lme4 1.1_12 r3.3.2_0 defaults r-lubridate 1.6.0 r3.3.2_0 defaults r-magrittr 1.5 r3.3.2_2 defaults r-maps 3.1.1 r3.3.2_0 defaults r-markdown 0.7.7 r3.3.2_2 defaults r-mass 7.3_45 r3.3.2_0 defaults r-matrix 1.2_7.1 r3.3.2_0 defaults r-matrixmodels 0.4_1 r3.3.2_0 defaults r-mgcv 1.8_16 r3.3.2_0 defaults r-mime 0.5 r3.3.2_0 defaults r-minqa 1.2.4 r3.3.2_2 defaults r-mnormt 1.5_5 r3.3.2_0 defaults r-modelmetrics 1.1.0 r3.3.2_0 defaults r-modelr 0.1.0 r3.3.2_0 defaults r-munsell 0.4.3 r3.3.2_0 defaults r-nlme 3.1_128 r3.3.2_0 defaults r-nloptr 1.0.4 r3.3.2_2 defaults r-nnet 7.3_12 r3.3.2_0 defaults r-openssl 0.9.5 r3.3.2_0 defaults r-packrat 0.4.8_1 r3.3.2_0 defaults r-pbdzmq 0.2_4 r3.3.2_0 defaults r-pbkrtest 0.4_6 r3.3.2_0 defaults r-pki 0.1_3 r3.3.2_0 defaults r-plyr 1.8.4 r3.3.2_0 defaults r-pryr 0.1.2 r3.3.2_0 defaults r-psych 1.6.9 r3.3.2_0 defaults r-purrr 0.2.2 r3.3.2_0 defaults r-quantmod 0.4_7 r3.3.2_0 defaults r-quantreg 5.29 r3.3.2_0 defaults r-r6 2.2.0 r3.3.2_0 defaults r-randomforest 4.6_12 r3.3.2_0 defaults r-rbokeh 0.5.0 r3.3.2_0 defaults r-rcolorbrewer 1.1_2 r3.3.2_3 defaults r-rcpp 0.12.8 r3.3.2_0 defaults r-rcppeigen 0.3.2.9.0 r3.3.2_0 defaults r-rcurl 1.95_4.8 r3.3.2_0 defaults r-readr 1.0.0 r3.3.2_0 defaults r-readxl 0.1.1 r3.3.2_0 defaults r-recommended 3.3.2 r3.3.2_0 defaults r-repr 0.10 r3.3.2_0 defaults r-reshape2 1.4.2 r3.3.2_0 defaults r-rjsonio 1.3_0 r3.3.2_2 defaults r-rmarkdown 1.3 r3.3.2_0 defaults r-rpart 4.1_10 r3.3.2_0 defaults r-rprojroot 1.1 r3.3.2_0 defaults r-rsconnect 0.7 r3.3.2_0 defaults r-rstudioapi 0.6 r3.3.2_0 defaults r-rvest 0.3.2 r3.3.2_0 defaults r-scales 0.4.1 r3.3.2_0 defaults r-selectr 0.3_0 r3.3.2_0 defaults r-shiny 0.14.2 r3.3.2_0 defaults r-sourcetools 0.1.5 r3.3.2_0 defaults r-sparsem 1.74 r3.3.2_0 defaults r-spatial 7.3_11 r3.3.2_0 defaults r-stringi 1.1.2 r3.3.2_0 defaults r-stringr 1.1.0 r3.3.2_0 defaults r-survival 2.40_1 r3.3.2_0 defaults r-tibble 1.2 r3.3.2_0 defaults r-tidyr 0.6.0 r3.3.2_0 defaults r-tidyverse 1.0.0 r3.3.2_0 defaults r-ttr 0.23_1 r3.3.2_0 defaults r-uuid 0.1_2 r3.3.2_0 defaults r-xml2 1.0.0 r3.3.2_0 defaults r-xtable 1.8_2 r3.3.2_0 defaults r-xts 0.9_7 r3.3.2_2 defaults r-yaml 2.1.14 r3.3.2_0 defaults r-zoo 1.7_13 r3.3.2_0 defaults readline 6.2 2 defaults redis 3.2.0 0 defaults redis-py 2.10.5 py36_0 defaults requests 2.12.4 py36_0 defaults requests 2.13.0 rope 0.9.4 py36_1 defaults rstudio 1.0.136 1 defaults ruamel_yaml 0.11.14 py36_1 defaults scikit-image 0.12.3 np111py36_1 defaults scikit-learn 0.18.1 np111py36_1 defaults scipy 0.18.1 np111py36_1 defaults seaborn 0.7.1 py36_0 defaults setuptools 27.2.0 py36_0 defaults simplegeneric 0.8.1 py36_1 defaults singledispatch 3.4.0.3 py36_0 defaults sip 4.18 py36_0 defaults six 1.10.0 py36_0 defaults snowballstemmer 1.2.1 py36_0 defaults sockjs-tornado 1.0.3 py36_0 defaults sphinx 1.5.1 py36_0 defaults Sphinx 1.5.2 spyder 3.1.2 py36_0 defaults spyder 3.1.3 sqlalchemy 1.1.5 py36_0 defaults sqlite 3.13.0 0 defaults statsmodels 0.6.1 np111py36_1 defaults sympy 1.0 py36_0 defaults terminado 0.6 py36_0 defaults testpath 0.3 tk 8.5.18 0 defaults toolz 0.8.2 py36_0 defaults tornado 4.4.2 py36_0 defaults traitlets 4.3.1 py36_0 defaults unicodecsv 0.14.1 py36_0 defaults wcwidth 0.1.7 py36_0 defaults werkzeug 0.11.15 py36_0 defaults wheel 0.29.0 py36_0 defaults widgetsnbextension 1.2.6 py36_0 defaults wrapt 1.10.8 py36_0 defaults xlrd 1.0.0 py36_0 defaults xlsxwriter 0.9.6 py36_0 defaults xlwt 1.2.0 py36_0 defaults xz 5.2.2 1 defaults yaml 0.1.6 0 defaults zeromq 4.1.5 0 defaults zlib 1.2.8 3 defaults comp@AbNormal:~/Apps/anaconda3$

mingwandroid commented 7 years ago

I would prefer not to have to open anaconda-navigator each time I want to run RStudio, an navigator is very slooow opening and occupies quite a bite of screen.

Sure, from a console window, please try:

source /home/comp/Apps/anaconda3/bin/activate
rstudio

I suspect something may go wrong, but hopefully we can get you up and running. Thanks.

spmolnar commented 7 years ago

On 02/22/2017 02:47 PM, Ray Donnelly wrote:

|source /home/comp/Apps/anaconda3/bin/activate|

Here's what happened:

comp@AbNormal:~$ source /home/comp/Apps/anaconda3/bin/activate rstudio Traceback (most recent call last): File "/home/comp/Apps/anaconda3/bin/conda", line 6, in sys.exit(conda.cli.main()) File "/home/comp/Apps/anaconda3/lib/python3.6/site-packages/conda/cli/main.py", line 151, in main activate.main() File "/home/comp/Apps/anaconda3/lib/python3.6/site-packages/conda/cli/activate.py", line 160, in main prefix = prefix_from_arg(sys.argv[3], shelldict=shelldict) File "/home/comp/Apps/anaconda3/lib/python3.6/site-packages/conda/cli/activate.py", line 60, in prefix_from_arg prefix = locate_prefix_by_name(context, arg.replace('/', os.path.sep)) File "/home/comp/Apps/anaconda3/lib/python3.6/site-packages/conda/base/context.py", line 569, in locate_prefix_by_name raise CondaEnvironmentNotFoundError(name) conda.exceptions.CondaEnvironmentNotFoundError: Could not find environment: rstudio . You can list all discoverable environments with conda info --envs.

conda environments:

# root * /home/comp/Apps/psi4conda

comp@AbNormal:~$

-- Stephen P. Molnar, Ph.D. Life is a fuzzy set www.molecular-modeling.net Stochastic and multivariate (614)312-7528 (c) Skype: smolnar1

mingwandroid commented 7 years ago

I meant for you to enter two separate commands into your console shell. First: source /home/comp/Apps/anaconda3/bin/activate and then after that rstudio

spmolnar commented 7 years ago

On 02/22/2017 04:39 PM, Ray Donnelly wrote:

I meant for you to enter two separate commands into your console shell: |source /home/comp/Apps/anaconda3/bin/activate| and then after that |rstudio|.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ContinuumIO/anaconda-issues/issues/1472#issuecomment-281812680, or mute the thread https://github.com/notifications/unsubscribe-auth/ADEWIt0srqFB6I03kg8GvfidzV1ULXcOks5rfKr_gaJpZM4MIuwj.

Ah, my lack of knowledge.

That worked.

Many thanks.

-- Stephen P. Molnar, Ph.D. Life is a fuzzy set www.molecular-modeling.net Stochastic and multivariate (614)312-7528 (c) Skype: smolnar1