Unable to load R kernel in Jupyter notebook

[glimmerphoenix]

[Moving issue here from jupyter/notebook issue track after @ccordoba12 request; should be assigned to @mingwandroid ]

Hello,

I'm running Ubuntu Server 16.04 64-bit.

After a fresh installation of R packages in Anaconda within a new environment, through conda install -c r r-essentials, I get the following error when trying to launch a new R notebook in jupyter-notebook:

(datascience) jfelipe@bastion:~$ conda info
Current conda install:                                                                                                                                                  

               platform : linux-64                                                                                                                                      
          conda version : 4.2.9                                                                                                                                         
       conda is private : False                                                                                                                                         
      conda-env version : 4.2.9                                                                                                                                         
    conda-build version : 2.0.2                                                                                                                                         
         python version : 3.5.2.final.0                                                                                                                                 
       requests version : 2.11.1                                                                                                                                        
       root environment : /home/jfelipe/anaconda3  (writable)                                                                                                           
    default environment : /home/jfelipe/anaconda3/envs/datascience                                                                                                      
       envs directories : /home/jfelipe/anaconda3/envs                                                                                                                  
          package cache : /home/jfelipe/anaconda3/pkgs                                                                                                                  
           channel URLs : https://repo.continuum.io/pkgs/free/linux-64/                                                                                                 
                          https://repo.continuum.io/pkgs/free/noarch/                                                                                                   
                          https://repo.continuum.io/pkgs/pro/linux-64/                                                                                                  
                          https://repo.continuum.io/pkgs/pro/noarch/                                                                                                    
            config file : None
           offline mode : False
----

[I 11:35:49.112 NotebookApp] [nb_conda_kernels] enabled, 5 kernels found
[I 11:35:49.714 NotebookApp] [nb_conda] enabled
[I 11:35:49.755 NotebookApp] [nb_anacondacloud] enabled
[I 11:35:49.800 NotebookApp] ✓ nbpresent HTML export ENABLED
[W 11:35:49.800 NotebookApp] ✗ nbpresent PDF export DISABLED: No module named 'nbbrowserpdf'
[I 11:35:49.804 NotebookApp] Serving notebooks from local directory: /home/jfelipe
[I 11:35:49.804 NotebookApp] 0 active kernels 
[I 11:35:49.804 NotebookApp] The Jupyter Notebook is running at: http://localhost:8888/
[I 11:35:49.804 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[I 11:35:57.076 NotebookApp] Creating new notebook in 
[I 11:35:58.202 NotebookApp] Kernel started: 4a702202-7a84-4045-8ea0-c85501157525
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/jfelipe/R/x86_64-pc-linux-gnu-library/3.3/stringi/libs/stringi.so':
  /home/jfelipe/anaconda3/envs/datascience/lib/R/bin/exec/../../lib/../.././libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /home/jfelipe/R/x86_64-pc-linux-gnu-library/3.3/stringi/libs/stringi.so)
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> 
Ejecución interrumpida
[I 11:36:01.203 NotebookApp] KernelRestarter: restarting kernel (1/5)
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/jfelipe/R/x86_64-pc-linux-gnu-library/3.3/stringi/libs/stringi.so':
  /home/jfelipe/anaconda3/envs/datascience/lib/R/bin/exec/../../lib/../.././libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /home/jfelipe/R/x86_64-pc-linux-gnu-library/3.3/stringi/libs/stringi.so)
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> 
Ejecución interrumpida
[I 11:36:04.214 NotebookApp] KernelRestarter: restarting kernel (2/5)
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/jfelipe/R/x86_64-pc-linux-gnu-library/3.3/stringi/libs/stringi.so':
  /home/jfelipe/anaconda3/envs/datascience/lib/R/bin/exec/../../lib/../.././libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /home/jfelipe/R/x86_64-pc-linux-gnu-library/3.3/stringi/libs/stringi.so)
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> 
Ejecución interrumpida
[I 11:36:07.225 NotebookApp] KernelRestarter: restarting kernel (3/5)
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/jfelipe/R/x86_64-pc-linux-gnu-library/3.3/stringi/libs/stringi.so':                                                                                                      
  /home/jfelipe/anaconda3/envs/datascience/lib/R/bin/exec/../../lib/../.././libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /home/jfelipe/R/x86_64-pc-linux-gnu-library/3.3/stringi/libs/stringi.so)                                                                                                                                                                                                            
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne ->                                                                                                                                            
Ejecución interrumpida                                                                                                                                                                                         
[W 11:36:08.571 NotebookApp] Timeout waiting for kernel_info reply from 4a702202-7a84-4045-8ea0-c85501157525                                                                                                   
[I 11:36:10.236 NotebookApp] KernelRestarter: restarting kernel (4/5)                                                                                                                                          
WARNING:root:kernel 4a702202-7a84-4045-8ea0-c85501157525 restarted                                                                                                                                             
Error in dyn.load(file, DLLpath = DLLpath, ...) :                                                                                                                                                              
  unable to load shared object '/home/jfelipe/R/x86_64-pc-linux-gnu-library/3.3/stringi/libs/stringi.so':                                                                                                      
  /home/jfelipe/anaconda3/envs/datascience/lib/R/bin/exec/../../lib/../.././libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /home/jfelipe/R/x86_64-pc-linux-gnu-library/3.3/stringi/libs/stringi.so)                                                                                                                                                                                                            
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne ->                                                                                                                                            
Ejecución interrumpida                                                                                                                                                                                         
[W 11:36:13.249 NotebookApp] KernelRestarter: restart failed                                                                                                                                                   
[W 11:36:13.250 NotebookApp] Kernel 4a702202-7a84-4045-8ea0-c85501157525 died, removing from map.                                                                                                              
ERROR:root:kernel 4a702202-7a84-4045-8ea0-c85501157525 restarted failed!                                                                                                                                       
[W 11:36:13.328 NotebookApp] Kernel deleted before session                                                                                                                                                     
[W 11:36:13.329 NotebookApp] 410 DELETE /api/sessions/eb491838-b879-497c-87cc-cdfa85d8db67 (127.0.0.1) 3.50ms referer=http://localhost:8888/notebooks/Untitled.ipynb?kernel_name=conda-env-datascience-r

Not sure, but libstdc++.so.6 in Anaconda seems to point to CXXABI_1.3.8, which is gcc-4.9. Ubuntu Server 16.04 64-bit comes with gcc 5.4.0 by default, more precisely gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.2).

BTW, I don't get any errors when loading ggplot2 (which also depends on stringi) in R outside Anaconda.

[glimmerphoenix]

Additional info:

I uninstalled stringi from the baseline R library in my system. After that, I can open R notebooks in Jupyter without errors. However, I don't think that you should be forced to uninstall any package from the baseline R library in your system when the whole point of using Anaconda is basically to encapsulate all dependencies in your working environment.

I have set up R with Jupyter notebooks in Anaconda many times previously (both in Linux and Windows). This is the first time I run into this problem.

My big doubt is: if Anaconda is (apparently) installing its own version of all R packages, aside from any other R installation in your system, why is there any conflict between stringi packages in both locations? It should only see what is installed inside the Anaconda environment. In fact, you don't need to follow IRkernel linking instructions anymore.

Thanks in advance for your help with this issue. I think this can be a serious problem, as it is very likely that many users willing work with R notebooks in Jupyter will also probably have R and RStudio already installed.

[mingwandroid]

It seems to me that Ubuntu 16.04 64-bit has set R_LIBS or something like that? This is not the recommended way to identify the system R install path since that gets precedence in all R instances.

How did you install your baseline R library?

[glimmerphoenix]

1. Baseline installation of R and recommended R packages: following the suggested procedure from the official documentation of the R project.
2. Additional packages (such as ggplot2, dplyr, tidyr, etc.): Directly in RStudio, through the "Packages" tab.

For what it is worth, RStudio returns:

> .libPaths()
[1] "/home/jfelipe/R/x86_64-pc-linux-gnu-library/3.3"
[2] "/usr/local/lib/R/site-library"                  
[3] "/usr/lib/R/site-library"                        
[4] "/usr/lib/R/library" 

No clue about my conda environment's R library, as (I think) it should be. However, the command-line R called inside my datascience conda environment shows:

> .libPaths()
[1] "/home/jfelipe/R/x86_64-pc-linux-gnu-library/3.3"       
[2] "/home/jfelipe/anaconda3/envs/datascience/lib/R/library"

Indeed, it seems that the baseline R library path is taking precedence over the specific R library path for conda.

[mingwandroid]

Looking into this more, if I mkdir -p ~/R/x86_64-pc-linux-gnu-library/3.3, then launch R from conda, and do .libPaths(), then I get:

[1] "/root/R/x86_64-pc-linux-gnu-library/3.3"
[2] "/root/r_3_3_1-x64-3.5/lib/R/library"

This means that I most likely need to patch r-base to prevent this from happening.

[mingwandroid]

If you edit ${CONDA_PREFIX}/lib/R/etc/Renviron and comment-out:

R_LIBS_USER=${R_LIBS_USER-'~/R/x86_64-pc-linux-gnu-library/3.3'}

then you should be able to proceed. I will work on a permanent fix next time I rebuild R.

[glimmerphoenix]

@mingwandroid Thanks a lot for your suggestions.

I have commented out the line you mention. The result is that I can open an R notebook in Jupyter and perform basic operations with standard functions in r-base (sum, mean, etc.).

However, I cannot load in the notebook any additional library (such as ggplot2). I tried to edit the same line in ${CONDA_PREFIX}/lib/R/etc/Renviron, to point to the local library inside my conda environment with the same result.

In any case, I will wait for a permanent fix on the next rebuild. I will also try to double-check if the same problem occurs in Windows platforms.

Again, many thanks for your help and support with this issue.

[mingwandroid]

To use ggplot2, did you install it with conda as follows:

conda install -c r r-ggplot2

.. because these two issues do not, on the face of it, seem related.

[glimmerphoenix]

@mingwandroid According to https://www.continuum.io/blog/developer/jupyter-and-conda-r:

The Anaconda team has created an “R Essentials” bundle with the IRKernel and over 80 of the most used R packages for data science, including dplyr, shiny, ggplot2, tidyr, caret and nnet.

Just in case, I have just double-checked if ggplot2 is already installed:

(datascience) jfelipe@bastion:~/anaconda3$ conda install -c r r-ggplot2
Fetching package metadata .........
Solving package specifications: ..........

# All requested packages already installed.
# packages in environment at /home/jfelipe/anaconda3/envs/datascience:
#
r-ggplot2                 2.1.0                  r3.3.1_0    r

Paying attention, the library ggplot2 does seems to load (no errors when I call library(ggplot2)); but when I try to create a simple boxplot I get:

library(ggplot2)
p <- ggplot(mpg, aes(class, hwy))
p + geom_boxplot()

Notebook Validation failed: 'Error in grid.Call(L_textBounds, as.graphicsAnnot(x$label), 
x$x, x$y, : X11 font -adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*, face 1 at size 9 could
not be loaded\nTraceback:\n' is not of type 'array':
"Error in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : 
X11 font -adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*, face 1 at size 9 could not be loaded
\nTraceback:\n"

In any case, please don't spend time on this notice until the first error is fixed, unless it is clear that both things are connected. I don't want to mix unrelated issues.

[glimmerphoenix]

I have updated Anaconda and its R packages (with conda update -c r r-essentials) and I can open, edit and run R notebooks correctly. Thanks a lot for fixing this.

[mingwandroid]

Thanks for the feedback.

[diegogarcilazo]

I had the same problem installing the Anaconda3-4.3.1-Linux-x86_64.sh in Debian jessie and I was able to solve it with your help. Thank you.

[gitclem]

I'm having the same problem. R in Jupyter was working a few days ago. I'm guessing that I recently updated caused the problem.

For better or worse, I've installed both anaconda 2 & 3 (in the off chance I decide to switch over to python 3 some day). I had also installed R outside of anaconda:

It does appear that R under Jupyter is also behind a few versions.
/usr/bin/R -v shows 3.3.5 /usr/local/anaconda2/bin/R -v shows 3.3.2 /usr/local/anaconda2/bin/conda --version shows 4.3.18 /usr/local/anaconda2/bin/anaconda --version 1.6.0

Jupyter shows these errors:

[I 18:44:12.177 NotebookApp] KernelRestarter: restarting kernel (1/5)
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/usr/local/anaconda2/lib/R/library/stringi/libs/stringi.so':
  /usr/local/anaconda2/lib/R/bin/exec/../../lib/../.././libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /usr/local/anaconda2/lib/R/library/stringi/libs/stringi.so)
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted

Now, I have found the problematic stringi.so file is located in 5 places on my machine:

find . -name stringi.so -exec ls -l {} \; 
-rwxrwxr-x 2  897735 Dec  6 15:21 ./usr/local/anaconda3/pkgs/r-stringi-1.1.2-r3.3.2_0/lib/R/library/stringi/libs/stringi.so
-rwxrwxr-x 2  897735 Dec  6 15:21 ./usr/local/anaconda3/lib/R/library/stringi/libs/stringi.so
-rwxrwxr-x 1  897735 Dec  6 15:21 ./usr/local/anaconda2/pkgs/r-stringi-1.1.2-r3.3.2_0/lib/R/library/stringi/libs/stringi.so
-rwxr-xr-x 1  7127312 May 17 00:28 ./usr/local/anaconda2/lib/R/library/stringi/libs/stringi.so
-rwxrwxr-x 1  5053168 May 11 18:44 ./usr/local/lib/R/site-library/stringi/libs/stringi.so

One of which appears to be out of sync? (to new??) I wonder if I just can't copy one of the versions over the other? (I'm not sure which I should though...)

strings /usr/local/anaconda2/pkgs/r-stringi-1.1.2-r3.3.2_0/lib/R/library/stringi/libs/stringi.so |grep CXXABI CXXABI_1.3.1 CXXABI_1.3 [etc]

strings /usr/local/anaconda2/lib/R/library/stringi/libs/stringi.so | grep CXXABI CXXABI_1.3.8 CXXABI_1.3.1 CXXABI_1.3 [etc]

strings /usr/local/lib/R/site-library/stringi/libs/stringi.so | grep CXXABI CXXABI_1.3.8 CXXABI_1.3.1 CXXABI_1.3

Config info:

 conda info
Current conda install:

               platform : linux-64
          conda version : 4.3.18
       conda is private : False
      conda-env version : 4.3.18
    conda-build version : not installed
         python version : 2.7.13.final.0
       requests version : 2.12.4
       root environment : /usr/local/anaconda2  (writable)
    default environment : /usr/local/anaconda2
       envs directories : /usr/local/anaconda2/envs
                          /home/clement/.conda/envs
          package cache : /usr/local/anaconda2/pkgs
                          /home/clement/.conda/pkgs
           channel URLs : 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 : None
           offline mode : False
             user-agent : conda/4.3.18 requests/2.12.4 CPython/2.7.13 Linux/4.10.0-21-generic debian/stretch/sid glibc/2.24    
                UID:GID : 1000:1000

[mingwandroid]

https://github.com/ContinuumIO/anaconda-issues/issues/1133#issuecomment-251249756

[dorcoh]

Hi, I got the same issue except that (I guess) it always looks for libicui18n.so.54 :

[ Ubuntu 16.04 ]

[I 20:44:32.136 NotebookApp] Kernel started: ed62bf5e-f3ac-4188-8326-41dc78c3477a
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/deebee/anaconda2/lib/R/library/stringi/libs/stringi.so':
  libicui18n.so.54: cannot open shared object file: No such file or directory
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted

I followed this thread and created a new environment then installed r-essentials ( as @glimmerphoenix wrote. Tried also to comment out that line in Renviron as @mingwandroid mentioned, or to change the paths there to my environment and such. I also tried to install icu=54 with no help

conda list | grep r-essentials
r-essentials              1.6.0                  r3.4.1_0    r

/usr/bin/R -v
R version 3.4.1

~/anaconda2/bin/R -v
R version 3.3.2 

Thanks in advance for your help

[mingwandroid]

You are not using the latest R. 3.4.1 was released last week. In fact you seem to have an odd mix of 3.4.1 and 3.3.2, perhaps try conda update --all.

I'm guessing you have some packages from conda-forge too? Can you show the output from conda info and conda list --show-channel-urls please?

[dorcoh]

Hi thanks for the fast reply, I do have conda-forge packages too but in main env (I read in other thread it causes misbehaviour, how do I delete pkgs by specific channel?). I just did conda update --all and tried to run jupyter from my env and the main env but it dies again

output after update:

Current conda install:

               platform : linux-64
          conda version : 4.3.25
       conda is private : False
      conda-env version : 4.3.25
    conda-build version : 1.20.0
         python version : 2.7.12.final.0
       requests version : 2.13.0
       root environment : /home/deebee/anaconda2  (writable)
    default environment : /home/deebee/anaconda2/envs/madlan
       envs directories : /home/deebee/anaconda2/envs
                          /home/deebee/.conda/envs
          package cache : /home/deebee/anaconda2/pkgs
                          /home/deebee/.conda/pkgs
           channel URLs : 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 : None
             netrc file : None
           offline mode : False
             user-agent : conda/4.3.25 requests/2.13.0 CPython/2.7.12 Linux/4.4.0-62-generic debian/stretch/sid glibc/2.23    
                UID:GID : 1000:1000

list from my env

# packages in environment at /home/deebee/anaconda2/envs/madlan:
#
backports                 1.0                      py27_0    defaults
backports_abc             0.5                      py27_0    defaults
bleach                    1.5.0                    py27_0    defaults
bzip2                     1.0.6                         3    defaults
cairo                     1.14.8                        0    defaults
configparser              3.5.0                    py27_0    defaults
curl                      7.54.1                        0    defaults
dbus                      1.10.20                       0    defaults
decorator                 4.1.2                    py27_0    defaults
entrypoints               0.2.3                    py27_0    defaults
enum34                    1.1.6                    py27_0    defaults
expat                     2.1.0                         0    defaults
fontconfig                2.12.1                        3    defaults
freetype                  2.5.5                         2    defaults
functools32               3.2.3.2                  py27_0    defaults
get_terminal_size         1.0.0                    py27_0    defaults
glib                      2.50.2                        1    defaults
gmp                       6.1.0                         0    defaults
gsl                       2.2.1                         0    defaults
gst-plugins-base          1.8.0                         0    defaults
gstreamer                 1.8.0                         0    defaults
harfbuzz                  0.9.39                        2    defaults
html5lib                  0.9999999                py27_0    defaults
icu                       54.1                          0    defaults
ipykernel                 4.6.1                    py27_0    defaults
ipython                   5.3.0                    py27_0    defaults
ipython_genutils          0.2.0                    py27_0    defaults
ipywidgets                6.0.0                    py27_0    defaults
jbig                      2.1                           0    defaults
jinja2                    2.9.6                    py27_0    defaults
jpeg                      9b                            0    defaults
jsonschema                2.6.0                    py27_0    defaults
jupyter                   1.0.0                    py27_3    defaults
jupyter_client            5.1.0                    py27_0    defaults
jupyter_console           5.2.0                    py27_0    defaults
jupyter_core              4.3.0                    py27_0    defaults
krb5                      1.13.2                        0    defaults
libffi                    3.2.1                         1    defaults
libgcc                    5.2.0                         0    defaults
libiconv                  1.14                          0    defaults
libpng                    1.6.27                        0    defaults
libsodium                 1.0.10                        0    defaults
libssh2                   1.8.0                         0    defaults
libtiff                   4.0.6                         3    defaults
libxcb                    1.12                          1    defaults
libxml2                   2.9.4                         0    defaults
markupsafe                1.0                      py27_0    defaults
mistune                   0.7.4                    py27_0    defaults
nbconvert                 5.2.1                    py27_0    defaults
nbformat                  4.4.0                    py27_0    defaults
ncurses                   5.9                          10    defaults
notebook                  5.0.0                    py27_0    defaults
openssl                   1.0.2l                        0    defaults
pandoc                    1.15.0.6                      0    defaults
pandocfilters             1.4.1                    py27_0    defaults
pango                     1.40.3                        1    defaults
path.py                   10.3.1                   py27_0    defaults
pathlib2                  2.3.0                    py27_0    defaults
pcre                      8.39                          1    defaults
pexpect                   4.2.1                    py27_0    defaults
pickleshare               0.7.4                    py27_0    defaults
pip                       9.0.1                    py27_1    defaults
pixman                    0.34.0                        0    defaults
prompt_toolkit            1.0.15                   py27_0    defaults
ptyprocess                0.5.2                    py27_0    defaults
pygments                  2.2.0                    py27_0    defaults
pyqt                      5.6.0                    py27_2    defaults
python                    2.7.13                        0    defaults
python-dateutil           2.6.1                    py27_0    defaults
pyzmq                     16.0.2                   py27_0    defaults
qt                        5.6.2                         5    defaults
qtconsole                 4.3.1                    py27_0    defaults
r-assertthat              0.2.0                  r3.4.1_0    defaults
r-backports               1.1.0                  r3.4.1_0    defaults
r-base                    3.4.1                         0    defaults
r-base64enc               0.1_3                  r3.4.1_0    defaults
r-bh                      1.62.0_1               r3.4.1_0    defaults
r-bindr                   0.1                    r3.4.1_0    defaults
r-bindrcpp                0.2                    r3.4.1_0    defaults
r-bitops                  1.0_6                  r3.4.1_2    defaults
r-boot                    1.3_19                 r3.4.1_0    defaults
r-broom                   0.4.2                  r3.4.1_0    defaults
r-car                     2.1_4                  r3.4.1_0    defaults
r-caret                   6.0_76                 r3.4.1_0    defaults
r-catools                 1.17.1                 r3.4.1_2    defaults
r-cellranger              1.1.0                  r3.4.1_0    defaults
r-class                   7.3_14                 r3.4.1_0    defaults
r-cluster                 2.0.6                  r3.4.1_0    defaults
r-codetools               0.2_15                 r3.4.1_0    defaults
r-colorspace              1.3_2                  r3.4.1_0    defaults
r-crayon                  1.3.2                  r3.4.1_0    defaults
r-curl                    2.6                    r3.4.1_0    defaults
r-data.table              1.10.4                 r3.4.1_0    defaults
r-dbi                     0.6_1                  r3.4.1_0    defaults
r-dichromat               2.0_0                  r3.4.1_2    defaults
r-digest                  0.6.12                 r3.4.1_0    defaults
r-dplyr                   0.7.0                  r3.4.1_0    defaults
r-essentials              1.6.0                  r3.4.1_0    defaults
r-evaluate                0.10                   r3.4.1_0    defaults
r-forcats                 0.2.0                  r3.4.1_0    defaults
r-foreach                 1.4.3                  r3.4.1_0    defaults
r-foreign                 0.8_68                 r3.4.1_0    defaults
r-formatr                 1.5                    r3.4.1_0    defaults
r-ggplot2                 2.2.1                  r3.4.1_0    defaults
r-gistr                   0.4.0                  r3.4.1_0    defaults
r-glmnet                  2.0_10                 r3.4.1_0    defaults
r-glue                    1.1.1                  r3.4.1_0    defaults
r-gtable                  0.2.0                  r3.4.1_0    defaults
r-haven                   1.0.0                  r3.4.1_0    defaults
r-hexbin                  1.27.1                 r3.4.1_0    defaults
r-highr                   0.6                    r3.4.1_0    defaults
r-hms                     0.3                    r3.4.1_0    defaults
r-htmltools               0.3.6                  r3.4.1_0    defaults
r-htmlwidgets             0.8                    r3.4.1_1    defaults
r-httpuv                  1.3.3                  r3.4.1_0    defaults
r-httr                    1.2.1                  r3.4.1_0    defaults
r-irdisplay               0.4.4                  r3.4.1_0    defaults
r-irkernel                0.7.1                  r3.4.1_0    defaults
r-iterators               1.0.8                  r3.4.1_0    defaults
r-jsonlite                1.5                    r3.4.1_0    defaults
r-kernsmooth              2.23_15                r3.4.1_0    defaults
r-knitr                   1.16                   r3.4.1_0    defaults
r-labeling                0.3                    r3.4.1_2    defaults
r-lattice                 0.20_35                r3.4.1_0    defaults
r-lazyeval                0.2.0                  r3.4.1_0    defaults
r-lme4                    1.1_13                 r3.4.1_0    defaults
r-lubridate               1.6.0                  r3.4.1_0    defaults
r-magrittr                1.5                    r3.4.1_2    defaults
r-maps                    3.2.0                  r3.4.1_0    defaults
r-markdown                0.8                    r3.4.1_0    defaults
r-mass                    7.3_47                 r3.4.1_0    defaults
r-matrix                  1.2_10                 r3.4.1_0    defaults
r-matrixmodels            0.4_1                  r3.4.1_0    defaults
r-mgcv                    1.8_17                 r3.4.1_0    defaults
r-mime                    0.5                    r3.4.1_0    defaults
r-minqa                   1.2.4                  r3.4.1_2    defaults
r-mnormt                  1.5_5                  r3.4.1_0    defaults
r-modelmetrics            1.1.0                  r3.4.1_0    defaults
r-modelr                  0.1.0                  r3.4.1_0    defaults
r-munsell                 0.4.3                  r3.4.1_0    defaults
r-nlme                    3.1_131                r3.4.1_0    defaults
r-nloptr                  1.0.4                  r3.4.1_2    defaults
r-nnet                    7.3_12                 r3.4.1_0    defaults
r-openssl                 0.9.6                  r3.4.1_0    defaults
r-pbdzmq                  0.2_6                  r3.4.1_0    defaults
r-pbkrtest                0.4_7                  r3.4.1_0    defaults
r-pkgconfig               2.0.1                  r3.4.1_0    defaults
r-plogr                   0.1_1                  r3.4.1_0    defaults
r-plyr                    1.8.4                  r3.4.1_0    defaults
r-pryr                    0.1.2                  r3.4.1_0    defaults
r-psych                   1.7.5                  r3.4.1_0    defaults
r-purrr                   0.2.2.2                r3.4.1_0    defaults
r-quantmod                0.4_9                  r3.4.1_0    defaults
r-quantreg                5.33                   r3.4.1_0    defaults
r-r6                      2.2.1                  r3.4.1_0    defaults
r-randomforest            4.6_12                 r3.4.1_0    defaults
r-rbokeh                  0.5.0                  r3.4.1_0    defaults
r-rcolorbrewer            1.1_2                  r3.4.1_3    defaults
r-rcpp                    0.12.11                r3.4.1_0    defaults
r-rcppeigen               0.3.3.3.0              r3.4.1_0    defaults
r-readr                   1.1.1                  r3.4.1_0    defaults
r-readxl                  1.0.0                  r3.4.1_0    defaults
r-recommended             3.4.1                  r3.4.1_0    defaults
r-rematch                 1.0.1                  r3.4.1_0    defaults
r-repr                    0.10                   r3.4.1_0    defaults
r-reshape2                1.4.2                  r3.4.1_0    defaults
r-rlang                   0.1.1                  r3.4.1_0    defaults
r-rmarkdown               1.5                    r3.4.1_0    defaults
r-rpart                   4.1_11                 r3.4.1_0    defaults
r-rprojroot               1.2                    r3.4.1_0    defaults
r-rvest                   0.3.2                  r3.4.1_0    defaults
r-scales                  0.4.1                  r3.4.1_0    defaults
r-selectr                 0.3_1                  r3.4.1_0    defaults
r-shiny                   1.0.3                  r3.4.1_0    defaults
r-sourcetools             0.1.6                  r3.4.1_0    defaults
r-sparsem                 1.77                   r3.4.1_0    defaults
r-spatial                 7.3_11                 r3.4.1_0    defaults
r-stringi                 1.1.5                  r3.4.1_0    defaults
r-stringr                 1.2.0                  r3.4.1_0    defaults
r-survival                2.41_3                 r3.4.1_0    defaults
r-tibble                  1.3.3                  r3.4.1_0    defaults
r-tidyr                   0.6.3                  r3.4.1_0    defaults
r-tidyverse               1.1.1                  r3.4.1_0    defaults
r-ttr                     0.23_1                 r3.4.1_0    defaults
r-uuid                    0.1_2                  r3.4.1_0    defaults
r-xml2                    1.1.1                  r3.4.1_0    defaults
r-xtable                  1.8_2                  r3.4.1_0    defaults
r-xts                     0.9_7                  r3.4.1_2    defaults
r-yaml                    2.1.14                 r3.4.1_0    defaults
r-zoo                     1.8_0                  r3.4.1_0    defaults
readline                  6.2                           2    defaults
scandir                   1.5                      py27_0    defaults
setuptools                27.2.0                   py27_0    defaults
simplegeneric             0.8.1                    py27_1    defaults
singledispatch            3.4.0.3                  py27_0    defaults
sip                       4.18                     py27_0    defaults
six                       1.10.0                   py27_0    defaults
sqlite                    3.13.0                        0    defaults
ssl_match_hostname        3.5.0.1                  py27_0    defaults
terminado                 0.6                      py27_0    defaults
testpath                  0.3.1                    py27_0    defaults
tk                        8.5.18                        0    defaults
tornado                   4.5.1                    py27_0    defaults
traitlets                 4.3.2                    py27_0    defaults
wcwidth                   0.1.7                    py27_0    defaults
wheel                     0.29.0                   py27_0    defaults
widgetsnbextension        2.0.0                    py27_0    defaults
xz                        5.2.3                         0    defaults
zeromq                    4.1.5                         0    defaults
zlib                      1.2.11                        0    defaults

in main env:

# packages in environment at /home/deebee/anaconda2:
#
alabaster                 0.7.7                    py27_0    defaults
anaconda                  custom                   py27_0    defaults
anaconda-clean            1.1.0                    py27_0    defaults
anaconda-client           1.4.0                    py27_0    defaults
anaconda-navigator        1.1.0                    py27_0    defaults
argcomplete               1.0.0                    py27_1    defaults
astropy                   1.1.2               np110py27_0    defaults
babel                     2.2.0                    py27_0    defaults
backports_abc             0.4                      py27_0    defaults
beautifulsoup4            4.4.1                    py27_0    defaults
bitarray                  0.8.1                    py27_0    defaults
blaze                     0.9.1                    py27_0    defaults
bokeh                     0.11.1                   py27_0    defaults
boto                      2.39.0                   py27_0    defaults
bottleneck                1.2.0               np110py27_0    conda-forge
bzip2                     1.0.6                         3    defaults
cairo                     1.12.18                       8    conda-forge
cdecimal                  2.3                      py27_0    defaults
cffi                      1.5.2                    py27_0    defaults
chest                     0.2.3                    py27_0    defaults
cloudpickle               0.1.1                    py27_0    defaults
clyent                    1.2.1                    py27_0    defaults
colorama                  0.3.7                    py27_0    defaults
conda                     4.3.25                   py27_0    defaults
conda-build               1.20.0                   py27_0    defaults
conda-env                 2.6.0                         0    defaults
conda-manager             0.3.1                    py27_0    defaults
configobj                 5.0.6                    py27_0    defaults
cryptography              1.7.1                    py27_0    defaults
curl                      7.45.0                        0    defaults
cycler                    0.10.0                   py27_0    defaults
cython                    0.23.4                   py27_0    defaults
cytoolz                   0.7.5                    py27_0    defaults
dask                      0.8.1                    py27_0    defaults
datashape                 0.5.1                    py27_0    defaults
decorator                 4.0.9                    py27_0    defaults
dill                      0.2.4                    py27_0    defaults
docutils                  0.12                     py27_0    defaults
dynd-python               0.7.2                    py27_0    defaults
enum34                    1.1.2                    py27_0    defaults
et_xmlfile                1.0.1                    py27_0    defaults
fastcache                 1.0.2                    py27_0    defaults
flask                     0.10.1                   py27_1    defaults
flask-cors                2.1.2                    py27_0    defaults
fontconfig                2.11.1                        6    conda-forge
freetype                  2.6.3                         1    conda-forge
funcsigs                  0.4                      py27_0    defaults
functools32               3.2.3.2                  py27_1    conda-forge
futures                   3.0.3                    py27_0    defaults
gevent                    1.1.0                    py27_0    defaults
glib                      2.43.0                        1    defaults
gmp                       6.1.2                         0    conda-forge
gmplot                    1.1.1                     <pip>
greenlet                  0.4.9                    py27_0    defaults
grin                      1.2.1                    py27_1    defaults
gsl                       2.2.1                         0    defaults
h5py                      2.6.0               np110py27_3    conda-forge
harfbuzz                  0.9.39                        1    defaults
hdf5                      1.8.15.1                      2    defaults
heapdict                  1.0.0                    py27_0    defaults
httplib2                  0.9.2                     <pip>
icu                       56.1                          4    conda-forge
idna                      2.1                       <pip>
idna                      2.0                      py27_0    defaults
ipaddress                 1.0.14                   py27_0    defaults
ipykernel                 4.3.1                    py27_0    defaults
ipython                   4.1.2                    py27_1    defaults
ipython_genutils          0.1.0                    py27_0    defaults
ipywidgets                4.1.1                    py27_0    defaults
itsdangerous              0.24                     py27_0    defaults
jbig                      2.1                           0    defaults
jdcal                     1.2                      py27_0    defaults
jedi                      0.9.0                    py27_0    defaults
jinja2                    2.8                      py27_0    defaults
jpeg                      9b                            0    conda-forge
jsonschema                2.4.0                    py27_0    defaults
jupyter                   1.0.0                    py27_3    defaults
jupyter_client            4.2.2                    py27_0    defaults
jupyter_console           4.1.1                    py27_0    defaults
jupyter_core              4.1.0                    py27_0    defaults
keras                     2.0.6                    py27_0    conda-forge
libdynd                   0.7.2                         0    defaults
libffi                    3.0.13                        0    defaults
libgcc                    5.2.0                         0    defaults
libgfortran               1.0                           0    defaults
libiconv                  1.14                          4    conda-forge
libpng                    1.6.28                        1    conda-forge
libsodium                 1.0.3                         0    defaults
libtiff                   4.0.6                         7    conda-forge
libxml2                   2.9.2                         0    defaults
libxslt                   1.1.28                        0    defaults
llvmlite                  0.9.0                    py27_0    defaults
locket                    0.2.0                    py27_0    defaults
lxml                      3.6.0                    py27_0    defaults
markupsafe                0.23                     py27_0    defaults
matplotlib                2.0.0               np110py27_1    conda-forge
mistune                   0.7.2                    py27_0    defaults
mkl                       11.3.3                        0    defaults
mkl-rt                    11.1                         p0    defaults
mkl-service               1.0.0                   py27_p2    defaults
mpmath                    0.19                     py27_0    defaults
multipledispatch          0.4.8                    py27_0    defaults
nbconvert                 4.1.0                    py27_0    defaults
nbformat                  4.0.1                    py27_0    defaults
ncurses                   5.9                          10    defaults
networkx                  1.9.1                    py27_0    defaults
nlopt                     2.4.2                    py27_1    conda-forge
nltk                      3.2                      py27_0    defaults
nose                      1.3.7                    py27_0    defaults
notebook                  5.0.0                    py27_0    defaults
numba                     0.24.0              np110py27_0    defaults
numexpr                   2.5.2               np110py27_1    defaults
numpy                     1.12.1                    <pip>
numpy                     1.10.4                   py27_2    defaults
oauth                     1.0.1                     <pip>
odo                       0.4.2                    py27_0    defaults
olefile                   0.44                     py27_0    conda-forge
openblas                  0.2.14                        3    defaults
openpyxl                  2.3.2                    py27_0    defaults
openssl                   1.0.2g                        0    defaults
pandas                    0.20.3                   py27_1    conda-forge
pango                     1.40.1                        0    conda-forge
paramiko                  2.0.0                     <pip>
partd                     0.3.2                    py27_1    defaults
patchelf                  0.8                           0    defaults
path.py                   8.1.2                    py27_1    defaults
patsy                     0.4.1                    py27_0    defaults
pcre                      8.39                          1    defaults
pep8                      1.7.0                    py27_0    defaults
pexpect                   4.0.1                    py27_0    defaults
pickleshare               0.5                      py27_0    defaults
pillow                    4.0.0                    py27_1    conda-forge
pip                       8.1.1                    py27_1    defaults
pip                       9.0.1                     <pip>
pixman                    0.32.6                        0    defaults
ply                       3.8                      py27_0    defaults
proj4                     4.9.2                         0    defaults
protobuf                  3.3.0                     <pip>
psutil                    4.1.0                    py27_0    defaults
ptyprocess                0.5                      py27_0    defaults
py                        1.4.31                   py27_0    defaults
py2cairo                  1.10.0                   py27_2    defaults
pyasn1                    0.1.9                    py27_0    defaults
pycairo                   1.10.0                   py27_0    defaults
pycosat                   0.6.1                    py27_0    defaults
pycparser                 2.14                     py27_0    defaults
pycrypto                  2.6.1                    py27_0    defaults
pycryptosat               4.5.3                     <pip>
pycurl                    7.19.5.3                 py27_0    defaults
pyflakes                  1.1.0                    py27_0    defaults
pygments                  2.1.1                    py27_0    defaults
PyOpenGL                  3.1.0                     <pip>
PyOpenGL-accelerate       3.1.0                     <pip>
PyOpenGL-Demo             3.0.0                     <pip>
PyOpenGL-Demo             3.0.1b1                   <pip>
pyopenssl                 16.2.0                   py27_0    conda-forge
pyparsing                 2.0.3                     <pip>
pyparsing                 2.0.3                    py27_0    defaults
pyqt                      4.11.4                   py27_1    defaults
pytables                  3.2.2               np110py27_1    defaults
pytest                    2.8.5                    py27_0    defaults
python                    2.7.12                        1    defaults
python-dateutil           2.5.1                    py27_0    defaults
pytz                      2016.2                   py27_0    defaults
pyyaml                    3.11                     py27_1    defaults
pyzmq                     15.2.0                   py27_0    defaults
qt                        4.8.7                         1    defaults
qtawesome                 0.3.2                    py27_0    defaults
qtconsole                 4.2.0                    py27_0    defaults
qtpy                      1.0                      py27_0    defaults
r                         3.3.2                  r3.3.2_0    conda-forge
r-assertthat              0.1                    r3.3.2_0    conda-forge
r-backports               1.0.5                  r3.3.2_0    conda-forge
r-base                    3.3.2                         2    conda-forge
r-base64enc               0.1_3                  r3.3.2_0    conda-forge
r-bh                      1.62.0_1               r3.3.2_0    conda-forge
r-bitops                  1.0_6                  r3.3.2_0    conda-forge
r-boot                    1.3_18                 r3.3.2_0    conda-forge
r-broom                   0.4.2                  r3.3.2_0    conda-forge
r-car                     2.1_4                  r3.3.2_0    conda-forge
r-caret                   6.0_76                 r3.3.2_0    conda-forge
r-catools                 1.17.1                 r3.3.2_0    conda-forge
r-class                   7.3_14                 r3.3.2_0    conda-forge
r-cluster                 2.0.6                  r3.3.2_0    conda-forge
r-codetools               0.2_15                 r3.3.2_0    conda-forge
r-colorspace              1.3_2                  r3.3.2_0    conda-forge
r-crayon                  1.3.2                  r3.3.2_0    conda-forge
r-curl                    2.4                    r3.3.2_0    conda-forge
r-data.table              1.10.4                 r3.3.2_0    conda-forge
r-dbi                     0.6_1                  r3.3.2_0    conda-forge
r-dichromat               2.0_0                  r3.3.2_0    conda-forge
r-digest                  0.6.10                 r3.3.2_0    conda-forge
r-doparallel              1.0.10                 r3.3.2_0    conda-forge
r-dplyr                   0.5.0                  r3.3.2_0    conda-forge
r-dt                      0.2                    r3.3.2_0    conda-forge
r-e1071                   1.6_8                  r3.3.2_0    conda-forge
r-essentials              1.5.2                  r3.3.2_0    r
r-evaluate                0.10                   r3.3.2_0    conda-forge
r-forcats                 0.1.1                  r3.3.2_0    r
r-foreach                 1.4.3                  r3.3.2_0    conda-forge
r-foreign                 0.8_67                 r3.3.2_0    conda-forge
r-formatr                 1.4                    r3.3.2_0    r
r-geosphere               1.5_5                  r3.3.2_0    conda-forge
r-ggmap                   2.6.1                  r3.3.2_0    conda-forge
r-ggplot2                 2.2.1                  r3.3.2_0    conda-forge
r-gistr                   0.4.0                  r3.3.2_0    conda-forge
r-glmnet                  2.0_5                  r3.3.2_0    conda-forge
r-gridbase                0.4_7                  r3.3.2_0    conda-forge
r-gtable                  0.2.0                  r3.3.2_0    conda-forge
r-haven                   1.0.0                  r3.3.2_0    r
r-hexbin                  1.27.1                 r3.3.2_0    conda-forge
r-highcharter             0.5.0                  r3.3.2_0    conda-forge
r-highr                   0.6                    r3.3.2_0    conda-forge
r-hms                     0.3                    r3.3.2_0    r
r-htmltools               0.3.6                  r3.3.2_0    conda-forge
r-htmlwidgets             0.8                    r3.3.2_0    conda-forge
r-httpuv                  1.3.3                  r3.3.2_0    conda-forge
r-httr                    1.2.1                  r3.3.2_0    conda-forge
r-igraph                  1.0.1                  r3.3.2_0    conda-forge
r-irdisplay               0.4.4                  r3.3.2_0    conda-forge
r-irkernel                0.7.1                  r3.3.2_0    r
r-irlba                   2.1.2                  r3.3.2_0    conda-forge
r-iterators               1.0.8                  r3.3.2_0    conda-forge
r-jpeg                    0.1_8                  r3.3.2_0    conda-forge
r-jsonlite                1.4                    r3.3.2_0    conda-forge
r-kernsmooth              2.23_15                r3.3.2_0    conda-forge
r-knitr                   1.16                   r3.3.2_0    conda-forge
r-labeling                0.3                    r3.3.2_0    conda-forge
r-lattice                 0.20_34                r3.3.2_0    conda-forge
r-lazyeval                0.2.0                  r3.3.2_0    conda-forge
r-lme4                    1.1_13                 r3.3.2_0    conda-forge
r-lubridate               1.6.0                  r3.3.2_0    r
r-magrittr                1.5                    r3.3.2_0    conda-forge
r-mapproj                 1.2_4                  r3.3.2_0    conda-forge
r-maps                    3.2.0                  r3.3.2_0    conda-forge
r-markdown                0.8                    r3.3.2_0    conda-forge
r-mass                    7.3_45                 r3.3.2_0    conda-forge
r-matrix                  1.2_7.1                r3.3.2_0    conda-forge
r-matrixmodels            0.4_1                  r3.3.2_0    conda-forge
r-memoise                 1.1.0                  r3.3.2_0    conda-forge
r-mgcv                    1.8_17                 r3.3.2_0    conda-forge
r-mime                    0.5                    r3.3.2_0    conda-forge
r-minqa                   1.2.4                  r3.3.2_0    conda-forge
r-mnormt                  1.5_5                  r3.3.2_0    conda-forge
r-modelmetrics            1.1.0                  r3.3.2_0    conda-forge
r-modelr                  0.1.0                  r3.3.2_0    r
r-munsell                 0.4.3                  r3.3.2_0    conda-forge
r-nlme                    3.1_131                r3.3.2_0    conda-forge
r-nloptr                  1.0.4                  r3.3.2_0    conda-forge
r-nmf                     0.20.6                 r3.3.2_0    conda-forge
r-nnet                    7.3_12                 r3.3.2_0    conda-forge
r-openssl                 0.9.6                  r3.3.2_1    conda-forge
r-pbdzmq                  0.2_4                  r3.3.2_0    conda-forge
r-pbkrtest                0.4_7                  r3.3.2_0    conda-forge
r-pkgmaker                0.22                   r3.3.2_0    conda-forge
r-plotly                  4.5.6                  r3.3.2_0    bioconda
r-plyr                    1.8.4                  r3.3.2_0    conda-forge
r-png                     0.1_7                  r3.3.2_0    conda-forge
r-proto                   1.0.0                  r3.3.2_0    conda-forge
r-pryr                    0.1.2                  r3.3.2_0    conda-forge
r-psych                   1.7.3.21               r3.3.2_0    conda-forge
r-purrr                   0.2.2                         1    bioconda
r-quantmod                0.4_8                  r3.3.2_0    conda-forge
r-quantreg                5.33                   r3.3.2_0    conda-forge
r-r6                      2.2.0                  r3.3.2_0    conda-forge
r-randomforest            4.6_12                 r3.3.2_0    conda-forge
r-rbokeh                  0.5.0                  r3.3.2_0    conda-forge
r-rcolorbrewer            1.1_2                  r3.3.2_0    conda-forge
r-rcpp                    0.12.10                r3.3.2_0    conda-forge
r-rcppeigen               0.3.2.9.1              r3.3.2_0    conda-forge
r-readr                   1.0.0                  r3.3.2_0    r
r-readxl                  0.1.1                  r3.3.2_0    r
r-recommended             3.3.2                  r3.3.2_0    conda-forge
r-registry                0.3                    r3.3.2_0    conda-forge
r-repr                    0.10                   r3.3.2_0    conda-forge
r-reshape2                1.4.2                  r3.3.2_0    conda-forge
r-rgooglemaps             1.4.1                  r3.3.2_0    conda-forge
r-rjson                   0.2.15                 r3.3.2_0    conda-forge
r-rlist                   0.4.6.1                r3.3.2_0    conda-forge
r-rmarkdown               1.6                    r3.3.2_1    conda-forge
r-rngtools                1.2.4                  r3.3.2_0    conda-forge
r-rpart                   4.1_10                 r3.3.2_0    conda-forge
r-rprojroot               1.2                    r3.3.2_0    conda-forge
r-rvest                   0.3.2                  r3.3.2_0    r
r-scales                  0.4.1                  r3.3.2_0    conda-forge
r-selectr                 0.3_0                  r3.3.2_0    r
r-shiny                   1.0.3                  r3.3.2_0    conda-forge
r-sourcetools             0.1.6                  r3.3.2_0    conda-forge
r-sp                      1.2_4                  r3.3.2_0    conda-forge
r-sparsem                 1.76                   r3.3.2_0    conda-forge
r-spatial                 7.3_11                 r3.3.2_0    conda-forge
r-stringi                 1.1.2                  r3.3.2_0    r
r-stringr                 1.2.0                  r3.3.2_0    conda-forge
r-survival                2.40_1                 r3.3.2_0    conda-forge
r-tibble                  1.2                    r3.3.2_0    r
r-tidyr                   0.6.1                  r3.3.2_0    conda-forge
r-tidyverse               1.0.0                  r3.3.2_0    r
r-ttr                     0.23_1                 r3.3.2_0    conda-forge
r-uuid                    0.1_2                  r3.3.2_0    conda-forge
r-viridislite             0.1.3                  r3.3.2_0    defaults
r-xml                     3.98_1.6               r3.3.2_0    conda-forge
r-xml2                    1.0.0                  r3.3.2_0    r
r-xtable                  1.8_2                  r3.3.2_0    conda-forge
r-xts                     0.9_7                  r3.3.2_0    conda-forge
r-yaml                    2.1.14                 r3.3.2_0    conda-forge
r-zoo                     1.7_14                 r3.3.2_0    conda-forge
readline                  6.2                           2    defaults
redis                     2.6.9                         0    defaults
redis-py                  2.10.3                   py27_0    defaults
requests                  2.13.0                   py27_0    conda-forge
rope                      0.9.4                    py27_1    defaults
ruamel_yaml               0.11.14                  py27_0    defaults
scikit-image              0.12.3              np110py27_0    conda-forge
scikit-learn              0.17.1              np110py27_2    defaults
scipy                     0.16.0                    <pip>
scipy                     0.16.0              np110py27_1    defaults
setuptools                20.3                     py27_0    defaults
simplegeneric             0.8.1                    py27_0    defaults
simplejson                3.8.2                     <pip>
singledispatch            3.4.0.3                  py27_0    defaults
sip                       4.16.9                   py27_0    defaults
six                       1.10.0                   py27_0    defaults
snowballstemmer           1.2.1                    py27_0    defaults
sockjs-tornado            1.0.1                    py27_0    defaults
sphinx                    1.3.5                    py27_0    defaults
sphinx_rtd_theme          0.1.9                    py27_0    defaults
spyder                    2.3.8                    py27_1    defaults
sqlalchemy                1.0.12                   py27_0    defaults
sqlite                    3.13.0                        0    defaults
ssl_match_hostname        3.4.0.2                  py27_0    defaults
statsmodels               0.8.0               np110py27_0    conda-forge
subprocess32              3.2.7                    py27_0    conda-forge
sympy                     1.0                      py27_0    defaults
tensorflow                1.1.0                     <pip>
tensorflow-gpu            1.1.0                     <pip>
terminado                 0.5                      py27_1    defaults
theano                    0.8.2                    py27_0    conda-forge
tk                        8.5.18                        0    defaults
toolz                     0.7.4                    py27_0    defaults
torch-0.2.0               1                         <pip>
torchvision               0.1.9                     <pip>
tornado                   4.3                      py27_0    defaults
traitlets                 4.2.1                    py27_0    defaults
uncompyle2                1.1                       <pip>
unicodecsv                0.14.1                   py27_0    defaults
util-linux                2.21                          0    defaults
Werkzeug                  0.12.2                    <pip>
werkzeug                  0.11.4                   py27_0    defaults
wheel                     0.29.0                   py27_0    defaults
xlrd                      0.9.4                    py27_0    defaults
xlsxwriter                0.8.4                    py27_0    defaults
xlwt                      1.0.0                    py27_0    defaults
xz                        5.2.3                         0    defaults
yaml                      0.1.6                         0    defaults
zeromq                    4.1.3                         0    defaults
zlib                      1.2.8                         0    defaults

Thanks

[mingwandroid]

OK, your /home/deebee/anaconda2/envs/madlan env looks OK to me.

From a shell without any conda or anaconda software on PATH, can you do: . /home/deebee/anaconda2/bin/activate home/deebee/anaconda2/envs/madlan

Then just try to run R from that shell? We need to take Jupyter out of the equation here and see if the problem manifests independently of that.

[dorcoh]

Ok it loads with 3.4.1

deebee@realm:~/anaconda2/envs/madlan/include$ env -i bash --noprofile --norc

bash-4.3$ . ~/anaconda2/bin/activate ~/anaconda2/envs/madlan                     
(/home/deebee/anaconda2/envs/madlan) bash-4.3$ R

R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 

[mingwandroid]

So something about how you launch it through Jupyter is at fault here? Can you launch Jupyter from the same shell instead?

[dorcoh]

I just tried to remove r-base (it was from channel conda-forge) from my main env and installed again (somehow it installed 3.3.1, even older) :

deebee@realm:~/anaconda2/envs/madlan/include$ conda remove r-base
Fetching package metadata .........
Solving package specifications: 
Package plan for package removal in environment /home/deebee/anaconda2:

The following packages will be REMOVED:

    r-base: 3.3.2-2 conda-forge

Proceed ([y]/n)? y

deebee@realm:~/anaconda2/envs/madlan/include$ conda install -c r r-base
Fetching package metadata ...........
Solving package specifications: .

Package plan for installation in environment /home/deebee/anaconda2:

The following NEW packages will be INSTALLED:

    r-base:     3.3.1-5           r          

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

    cairo:      1.12.18-8         conda-forge --> 1.12.18-6        
    fontconfig: 2.11.1-6          conda-forge --> 2.11.1-6         
    freetype:   2.6.3-1           conda-forge --> 2.5.5-2          
    icu:        56.1-4            conda-forge --> 54.1-0           
    jpeg:       9b-0              conda-forge --> 8d-2             
    libtiff:    4.0.6-7           conda-forge --> 4.0.6-2          
    matplotlib: 2.0.0-np110py27_1 conda-forge --> 1.5.1-np110py27_0
    pango:      1.40.1-0          conda-forge --> 1.39.0-1         
    pillow:     4.0.0-py27_1      conda-forge --> 3.4.2-py27_0

and suddenly it works (from my main env, and the clean shell too), what do you think caused this? btw, why it doesn't update to 3.4.1 as in https://anaconda.org/r/r-base should I just try to re-install conda and all it's packages? or just conda-forge packages?

Thanks

[mingwandroid]

Conda has removed all packages from conda-forge from your main env here because conda-forge has been removed from the channels it considers, so now you are back to an entirely defaults based environment and that means there are no binary compatibility issues anymore.

It's probably best to know what your goals are here, all I can say for sure is that you cannot mix software from conda-forge with software from defaults in the same environment and expect it to work properly.

[nick-youngblut]

I've followed the instructions on bioconda about setting up channel order and I'm getting the same error:

Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/ebio/abt3_projects/software/dev/miniconda3/lib/R/library/stringi/libs/stringi.so':
  libicui18n.so.58: cannot open shared object file: No such file or directory
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted

I used a simple install script to set up 2 environments (1 for python2 & 1 for python3):

#!/bin/bash
# miniconda install & setup

# set vars
VERSION=0.2.0
LOG="miniconda_setup.log"
CONDA_URL="https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh"
# paraent directory (install directory)
PARENT_DIR=$(dirname `pwd`)
INSTALL_DIR=$PARENT_DIR"/miniconda3"
CONDA_PATH=$INSTALL_DIR"/bin"

# preamble
echo ""
echo "NOTE: install log written to: "$LOG
echo ""
echo "#-- miniconda_setup.sh log --#" > $LOG
echo "# miniconda_setup version: "$VERSION | tee -a $LOG

# download
echo "# Downloading miniconda" | tee -a $LOG
wget -nv $CONDA_URL 2>> $LOG 1>&2

# install
echo "# Running miniconda installer" | tee -a $LOG
bash Miniconda3-latest-Linux-x86_64.sh -b -p $INSTALL_DIR 2>> $LOG 1>&2
## delete installer
rm -f Miniconda3-latest-Linux-x86_64.sh

# add conda to PATH
echo "# Adding conda to PATH" | tee -a $LOG
export PATH=$CONDA_PATH:$PATH

# adding channels
echo "# Adding conda channels" | tee -a $LOG
conda config --add channels r
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

# creating conda envs
echo "# Creating conda environemnts" | tee -a $LOG
conda create -q -y -n py3 python=3 2>> $LOG 1>&2
conda create -q -y -n py2 python=2 2>> $LOG 1>&2

echo "# Installing jupyter" | tee -a $LOG
conda install -q -y jupyter 2>> $LOG 1>&2

echo "# Installing nb_conda" | tee -a $LOG
conda install -q -y nb_conda 2>> $LOG 1>&2

echo "# Installing kernels" | tee -a $LOG
echo "## Adding kernels for conda environments" | tee -a $LOG
conda install -q -y -n py2 ipykernel nb_conda 2>> $LOG 1>&2
conda install -q -y -n py3 ipykernel nb_conda 2>> $LOG 1>&2

echo "# Installing R-base" | tee -a $LOG
conda install -q -y r-base 2>> $LOG 1>&2
conda install -q -y -n py2 r-base 2>> $LOG 1>&2
conda install -q -y -n py3 r-base 2>> $LOG 1>&2

echo "## Installing rpy2" | tee -a $LOG
conda install -q -y rpy2 2>> $LOG 1>&2
conda install -q -y -n py2 rpy2 2>> $LOG 1>&2
conda install -q -y -n py3 rpy2 2>> $LOG 1>&2

echo "## Installing irkernel" | tee -a $LOG
conda install -q -y r-irkernel 2>> $LOG 1>&2
conda install -q -y -n py2 r-irkernel 2>> $LOG 1>&2
conda install -q -y -n py3 r-irkernel 2>> $LOG 1>&2

The resulting environment looks like the following:

# packages in environment at /ebio/abt3_projects/software/dev/miniconda3:
#
asn1crypto                0.22.0           py36h265ca7c_1
bleach                    1.4.2                    py36_0    bioconda
bzip2                     1.0.6                         1    conda-forge
ca-certificates           2017.08.26           h1d4fec5_0
cairo                     1.14.8                        0
certifi                   2017.7.27.1      py36h8b7b77e_0
cffi                      1.10.0           py36had8d393_1
chardet                   3.0.4            py36h0f667ec_1
conda                     4.3.29                   py36_0    conda-forge
conda-env                 2.6.0                         0    conda-forge
cryptography              2.0.3            py36ha225213_1
curl                      7.55.1                        0    conda-forge
dbus                      1.10.22                       0    conda-forge
decorator                 4.1.2                    py36_0    conda-forge
entrypoints               0.2.3                    py36_1    conda-forge
expat                     2.2.1                         0    conda-forge
fontconfig                2.12.1                        3
freetype                  2.5.5                         2
gettext                   0.19.7                        1    conda-forge
glib                      2.50.2                        1
gmp                       6.1.2                         0    conda-forge
graphite2                 1.3.9                         0    conda-forge
gsl                       2.1                           2    conda-forge
gst-plugins-base          1.8.0                         0    conda-forge
gstreamer                 1.8.0                         1    conda-forge
harfbuzz                  0.9.39                        2
html5lib                  0.999999999              py36_0    conda-forge
icu                       54.1                          0
idna                      2.6              py36h82fb2a8_1
ipykernel                 4.6.1                    py36_0    conda-forge
ipython                   6.2.1                    py36_0    conda-forge
ipython_genutils          0.2.0                    py36_0    conda-forge
ipywidgets                7.0.3                    py36_1    conda-forge
jedi                      0.10.2                   py36_0    conda-forge
jinja2                    2.9.6                    py36_0    conda-forge
jpeg                      9b                            2    conda-forge
jsonschema                2.6.0                    py36_0    conda-forge
jupyter                   1.0.0                    py36_0    conda-forge
jupyter_client            5.1.0                    py36_0    conda-forge
jupyter_console           5.2.0                    py36_0    conda-forge
jupyter_core              4.4.0                      py_0    conda-forge
krb5                      1.14.2                        0    conda-forge
libedit                   3.1.20170329                  0    conda-forge
libffi                    3.2.1                h4deb6c0_3
libgcc                    7.2.0                h69d50b8_2
libgcc-ng                 7.2.0                h7cc24e2_2
libiconv                  1.14                          4    conda-forge
libpng                    1.6.28                        2    conda-forge
libsodium                 1.0.10                        0    conda-forge
libssh2                   1.8.0                         2    conda-forge
libstdcxx-ng              7.2.0                h7a57d05_2
libtiff                   4.0.7                         1    conda-forge
libxcb                    1.12                          1    conda-forge
libxml2                   2.9.4                         0
markupsafe                1.0                      py36_0    conda-forge
mistune                   0.8                      py36_0    conda-forge
nb_conda                  2.2.1                    py36_0    conda-forge
nb_conda_kernels          2.1.0                    py36_0    conda-forge
nbconvert                 5.3.1                      py_1    conda-forge
nbformat                  4.4.0                    py36_0    conda-forge
ncurses                   5.9                          10    conda-forge
notebook                  5.2.1                    py36_2    conda-forge
openssl                   1.0.2l               h077ae2c_5
pandoc                    2.0.0.1                       1    conda-forge
pandocfilters             1.4.1                    py36_0    conda-forge
pango                     1.40.3                        1
pcre                      8.39                          0    conda-forge
pexpect                   4.2.1                    py36_0    conda-forge
pickleshare               0.7.4                    py36_0    conda-forge
pip                       9.0.1            py36h8ec8b28_3
pixman                    0.34.0                        0    conda-forge
prompt_toolkit            1.0.15                   py36_0    conda-forge
ptyprocess                0.5.2                    py36_0    conda-forge
pycosat                   0.6.2            py36h1a0ea17_1
pycparser                 2.18             py36hf9f622e_1
pygments                  2.2.0                    py36_0    conda-forge
pyopenssl                 17.2.0           py36h5cc804b_0
pyqt                      5.6.0                    py36_4    conda-forge
pysocks                   1.6.7            py36hd97a5b1_1
python                    3.6.3                         1    conda-forge
python-dateutil           2.6.1                    py36_0    conda-forge
pyzmq                     16.0.2                   py36_2    conda-forge
qt                        5.6.2                         5
qtconsole                 4.3.1                    py36_0    conda-forge
r-base                    3.3.2                         1
r-crayon                  1.3.2                  r3.3.2_0    conda-forge
r-digest                  0.6.12                 r3.3.2_0    bioconda
r-evaluate                0.10                   r3.3.2_0    conda-forge
r-irdisplay               0.4.4                  r3.3.2_0    conda-forge
r-irkernel                0.8.7                  r3.3.2_0    conda-forge
r-jsonlite                0.9.19                 r3.3.2_1    bioconda
r-magrittr                1.5                    r3.3.2_0    conda-forge
r-pbdzmq                  0.2_6            r342h934a24f_0
r-r6                      2.2.0                  r3.3.2_0    conda-forge
r-repr                    0.10                   r3.3.2_0    conda-forge
r-stringi                 1.1.2                  r3.3.2_0    conda-forge
r-stringr                 1.2.0                  r3.3.2_0    conda-forge
r-uuid                    0.1_2                  r3.3.2_0    conda-forge
readline                  6.2                           0    conda-forge
requests                  2.18.4           py36he2e5f8d_1
rpy2                      2.7.8              py36r3.3.2_1    bioconda
ruamel_yaml               0.11.14          py36ha2fb22d_2
setuptools                36.5.0           py36he42e2e1_0
simplegeneric             0.8.1                    py36_0    conda-forge
singledispatch            3.4.0.3                  py36_0    conda-forge
sip                       4.18                     py36_1    conda-forge
six                       1.10.0           py36hcac75e4_1
sqlite                    3.13.0                        1    conda-forge
terminado                 0.6                      py36_0    conda-forge
testpath                  0.3.1                    py36_0    conda-forge
tk                        8.5.19                        2    conda-forge
tornado                   4.5.2                    py36_0    conda-forge
traitlets                 4.3.2                    py36_0    conda-forge
urllib3                   1.22             py36hbe7ace6_0
wcwidth                   0.1.7                    py36_0    conda-forge
webencodings              0.5                      py36_0    conda-forge
wheel                     0.29.0           py36he7f4e38_1
widgetsnbextension        3.0.6                    py36_0    conda-forge
xorg-libxau               1.0.8                         3    conda-forge
xorg-libxdmcp             1.1.2                         3    conda-forge
xz                        5.2.3                h2bcbf08_1
yaml                      0.1.7                h96e3832_1
zeromq                    4.2.1                         1    conda-forge
zlib                      1.2.11               hfbfcf68_1

I'm wondering where I went wrong and why more users aren't having this problem. As far as I can tell, I performed a very basic install with the channel order specified in the bioconda docs

conda update r-stringi states that I've got the most up-to-date version.

The only way that I've previously gotten R kernels to work is to install everything that I can from the "r" channel, but this isn't what the bioconda docs state on what to do, and I'm trying to use the "official" installation method if possible.

[nick-youngblut]

@mingwandroid: I can say for sure is that you cannot mix software from conda-forge with software from defaults in the same environment and expect it to work properly

Doesn't this mixing of conda-forge and defaults occur when a user uses the channel order specified by the bioconda docs? I'm confused on how you would avoid this mixture of default & conda-forge packages if channels are set as:

conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

[mingwandroid]

You cannot about missing with such a channel setup.

Bioconda's docs should advise you to use a separate env. here.

[nick-youngblut]

So instead of

conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

do you recommend just using the "defaults" channel or another channel?

As a note: conda update --all with the conda install & env-setup listed above did eliminate the libicui18n.so.58: cannot open shared object file error. The update changed a lot of packages from "default" to either "conda-forge" or "bioconda", so maybe I should just be using those channels?