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Using Anaconda Navigator 1.6.3, R Studio version 1.0.153 and R version 3.4.1.
MacBook Air Mac OS version 10.12.6
When launch R Studio with Navigator, I get the following error:
Error in tools::startDynamicHelp() : internet routines cannot be loaded
This R Studio was installed via conda with R Essentials
When I start an older version of R Studio outside of Anaconda Navigator (i.e. a Version of Rstudio I had before I installed the Anaconda version of R Studio) I do not get this problem
I get a similar error on a clean install of Anaconda 4.4.0 after doing conda install rpy2. This is on Mac OS Sierra, and the R version I get is 3.4.1. Specifically, when trying to install a package, I get an error:
> source("http://bioconductor.org/biocLite.R")
Error in file(filename, "r", encoding = encoding) :
internet routines cannot be loaded
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
unable to load shared object '/Users/sten/anaconda3/lib/R/modules//internet.so':
dlopen(/Users/sten/anaconda3/lib/R/modules//internet.so, 6): Library not loaded: @rpath/libssh2.1.dylib
Referenced from: /Users/sten/anaconda3/lib/R/modules//internet.so
Reason: image not found
On Sep 4, 2017, at 6:14 PM, Sten Linnarsson ***@***.***> wrote:
I get a similar error on a clean install of Anaconda 4.4.0 after doing "conda install rpy2". This is on Mac OS Sierra, and the R version I get is 3.4.1:
> source("http://bioconductor.org/biocLite.R")
Error in file(filename, "r", encoding = encoding) :
internet routines cannot be loaded
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
unable to load shared object '/Users/sten/anaconda3/lib/R/modules//internet.so':
dlopen(/Users/sten/anaconda3/lib/R/modules//internet.so, 6): Library not loaded: @rpath/libssh2.1.dylib
Referenced from: /Users/sten/anaconda3/lib/R/modules//internet.so
Reason: image not found
Note that @rpath <https://github.com/rpath> has nothing to do with R, but is a mechanism for finding shared libraries <https://developer.apple.com/library/content/documentation/DeveloperTools/Conceptual/DynamicLibraries/100-Articles/RunpathDependentLibraries.html> on Mac OS X.
Checking under ~/anaconda3/lib indeed there is no libssh2.1.dylib. After doing
conda install libssh2
it still doesn't work, but now it wants to load another library (libgssapi_krb5.2.2.dylib) which we can get by installing krb5:
conda install krb5
...and this solves the problem! At least on my machine.
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I have tried to fix the internet routines problem as well by copying conda install krb5 into R studio and trying to run it. I revieved the fallowing error messages
Error: unexpected symbol in "conda install"
Error: unexpected symbol in "conda install.packages"
I have macOS Sierra 10.12.4, Anaconda Navigator 1.6.2, and R Studio version 3.4.1
Ultimately I am trying to install caTools but I get the faloowing error message
Activity
mregensberg commentedon Aug 22, 2017
+1
update: separately installed RStudio + R 3.4.1 works fine.
slinnarsson commentedon Sep 4, 2017
I get a similar error on a clean install of Anaconda 4.4.0 after doing
conda install rpy2
. This is on Mac OS Sierra, and the R version I get is 3.4.1. Specifically, when trying to install a package, I get an error:Note that @rpath has nothing to do with R, but is a mechanism for finding shared libraries on Mac OS X.
Checking under
~/anaconda3/lib
indeed there is no libssh2.1.dylib. After doingit still doesn't work, but now it wants to load another library (
libgssapi_krb5.2.2.dylib
) which we can get by installing krb5:...and this solves the problem! At least on my machine.
In short, it seems there are two dependencies missing from
r-base
.mingwandroid commentedon Sep 4, 2017
Thanks @slinnarsson, I need to get this fixed ASAP.
Mikejs2178 commentedon Sep 4, 2017
mingwandroid commentedon Sep 4, 2017
This is open until I fix it properly.
lihp11 commentedon Sep 8, 2017
Thanks,it solved my problem!!!
mattsears18 commentedon Sep 11, 2017
thanks @slinnarsson, solved for me.
andreassandhi commentedon Sep 13, 2017
thanks @slinnarsson, solved for me.
wordbites commentedon Sep 13, 2017
Thank you @slinnarsson! It solved the problem I've stuck for 2 days!
StealthNameless commentedon Sep 16, 2017
Hello,
I have tried to fix the internet routines problem as well by copying conda install krb5 into R studio and trying to run it. I revieved the fallowing error messages
Error: unexpected symbol in "conda install"
Error: unexpected symbol in "conda install.packages"
I have macOS Sierra 10.12.4, Anaconda Navigator 1.6.2, and R Studio version 3.4.1
Ultimately I am trying to install caTools but I get the faloowing error message
caTools’ is not available (for R version 3.4.1)
All my packages are up to date.
slinnarsson commentedon Sep 17, 2017
@StealthNameless you need to run the conda comman in your terminal, not inside R studio.
jrumbut commentedon Sep 19, 2017
@slinnarsson You are a hero.
3 remaining items
zackkatz commentedon Sep 27, 2017
Thank you @slinnarsson, your solution worked for me.
doronator commentedon Oct 2, 2017
black magic, but it works!
codykingham commentedon Oct 16, 2017
When running
conda install libssh2
, Conda wants to downgrade my Python package to 3.5.4 from 3.6. Which I don't want.mingwandroid commentedon Oct 16, 2017
codykingham commentedon Oct 16, 2017
@mingwandroid It works. You're the wind in my sails today. ⛵️
mingwandroid commentedon Oct 26, 2017
This is fixed properly now. Make sure you are using the latest
conda
thenconda update r-essentials rstudio
.LilySnow commentedon Mar 6, 2018
@slinnarsson Thanks! Solved for me!
fengwei-li commentedon Jan 3, 2021
the above suggestions can not solve my problem.
however, I fix it through
cd ~/anaconda3/lib
(your anaconda3 lib PATH)rstudio
thesuperzapper commentedon Oct 2, 2024
If you are using RStudio Server, you might need to start it with the
--rsession-ld-library-path=/opt/conda/lib
command line argument.This is because RStudio ignores the servers
LD_LIBRARY_PATH
when starting R sessions.