Hello everyone,
I am very new to R and RStudio, and I am struggling to set up a conda environment with a specific R version, that I could then use with RStudio.
At first, I followed Anaconda guidelines (see Using R language with Anaconda — Anaconda documentation) by doing:
conda create -n r-environment r-essentials r-base
conda activate r-environment
However, the R installed version is then 3.6, whereas I would like to install R>=4.* because some of the libraries I will then use require a recent version of R.
Thus, I used coda-forge channel to install R within my conda environment:
conda create -n R-env
conda activate R-env
condac install -c conda-forge r-base=4.1.2 r-essentials
The installation goes smoothly, I can open a R terminal and install libraries.
Yet, once in my env I cannot launch RStudio (/usr/bin/rstudio), I got the following error:
R Session Startup Failure Report
RStudio Version
RStudio 2021.09.2+382, "Ghost Orchid" (fc9e2179, 2022-01-04) for CentOS 7
Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36
Error message
[No error available]
Process Output
The R session exited with code 1.
Error output:
/usr/lib/rstudio/bin/rsession: /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /data/users/pklein/Conda/miniconda3/envs/R-env/lib/R/lib/../../libicuuc.so.69)
/usr/lib/rstudio/bin/rsession: /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /data/users/pklein/Conda/miniconda3/envs/R-env/lib/R/lib/../../libicuuc.so.69)
/usr/lib/rstudio/bin/rsession: /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /data/users/pklein/Conda/miniconda3/envs/R-env/lib/R/lib/../../libicui18n.so.69)
/usr/lib/rstudio/bin/rsession: /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /data/users/pklein/Conda/miniconda3/envs/R-env/lib/R/lib/../../libicui18n.so.69)
Standard output:
[No output emitted]
Logs
/data/users/pklein/.local/share/rstudio/log/rsession-pklein.log
2022-02-07T09:05:44.257172Z [rsession-pklein] ERROR CLIENT EXCEPTION (rsession-pklein): (Error) : This API only accepts integers;|||http://127.0.0.1:24504/rstudio/AC5AADB35BD3AFF301FEFC583AAFE0E0.cache.js#-1::_verifyIntegers|||elemental2/dom/CSSProperties.java#1229::resize|||http://127.0.0.1:24504/rstudio/4032CB57FF3A58D9FCAE4CBA2130587E.cache.js#-1::fit|||org/rstudio/studio/client/workbench/views/terminal/xterm/XTermWidget.java#190::run|||com/google/gwt/user/client/Timer.java#124::fire|||rstudio-0.js#-1::eval|||com/google/gwt/core/client/impl/Impl.java#306::apply|||com/google/gwt/core/client/impl/Impl.java#345::entry0|||rstudio-0.js#-1::eval|||Client-ID: 33e600bb-c1b1-46bf-b562-ab5cba070b0e|||User-Agent: Mozilla/5.0 (X11 Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36
2022-02-07T12:56:56.153451Z [rsession-pklein] ERROR Parent terminated; LOGGED FROM: void {anonymous}::detectParentTermination() src/cpp/session/SessionMain.cpp:1431
2022-02-07T12:56:56.153451Z [rsession-pklein] ERROR Parent terminated; LOGGED FROM: void {anonymous}::detectParentTermination() src/cpp/session/SessionMain.cpp:1431
As suggested here (c++ - version `CXXABI_1.3.8' not found (required by ...) - Stack Overflow) I installed gcc>=9 with conda and updated my LD_LIBRARY_PATH env variable.
Do you have any suggestions ?
Thank you very much for your time !
Best,
Paul
PS: I also tried to install RStudio within my conda env but I read many messages saying that it was not maintained and quite buggy (RStudio crash on open (downloaded with Anaconda) - #3 by Jmf369 Rstudio asking to save something on startup, failing to launch)