Otherwise, Rstudio is extremely limiting, in does not see you library path or anything else that is not added at the config file on startup. Only in this case Rstudio will be able to know where the gcc libraries are. In the past, the Rstan that has been installed works because it was compiled it with a gcc version which matches the R version Rstudio is using. The GLIBXX library for the gcc version you want is at /stornext/System/data/apps/gcc/gcc-7.3.0/lib64/libstdc++.so. It is instead looking at the system’s gcc library, which is version 4.8.5 and located at /usr/lib64/. usr/lib64/libstdc++.so.6 : version `GLIBCXX_3.4.20’ not found (required by … Unable to load shared object ‘/stornext/HPCScratch/home/mangiola.s/R/x86_64-pc-linux-gnu- library/3.5/rstan/libs/rstan.so’: If you see your error trace, the glibxx library your Rstan is looking at is not the one from gcc 7.3.0: For your Rstan to work, Rstduio has to be able to see the shared libraries that come with gcc 7.3.0. You are forcing Rstan to compile with a version of gcc that rstudio has no idea where it is. It seems more an issue with Rstudio, being not as powerful as R My IT admin told similar thing (his suggestion did not work at the end and he told me that there are no current solutions). I also had to abandon (for the moment) the installation of Rstan + Rstudio server on the cluster. Like I said, I realize this isn’t strictly an rstan issue but I’d appreciate any advice anyone can offer. So I am somewhat stuck (at least in terms of using rstudio server, which I have a strong preference for). I am apparently not the first person to have this issue, but it seems like all of the solutions require a global change to the RStudio Server configuration and making a system wide change for this issue is probably not going to be possible. The administrator confirmed that if LD_LIBRARY_PATH is set in in the global RStudio Server configuration file (in a test environment) everything seems to work correctly. It seems as if rstudio is not respecting my LD_LIBRARY_PATH. PATH = /usr/local/gcc/7.2.0/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin Here is some potentially relevant output: This occurs despite being able to successfully reinstall rstan through rstudio. lib64/libstdc++.so.6: version `CXXABI_1.3.8’ not found (required by /home/cquirk/R/x86_64-redhat-linux-gnu-library/3.5/rstan/libs/rstan.so) Unable to load shared object ‘/home/cquirk/R/x86_64-redhat-linux-gnu-library/3.5/rstan/libs/rstan.so’: The issue I am having is that when trying to load rstan through rstudio server I get the following error:Įrror: package or namespace load failed for ‘rstan’ in dyn.load(file, DLLpath = DLLpath, …): Launching R from a bash terminal then correctly uses the new version of gcc and I can install and load rstan (2.18.2) successfully. In ~/.profile I load the newer gcc version. The only available gcc version was 4.8.5, so the administrators installed gcc version 7.2.0 for me. I am trying to get rstan setup on a linux cluster (RHEL 7.6). To be honest this is likely more of an rstudio question than an rstan question, but I am hoping there may be someone here who can help with my issue.
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