I've got a server running RStudio, and recently another user updated what version of gcc was on it for another project. I attempted to install Rcpp, and get the following error:
Error: package or namespace load failed for ‘Rcpp’ in dyn.load(file,
DLLpath = DLLpath, ...): unable to load shared object
'/home/username/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/libs/Rcpp.so':
/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by
/home/username/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/libs/Rcpp.so)
Error: loading failed Execution halted ERROR: loading failed
Oddly, this doesn't occur when using R from the command line, which makes me think that RStudio Server is having trouble finding GLIBCXX_3.4.20, rather than it being genuinely missing.
Does anyone know how to sort this error out?
Related
I'm not too familiar with R and are using it for Uni, and we need this asreml package for one of our classes. When I try installing it this error comes up:
Error: package or namespace load failed for ‘asreml’:
.onLoad failed in loadNamespace() for 'asreml', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/00LOCK-asreml/00new/asreml/libs/libvsninet.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/00LOCK-asreml/00new/asreml/libs/libvsninet.so, 0x0006): tried: '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/00LOCK-asreml/00new/asreml/libs/libvsninet.so' (mach-o file, but is an incompatible architecture (have (x86_64), need (arm64e)))
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/asreml’
Warning in install.packages :
installation of package ‘/Users/Cami/Downloads/asreml-4.1.0.176-macOS-10.13.2-R4.2.tar.gz’ had non-zero exit status
I tried installing it on R both with a full path to the file and with a working directory set up. I've also tried to install it directly through the computer terminal, however, the same error comes up. A tutor in class has also tried to open a library for the package through the terminal on my laptop and it also didn't work. Neither of us are sure of what 'libvsninet.so' means. I've also tried to disinstall and reinstall both R and RStudio, but the result is the same.
I'm having trouble loading rgdal in RStudio. I tried the usual command install.packages and when prompted with
"Do you want to install from sources the package which needs compilation (Yes/no/cancel)"
I've tried both yes and no. However I continue to get a cryptic error message when I try to load the library for use. It is:
Error: package or namespace load failed for ‘rgdal’ in dyn.load(file, DLLpath = >DLLpath, ...):
unable to load shared object >'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rgdal/libs/rgdal.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rgdal/libs/rgdal.so, 6): Symbol not found: _sqlite3_column_table_name
Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rgdal/libs/rgdal.so (which was built for Mac OS X 10.13)
Expected in: /usr/lib/libsqlite3.dylib
in /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rgdal/libs/rgdal.so
I'm trying to install the Homals package - library(homals), but keep getting this error message:
library(homals)
Error : .onLoad failed in loadNamespace() for 'rgl', details: call:
dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared
object
'/Library/Frameworks/R.framework/Versions/3.3/Resources/library/rgl/libs/rgl.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.3/Resources/library/rgl/libs/rgl.so,
6): Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/rgl/libs/rgl.so
Reason: image not found Error: package or namespace load failed for
‘homals’
I have a couple of my colleagues to run the same code, the same thing happens. I have re-install R studio to the newest version.
install.packages("rgl")
install.packages("homals")
library(homals)
Any solutions for this? thank you.
I was able to successfully install on both Windows and Mac. I believe the root cause here is that you have R version 3.3 installed when you require at least v3.5.3 as per below:
library(homals)
Warning message:
package ‘homals’ was built under R version 3.5.3
I am running R 3.5.0 on a Ubuntu 18.04 machine. Some Shiny app I am testing with this new environment uses the ReporteRsjars package and gives the following error message on loading this package:
Loading required package: ReporteRsjars
Error: package or namespace load failed for ‘ReporteRsjars’:
.onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/usr/local/lib/R/site-library/rJava/libs/rJava.so':
libjvm.so: cannot open shared object file: No such file or directory
Warning: Error in : package ‘ReporteRsjars’ could not be loaded
The file /usr/local/lib/R/site-library/rJava/libs/rJava.sohowever does exist.
Any help would be appreciated!
After quite some more trying I found the solution - and realized that I mis-interpreted the error message: The missing library was actually the libjvm.so which was not found. A symlink
ln -s /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server/libjvm.so /usr/lib
followed by a R CMD javareconfand a removal and re-installation of the rJavapackage did it for me.
I had some issues installing rJava first. Then I found this solution.
Unfortunately I get following error, when loading the package:
Error : .onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/informatik2/students/home/1jendryc/R/x86_64-pc-linux-gnu-library/3.1/rJava/libs/rJava.so':
libjvm.so: cannot open shared object file: No such file or directory
Error: package or namespace load failed for ‘rJava’
Still this file exists and even the path is correct
~/R/x86_64-pc-linux-gnu-library/3.1/rJava/libs$ ls
rJava.so
So I tried that approach, but it didn't worked.
I have no possibility to get root easily, cause I am working at my university at a pool computer.
Cheers.
Your issue is something different. What message says is that it can't find "libjvm.so". You need to properly configure Java, rJava and R. Take a look here
http://www.owsiak.org/?p=3671
where all the caveats are listed when it comes to working with R and Java.