I need to do symbolic computation with matrices in R, preferably using the rSymPy package. I am running everything on Mac OS. There is a problem with loading the rJava package, however. I get the following error:
Error: package or namespace load failed for ‘rJava’: .onLoad failed in loadNamespace() for 'rJava', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so': dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib Referenced from: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so Reason: image not found
I have read through Problems when trying to load a package in R due to rJava and Unable to load rJava on R, as well as other similar questions. This is very frustrating - any help would be appreciated!
My end goal here is to perform matrix reduction and manipulation in R with variables (i.e. symbolic matrix computations). If there are any other suggestions on how to do this in R, please let me know.
First thing to try is to run the following from a terminal:
R CMD javareconf
Related
I have a M1 Macbook Pro running OS Big Sur and just tried to install rjags and JAGS. I downloaded JAGS from https://sourceforge.net/projects/mcmc-jags/ without a problem, and ran install_packages("rjags"), but when I run library(rjags) I get this error:
Loading required package: coda
Error: package or namespace load failed for ‘rjags’:
.onLoad failed in loadNamespace() for 'rjags', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Users/afredston/Library/Caches/org.R-project.R/R/renv/cache/v5/R-4.1/aarch64-apple-darwin20/rjags/4-12/e8a71b3a154c8e68c152b4cfbebfdd97/rjags/libs/rjags.so':
dlopen(/Users/afredston/Library/Caches/org.R-project.R/R/renv/cache/v5/R-4.1/aarch64-apple-darwin20/rjags/4-12/e8a71b3a154c8e68c152b4cfbebfdd97/rjags/libs/rjags.so, 10): Library not loaded: /opt/R/arm64/lib/libjags.4.dylib
Referenced from: /Users/afredston/Library/Caches/org.R-project.R/R/renv/cache/v5/R-4.1/aarch64-apple-darwin20/rjags/4-12/e8a71b3a154c8e68c152b4cfbebfdd97/rjags/libs/rjags.so
Reason: image not found
I understand this means that R cannot "find" the installation of JAGS. I am using renv for this project, but even if I deactivate it and re-run install_packages("rjags") and library(rjags) I get the error (just with different file paths):
Loading required package: coda
Error: package or namespace load failed for ‘rjags’:
.onLoad failed in loadNamespace() for 'rjags', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/rjags/libs/rjags.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/rjags/libs/rjags.so, 10): Library not loaded: /opt/R/arm64/lib/libjags.4.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/rjags/libs/rjags.so
Reason: image not found
I'm a stats person without much back-end computer expertise so I'd appreciate help resolving this!
See here for a similar post.
So have you installed the correct version of JAGS on your Apple computer?
Essentially, rjags is an R interface and it needs an installed JAGS (a back-end you mentioned) to function.
Follow the instructions here to install JAGS on Apple computers with M1 chips.
Also from the link above (from JAGS development team):
A readme file is provided in the disk image - please do read it.
If you find that rjags fails to load after installation of JAGS,
make sure you have installed the Mavericks or El Capitan binary of
R from CRAN. If you really need the Snow Leopard build of R (or if
you compiled R yourself) you will have to compile JAGS from source.
If you have followed the instructions above (and in the relevant
README file) and are still having problems with installation of
these binaries, please let us know via the JAGS discussion forum.
PS: I would comment if I could, but I am new here and don't have enough points to do so.
I'm trying to load package gmm (running "library(gmm)") and get this error message below.
It seems unfixable, as it states that my gfortran/lib/libgomp.1.dylib has the wrong architecture? I'm guessing this is related to the new Mac architecture?
library(gmm)
Loading required package: sandwich
Error: package or namespace load failed for ‘gmm’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/gmm/libs/gmm.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/gmm/libs/gmm.so, 6): Library not loaded: /usr/local/gfortran/lib/libgomp.1.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/gmm/libs/gmm.so
Reason: no suitable image found. Did find:
**/usr/local/gfortran/lib/libgomp.1.dylib: mach-o, but wrong architecture**
/usr/local/gfortran/lib/libgomp.1.dylib: mach-o, but wrong architecture
I had the same issue on R version 4.1. Found a similar question here which points to installing (or updating) your gfortran installation here. Once I did that and restarted R, the gmm package was able to find the missing image(s) automatically when I loaded the package.
I keep getting the same error, for both first for XLConnect, (which I thought was a java problem) and now rJava (which is also not working). This is the error message I get when I library(rJava):
Error: package or namespace load failed for ‘rJava’: .onLoad failed
in loadNamespace() for 'rJava', details: call: dyn.load(file,
DLLpath = DLLpath, ...) error: unable to load shared object
'/Users/snyderk2/Library/R/3.4/library/rJava/libs/rJava.so':
dlopen(/Users/snyderk2/Library/R/3.4/library/rJava/libs/rJava.so, 6):
Library not loaded: #rpath/libjvm.dylib Referenced from:
/Users/snyderk2/Library/R/3.4/library/rJava/libs/rJava.so Reason:
image not found
I am new to R, and just need to figure out how to get these packages working, thanks!
Try (check your java version and change accordingly):
Sys.setenv(JAVA_HOME = "C:/Program Files/Java/jre-9.0.1")
And then load library.
Install package xlsx if you are trying to access Excel file by entering install.packages("xlsx", dependencies = T) in your console.
Another R package for working with excel data which does not require rJava is openxlsx. I've found it works faster than java-based packages, which is a nice bonus.
I am having problems loading rugarch package on R and I really need that package for my thesis.
I have no problem installing it. But when I try to load it I receive the following error message:
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 ‘rugarch’
Any suggestions ?
Any help would be appreciated.
This answer is a bit late but for other people searching for a solution. The solution that worked for me is to download and install XQuartz https://www.xquartz.org onto your Mac.
See Stackoverflow answers here and here
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.