I am trying to install the package "rjags" in R but am running into the following error:
Loading required package: rjags
Error : .onLoad failed in loadNamespace() for 'rjags', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.1/Resources/library/rjags/libs/rjags.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.1/Resources/library/rjags/libs/rjags.so, 10): Symbol not found: __ZN5RangeC1ERKSt6vectorIiSaIiEES4_
Referenced from: /Library/Frameworks/R.framework/Versions/3.1/Resources/library/rjags/libs/rjags.so
Expected in: /usr/local/lib/libjags.3.dylib
in /Library/Frameworks/R.framework/Versions/3.1/Resources/library/rjags/libs/rjags.so
Error: package ‘rjags’ could not be loaded
I've installed JAGS on my Mac (running Mavericks), and I am running R-3.1.2. I've tried installing from the url using the devtools package, as recommended by this site:
install_url("http://sourceforge.net/projects/mcmc-jags/files/rjags/3/rjags_3-2.tar.gz",
args="--configure-args='--with-jags-include=/Users/casallas/homebrew/opt/jags/include/JAGS
--with-jags-lib=/Users/casallas/homebrew/opt/jags/lib'
"
)
I've also gone through the instructions on this other site , trying the different versions of JAGS and receive the same error. I'm at a loss for what to try next and am sure the solution is simple. Does anyone have any insights? Thanks so much!
I found that while I was unable to install rjags from the url, if I installed the package from source on my computer I was successful. I did this by downloading the appropriate package from here (which for me was rjags_3-14.tgz) and ran the following command:
install.packages(path_to_file, repos = NULL, type="source")
The error:
Symbol not found: __ZN5RangeC1ERKSt6vectorIiSaIiEES4_
Is (nearly) always caused by a mismatch between standard libraries between the Mavericks build of R (actually rjags) and Snow Leopard build of JAGS (or vice versa). For more info see the instructions at https://sourceforge.net/projects/mcmc-jags/files/JAGS/3.x/Mac%20OS%20X/
I'm guessing that compiling the package yourself from source worked because it matched the version of the standard library that JAGS is using, but this will no longer match the version that R is using (although I'm not sure if this is a major problem, it is not recommended). You would be better to match the builds of R and JAGS and use the pre-built rjags library from CRAN.
It is interesting that you say you have tried both builds of JAGS but I suggest trying again along these lines:
1) Use .Platform$pkgType in R to confirm if it you are using mac.binary (SL) or mac.binary.mavericks (Mavericks) - or failing that re-install the Mavericks binary of R from CRAN
2) Exit R
3) Re-install the appropriate version of JAGS
4) Re-open R and re-install the rjags library from CRAN
5) Try library(rjags)
If this doesn't work can you provide more information so I can try and track down a possible problem with the JAGS builds?
Thanks,
Matt
Related
I am having difficulty installing the zenplots package in R. For some odd reason when I use install.packages('zenplots') on my machine (Mac OS Catalina V-10.15.7) it installs fine... but when I try and install it on my second machine (also Mac OS Catalina V-10.15.7) and if I try and install it on my institutes server I get the following error:
Warning in fun(libname, pkgname) : couldn't connect to display ":0"
Error : package or namespace load failed for ‘loon’: .onLoad failed
in loadNamespace() for 'loon', details: call:
structure(.External(.C_dotTcl, ...), class = "tclObj") error: [tcl]
couldn't connect to display ":0".
Error: unable to load R code in package ‘zenplots’ Execution halted
I have also tried to install directly from GitHub using remotes::install_github('great-northern-diver/zenplots', force = T) but I get the same error as above.
I have even tried using install.packages("zenplots", repos="http://R-Forge.R-project.org") which works but unfortunatley this version doesn't contain all the functions found in zenplots.
My R version is above version 3.4.0, which is required for zenplots and as per the documentation I have already installed the graph package from BioConductor.
Any suggestions as to what might be the issue here?
I would guess that the R on your server was compiled without some feature required by the library. My guess: it is missing either tcltk or X11 support. To check do the following:
capabilities()
And see which features return FALSE, meaning they are not enabled.
I've successfully installed rstan, but when I try to attach it with library(rstan) I get a pop-up window with the title "RGui (64-bit): Rgui.exe - Entry Point Not Found" and the message content
The procedure entry point EXTPTR_PTR could not be located in the dynamic link library C:\Users\MyName\Documents\R\win-library\4.0\Rcpp\libs\x64\Rcpp.dll.
In the R console itself I get
> library(rstan)
Loading required package: StanHeaders
Loading required package: ggplot2
Error: package or namespace load failed for ‘rstan’ in inDL(x, as.logical(local), as.logical(now), ...):
unable to load shared object 'C:/Users/Daniel/Documents/R/win-library/4.0/Rcpp/libs/x64/Rcpp.dll':
LoadLibrary failure: The specified procedure could not be found.
I'm running 4.0.0 (2020-04-24) 'Arbor Day', on a 64 bit Windows machine with Windows 10.
I thought this might have been an issue with Rtools (Rtools 4.0 not found during package installation), but having reinstalled rtools40 and properly added it to my path - and then reinstalling all of my packages to make sure there were no dependency issues - the problem with rstan persists. Any idea what might be going wrong here, and how I can get rstan working?
Quick ones:
Did you build it yourself from source, or did you install binaries?
You should probably upgrade to R 4.0.2 as there were known issues with 4.0.0 and 4.0.1.
There is no issue with Rcpp per se; it builds on Windows as it should (see CRAN check pages).
But we did have numerous reports on the issue in 2. So please upgrade R to 4.0.2 and try that.
We need to updata R. In your script does the following:
First install the package
install.packages("installr")
Then:
library(installr)
updateR()
After that we install the last R update.
This help me to fix the error of Can't load the library in Windows - EXTPTR_PTR could not be located in the dynamic library
I needed to install the R package quadprog, which only works for R with version 3.6.0. So I installed R (3.6.0 version), and open it with RStudio. But now I failed to load any libraries, even after I installed the packages successfully using install.packages("package_name"). Specifically, the libraries I need to load are caret, forecast and ggplot2. I tried re-installing R but it still does not work. The error message I get is
Error: package or namespace load failed for ‘forecast’ in
dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object
'/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/libs/Rcpp.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/libs/Rcpp.so,
6): Symbol not found: ___cxa_uncaught_exceptions Referenced from:
/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libc++.1.dylib
Expected in: /usr/lib/libc++abi.dylib in
/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libc++.1.dylib
After installing Rcpp package successfully with install.packages("Rcpp") , I still got the message above when I tried library(Rcpp). So I am completely stumbled here...(before upgrades, everything works fine except I cannot install quadprog, so cannot install forecast package as well). Can anyone please help me fix this issue?
Please see below the images showing that the packages are stored in the same directory path of the R.
I read that you need to recompile your old packages after upgrading to newer version of R. Run the following line in your R terminal
update.packages(ask=FALSE,
checkBuilt=TRUE,
repos="https://cloud.r-project.org")
Then
install.packages(c("Rcpp", "caret", "forecast", "ggplot2", "quadprog"),
dependencies=TRUE,
repos="https://cloud.r-project.org")
Had similar issue, restart R session and install Rcpp from source
install.packages("Rcpp", type="source")
then load the library
library(Rcpp)
if still getting the error, restart R session and try loading library again.
I ended up by getting and then google searching the exact error code :). I fixed it by installing the latest version of R from CRAN along with the latest version of Rstudio. What I think happened was that when I updated some packages R and Rstudio were out of sync.
I'm trying to install the package nloptr on Mac OS High Sierra in order to use many nice packages like lme4, and I'm using RStudio inside Anaconda, with R 3.4.2. I have also installed NLopt (downloaded from the NLopt website, not the development version. I have also installed Xcode command line tool. But I still can't install nloptr, and get this
Error: package or namespace load failed for ‘nloptr’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Users/lambda/anaconda3/lib/R/library/nloptr/libs/nloptr.so':
dlopen(/Users/lambda/anaconda3/lib/R/library/nloptr/libs/nloptr.so, 6): Symbol not found: _nlopt_add_equality_mconstraint
Referenced from: /Users/lambda/anaconda3/lib/R/library/nloptr/libs/nloptr.so
Expected in: flat namespace
in /Users/lambda/anaconda3/lib/R/library/nloptr/libs/nloptr.so
I already searched online for what to do, and did add the path where NLopt was installed to LD_LIBRARY_PATH in the /etc/ldpaths file, but I still get the same error. Yes, I have the same problem as in Trouble installing nloptr package on R 3.3.0, but I didn't find a solution that works there since the person who asked that question resolved it himself and I don't know what he meant when he said "installed as a root". Can anyone help?
Also, I got something like this when installing NLopt with CMake, and this happened to many different functions:
In file included from f77api.c:103:
./f77funcs.h:57:14: warning: 'nlopt_minimize_constrained' is deprecated
[-Wdeprecated-declarations]
*info = nlopt_minimize_constrained((nlopt_algorithm) *algorithm,
^
./nlopt.h:348:35: note: 'nlopt_minimize_constrained' has been explicitly marked
deprecated here
int maxeval, double maxtime) NLOPT_DEPRECATED;
^
./nlopt.h:320:43: note: expanded from macro 'NLOPT_DEPRECATED'
# define NLOPT_DEPRECATED __attribute__((deprecated))
^
Would this be why the library isn't loaded?
BTW, I have installed Rcpp and updated it. Rcpp works on my computer.
Update: I changed the default C and C++ compiler to clang4 downloaded from R project. I tried the installation again, and got a different error:
Error: package or namespace load failed for ‘nloptr’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Users/lambda/anaconda3/lib/R/library/nloptr/libs/nloptr.so':
dlopen(/Users/lambda/anaconda3/lib/R/library/nloptr/libs/nloptr.so, 6): Library not loaded: #rpath/libnlopt.0.dylib
Referenced from: /Users/lambda/anaconda3/lib/R/library/nloptr/libs/nloptr.so
Reason: image not found
Error: loading failed
I have tried to tell R where the library is by Sys.geteng(DYLD_LIBRARY_PATH = "/usr/local/lib"), but it didn't work. It actually appears that R does know where the shared library is, according to the messages I got from installation, but it just can't load it. Please help!
Never mind, I reinstalled Anaconda, and installed the standalone R and RStudio (not within Anaconda), and those packages all installed successfully. Maybe it's a bad idea to use the RStudio inside Anaconda.
Edit: For those who run into similar scenarios: I switched to Microsoft R Open (MRO), since I'm dealing a lot with linear algebra recently. Then when I tried to install nloptr in MRO, I got a similar error message that shared library failed to load because image not found. I reinstalled the CRAN R 3.4.3 and nloptr installed totally fine there. So I found where nloptr was installed in CRAN R 3.4.3 by .libPaths(), copied the nloptr folder to where MRO stores packages, and used the utility RSwitch to change the default version of R to MRO. Then I loaded nloptr in MRO, installed packages that depend on it, and used those packages; they worked fine. I don't know what's wrong with MRO that caused the error, but at least this worked.
I am having issues getting rjags the R package for R to call JAGS (Just Another Gibbs Sampler http://www-ice.iarc.fr/~martyn/software/jags/ ).
I am running Mac Os X. 10.5.8 Leopard and using R64 2.12.1. I compiled JAGS from the command line. Then I installed rjags in the R command line.
install.packages(rjags)
When I try to call rjags within R, I get the following error.
> library(rjags)
Error : .onLoad failed in loadNamespace() for 'rjags', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/2.12/Resources /library/rjags/libs/x86_64/rjags.so':
dlopen(/Library/Frameworks/R.framework/Versions/2.12/Resources/library/rjags/libs/x86_64/rjags.so, 10): Library not loaded: /usr/local/lib/libjags.2.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/2.12/Resources/library/rjags/libs/x86_64/rjags.so
Reason: no suitable image found. Did find:
/usr/local/lib/libjags.2.dylib: mach-o, but wrong architecture
/usr/local/lib/libjags.2.dylib: mach-o, but wrong architecture
Error: package/namespace load failed for 'rjags'
I am guessing there is some issue with rjags referencing an unknown file in the library, but I am not sure. I am a fairly novice at the command line and messing around with directories, so any help would be much appreciated.
I found (after downloading and installing the dmg from SourceForge) that the following commands worked for me:
wget http://cran.r-project.org/src/contrib/rjags_2.2.0-4.tar.gz
wget http://cran.r-project.org/src/contrib/R2jags_0.02-15.tar.gz
sudo R --with-jags-modules=/usr/local/lib/JAGS/modules-2.2.0 CMD INSTALL rjags_2.2.0-4.tar.gz
sudo R --with-jags-modules=/usr/local/lib/JAGS/modules-2.2.0 CMD INSTALL R2jags_0.02-15.tar.gz
sudo R --with-jags-modules=/usr/local/lib/JAGS/modules-2.2.0 --arch=i386 CMD INSTALL rjags_2.2.0-4.tar.gz
sudo R --with-jags-modules=/usr/local/lib/JAGS/modules-2.2.0 --arch=x86_64 CMD INSTALL rjags_2.2.0-4.tar.gz
They certainly aren't all necessary, but they were sufficient!
I had the same problem while running Rstudio 0.97.237 and R 2.15.2. The issue had something to do with JAGS.
The fix: Update to JAGS 3-3 by downloading and installing it from here.
I encountered the error: unable to load shared object '/Library/Frameworks/R.framework/Resources/modules//R_X11.so': on my Mac and DuckDuckGo led me to this post. I was using R from the command line, so I can't speak to how it works with RStudio although I'm pretty sure it's the fix for that too. I updated JAGS from the SourceForge link provided in another answer. I can at least verify that it worked for me, though the developer was unsigned (I needed to ignore a MacOS warning during the installation procedure).