I've been trying to solve this one for ages.
I want to use RQDA on my Mac. I have installed it (install.packages("RQDA")fine. But when I go to run it it asks if I need GTK+. I keep saying yes, but it fails.
library(RQDA)
Loading required package: RSQLite
Loading required package: gWidgetsRGtk2
Loading required package: RGtk2
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RGtk2/libs/RGtk2.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RGtk2/libs/RGtk2.so, 6):
Library not loaded: /usr/X11/lib/libXinerama.1.dylib
Referenced from: Library/Frameworks/GTK+.framework/Versions/2.24.X11/Resources/lib/libgtk-x11-2.0.0.dylib
Reason: image not found
Need GTK+ ? (Restart R after installing)
1: Install GTK+
2: Do not install GTK+
I have checked my library path and found that the package is there but in the 3.3 version. It is sitting there "RGtk2.so".
libPaths()
[1] "/Library/Frameworks/R.framework/Versions/3.3/Resources/library"
I have googled this to death. Any ideas would be much appreciated!
After you have installed the RQDA package, and you call the library RQDA, be careful because a popup window raises asking for install RGtk2+ components. But that window can be hidden by your open aplications over the desktop. Look for the popup window and answer yes for install. Once is installed, won't be more problems.
Install GTK from http://r.research.att.com/libs/GTK_2.24.17-X11.pkg. Make sure you have the latest XQuartz from https://www.xquartz.org/
Related
Not sure if relevant, but I'm getting this error after a recent update to Mac OS Monterey Version 12.5.1.
After trying library(plotKML) I get the following:
Error: package or namespace load failed for ‘plotKML’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Users/kchalkowski/Library/R/x86_64/4.1/library/lwgeom/libs/lwgeom.so':
dlopen(/Users/kchalkowski/Library/R/x86_64/4.1/library/lwgeom/libs/lwgeom.so, 0x0006): Library not loaded: '/usr/local/opt/proj/lib/libproj.22.dylib'
I checked the directory /usr/local/opt/proj/lib and sure enough, libproj.22.dylib is not there. Rather, another version is there in it's place: libproj.25.dylib.
Is there a way to get that older version of libproj? or a way to link plotKML to the correct dylib? I had a similar issue with sf, but was able to fix it with a brew reinstall of pkg-config gdal proj geos in the terminal, and uninstalling and reinstalling sf. I've tried uninstalling and reinstalling plotKML but to no avail.
Did a search for the name of the dynamic library and I think I actually just fixed it following advice here: https://github.com/flow-project/flow/issues/896
I used the following in the terminal but instead of 19/5, I replaced the versions of the libraries in the code here with the one I have (25) and the one plotKML wants (22), and it seems to be working now?:
ln -s /usr/local/opt/proj/lib/libproj.19.dylib /usr/local/opt/proj/lib/libproj.15.dylib
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'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.
Here's the error I get:
> 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 '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: #rpath/libjvm.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so
Reason: image not found
I see this is by no means a unique problem.. I've tried the solutions here, here and here. No success.
Some more details: I'm using R GUI, but I also can't load rJava through R terminal. I also didn't have any issue with rJava on R 3.3.s
You have two options here:
get older release of R and use precompiled version of rJava
get rJava sources and compile it for yourself
Note that rJava (most recent sources) require some features that are not embedded inside XCode and clang that is available via AppStore. You will need to do some low level stuff when it comes to building rJava package.
You can find detailed instruction here: http://www.owsiak.org/r-3-4-rjava-macos-and-even-more-mess/
If you decide to use older release of R, it's still a struggle to get it working, but way less to do: http://www.owsiak.org/r-java-rjava-and-macos-adventures/
JAVA_HOME path is different for different version of MAC OS.
In some cases there is /jre folder and in some cases it is not after /Home director manually go towards /server folder with CD command in terminal and using pwd copy the entire path use that to set the java.home then you can easily load rJava library. This is how I was able to fix the issue
options("java.home"="/Library/Java/JavaVirtualMachines/jdk-9.0.1.jdk/Contents/Home/lib")
Sys.setenv(LD_LIBRARY_PATH='$JAVA_HOME/server')
dyn.load('/Library/Java/JavaVirtualMachines/jdk-9.0.1.jdk/Contents/Home/lib/server/libjvm.dylib')
library(rJava)
I recently installed the latest version of R (3.4.0) and installed all of my packages, but for some reason rgdal will not load and I'm getting this message:
library(rgdal)
Error: package or namespace load failed for ‘rgdal’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rgdal/libs/rgdal.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rgdal/libs/rgdal.so, 6): Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rgdal/libs/rgdal.so
Reason: image not found
I went to the rgdal/libs directory and the rgdal.so file exists, but for some reason doesn't want to load. Anyone else have this issue or a similar one?
Try installing RStudio and re-download it from there or type install.packages("rgdal"). If none of these work try installing another package and see if you can run it, because it is either the directory, the package or the version of the package is not compatible with the version of the language.
Do you have GDAL OS X frameworks installed? If not, go to William Kyngesburye's site, download and install frameworks in the following order:
GDAL Complete
GSL Framework
FreeType
cairo
After completing this installation, go for steps 2 and 3 of this answer, and then, install rgdal from R.app using these specifications in the install.packages command.
It solved the problem for me, hope it helps you!
Seems to be related to my issue posted same day, Unable to load pgirmess library ("image not found") - R 3.4 in Mac OS .
I installed the previous version of R from CRAN (3.3.3), and it works fine. You can have both versions installed at the same time. Maybe not a long term solution but at least a temporary fix so your work can continue.