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
Related
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 have installed Oracle Instant Client 12.1.0.2.0 and am now trying to install ROracle 1.3-1 for R with the following command:
R CMD INSTALL --configure-args='--with-oci-lib=/usr/local/oracle/instantclient12 --with-oci-inc=/usr/local/oracle/instantclient12/sdk/include' ROracle_1.3-1.tar.gz
The Oracle Instant Client is installed in /usr/local/oracle/instantclient12
Unfortunately, I am getting the following error at the end of the ROracle install and have been having a difficult time figuring out what is going wrong:
** testing if installed package can be loaded
Error: package or namespace load failed for ‘ROracle’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/ROracle/libs/ROracle.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/ROracle/libs/ROracle.so, 6): Library not loaded: #rpath/libclntsh.dylib.12.1
Referenced from: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/ROracle/libs/ROracle.so
Reason: image not found
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/ROracle’
For whatever reason #rpath/libclntsh.dylib.12.1 can't be found and is preventing ROracle from being fully installed. I have tried putting a link to libclntsh.dylib.12.1 in ~/lib and /usr/lib but neither link worked. I have also tried pointing to the directory containing libclntsh.dylib.12.1 with the environment variables DYLD_FALLBACK_LIBRARY_PATH and DYLD_LIBRARY_PATH but those have not worked as well.
I am using MacOS High Sierra (10.13) and R 3.4.2.
The only way I have found so far to get around this problem is to put a link to libclntsh.dylib.12.1 in the framework lib directory for R. On my computer the R framework lib directory is located in /Library/Frameworks/R.framework/Resources/lib
My instant client is installed in /usr/local/oracle/instantclient12
So I use the following command to make the file link:
ln -s /usr/local/oracle/instantclient12/libclntsh.dylib.12.1 /Library/Frameworks/R.framework/Resources/lib/libclntsh.dylib.12.1
This resolves the ROracle install problem and I can now load the ROracle library in R without issue.
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.
I run RStudio Server on ubuntu 14.04. When trying to install the rgdal package I get the following error message:
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/admin2/R/x86_64-pc-linux-gnu- library/2.14/rgdal/libs/rgdal.so':
libnetcdf.so.6: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
I upgraded RStudio Server, R-Core and all Ubuntu packages to their latest versions but no success. I also tried apt-get install lib32stdc++6 as suggested here, but also no changes. I think it is a problem specific to GDAL and the indexing of shared libraries in unix. Can anyone help please?
Ok I got it done removing Gdal completly, compiling it from source again and setting library paths correctly as described here. Later adding /usr/local/lib/ to /etc/ld.so.conf and run sudo ldconfig as described here.