After upgrading to MacOS Mojave (10.14.1), I'm no longer able to install rJava for R version 3.5.1 with Java version "1.8.0_102" installed.
I tried the previous solution for MacOS 10.11 but it still did not work, giving this 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-9.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
Posting the solution I found in case it helps others -- I don't quite understand why this work or if it's the right way so looking for better alternatives!
This issue lead to this Apple forum where it's stated
For legacy software that looks for the macOS headers in the base system under /usr/include, please install the package file located at: /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14. pkg
To do this, open terminal and run these commands
cd /Library/Developer/CommandLineTools/Packages/
open macOS_SDK_headers_for_macOS_10.14.pkg
then follow prompts to install the package.
After this, in the terminal, configure rJava and install as in the previous answer
sudo R CMD javareconf
R -e "install.packages('rJava')"
and it should install without problem.
After installing JDK 11.04 LTS I rain into the same error in R Studio on Mojave
R was expecting Library not loaded: /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk
Despite running sudo R CMD javareconf the error still persisted
Therefore I browsed to /Library/Java/JavaVirtualMachines/ in finder and renamed the folder "jdk-11.0.4.jdk" to "jdk-11.0.1.jdk"
Restarted R and both library(rJava) and library(xlsx) now work.
Hope this helps someone
I ran into the exact problem. I solved it by:
Install the latest version of Java (dmg file)
Install rJava in Studio: install.packages("rJava")
In the terminal: sudo mv jdk-12.0.1.jdk jdk-11.0.1.jdk
Otherwise the following error will appear in Rstudio:
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
In Rstudio: library(rJava)
rJava should have been loaded without issues.
I ran into same issue, when i was trying to install "rJava" in my macOs (Mojave version).
Below steps i executed to resolve issue.
R version : 3.6.1
issue : configure: error: one or more Java tools are missing.
*** JDK is incomplete! Please make sure you have a complete JDK. JRE is not sufficient.
solution : execute below command in your terminal
$ /usr/libexec/java_home -V
Matching Java Virtual Machines (1):
1.8.0_162, x86_64: "Java SE 8" /Library/Java/JavaVirtualMachines/jdk1.8.0_221.jdk(your Java version)/Contents/Home
$ export JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_221.jdk/Contents/Home
$ export PATH=$JAVA_HOME/bin:$PATH
$ R CMD javareconf
$ R --quiet -e 'install.packages("rJava", type="source", repos="http://cran.us.r-project.org")'
Related
I tried to find solutions from previous posts, but they do not solve my problem.
I am using macOS High Sierra and have Java installed. Below is the error reported by Rstudio. Also, rJava, Mac, and R are really messy with each other. I found this post but still does not work.
https://github.com/MTFA/CohortEx/wiki/Run-rJava-with-RStudio-under-OSX-10.10,-10.11-(El-Capitan)-or-10.12-(Sierra)
///////////////////
library(RWeka)
Error: package or namespace load failed for ‘RWeka’:
.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
In addition: Warning message:
package ‘RWeka’ was built under R version 3.4.4
I met the same question and I found this is helpful.
Cannot load R xlsx package on Mac OS 10.11
1.In terminal enter the following to relink Java correctly:
sudo R CMD javareconf
2.Back in R (or RStudio) install the rJava package from source:
install.packages("rJava",type='source')
Then
library(rJava)
and
library(RWeka)
should work.
Bear in mind that I am computer illiterate and new to R. I have installed the rJava package in R studio version 1.0.143 and installed Java 8 (using MacOS Sierra). When I try to load the rJava package:
library(rJava)
I get the following error
Unable to find any JVMs matching version "(null)".
No Java runtime present, try --request to install.
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/cormac/Library/R/3.4/library/rJava/libs/rJava.so':
dlopen(/Users/cormac/Library/R/3.4/library/rJava/libs/rJava.so, 6):
Library not loaded: #rpath/libjvm.dylib
Referenced from:
/Users/cormac/Library/R/3.4/library/rJava/libs/rJava.so
Reason: image not found
In addition: Warning messages:
1: package ‘rJava’ was built under R version 3.4.2
2: running command '/usr/libexec/java_home' had status 1
Could somebody help me to interpret this error message? There is probably a very simple solution, but I am completely lost. Thank you!!
As noted in Unable to load rJava in RStudio, there is a very specific sequence of steps that must be taken to get rJava to work on a Macbook, as documented in rJava Issues #86.
Download and install Java from Oracle
Uninstall any previously installed version of rJava
Add JAVA_HOME to your .bashrc
Close & restart terminal, R and RStudio sessions so they pick up the updated JAVA_HOME
Use install.packages() to install rJava
See the URL link above for additional details on each step.
I was trying to install the rattle package in R and got this error message saying
configure: error: GTK version 2.8.0 required
ERROR: configuration failed for package ‘RGtk2’
Then I tried to fix the RGtk2 problem using this guide
http://marcoghislanzoni.com/blog/2014/08/29/solved-installing-rattle-r-3-1-mac-os-x-10-9/
I tried this code in the Mac OS terminal (but this is above my understanding) :
export PATH=/opt/local/bin:/opt/local/sbin:$PATH
sudo port selfupdate
sudo port install pkgconfig
export PATH=/opt/pkgconfig/bin:$PATH
sudo port install gtk2 +x11
export PKG_CONFIG_PATH=/opt/local/lib/pkgconfig
It gave me this answer
export PATH=/opt/local/bin:/opt/local/sbin:$PATH
ad-mac0630:~ caruc35$ sudo port selfupdate
Password:
Sorry, try again.
Password:
And locked down.
I also installed XCode command line tools from Apple and tried some stuff from the guide above. It didnt get the rattle package to work so I erased it.
After messing with this the rattle package does still not work and R seems not to work as it did before. For example i can´t load the xlsx package getting this error message:
Loading required package: 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/caruc35/Library/R/3.4/library/rJava/libs/rJava.so':
dlopen(/Users/caruc35/Library/R/3.4/library/rJava/libs/rJava.so, 6): Library not loaded: #rpath/libjvm.dylib
Referenced from: /Users/caruc35/Library/R/3.4/library/rJava/libs/rJava.so
Reason: image not found
Error: package ‘rJava’ could not be loaded
Did I mess up when trying to change PATH? Is there a way to reset everything back to normal?
I have tried reinstalling R but the same problems still occurs.
I'm using Ubuntu 16.04.
I have R running on my Jupyter notebook and all the packages comes with "R essentials" work fine.
However, when I try to install additional packages like "mice" or "bigmemory", the installation always fails. When it tries to do
** testing if installed package can be loaded
this is the error message that appears:
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/usr/anaconda3/lib/R/library/bigmemory/libs/bigmemory.so':
/home/usr/anaconda3/lib/R/library/Rcpp/libs/../../../../libstdc++.so.6: version 'GLIBCXX_3.4.20' not found (required by /home/usr/anaconda3/lib/R/library/bigmemory/libs/bigmemory.so)
I have tried sudo apt-get install libstdc++6
and it says my libstdc++6 is installed and already is the newest version. I don't know why the R installer cannot find it..
I figured it out!
I got frustrated and uninstalled anaconda3 completely rm -rf ~\anaconda3. After reinstalling it, I looked at the instruction for installing IRkernel. I saw this:
If this fails, search the output for something like:
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/Users/[you]/anaconda/lib/R/library/rzmq/libs/rzmq.so':
dlopen(/Users/[you]/anaconda/lib/R/library/rzmq/libs/rzmq.so, 6): Library not loaded: libzmq.5.dylib
Referenced from: /Users/[you]/anaconda/lib/R/library/rzmq/libs/rzmq.so
Reason: image not found
This would mean that the R binary package of rzmq was compiled against a different version of libzmq from the one on your system.
It can be fixed by installing from source
So following the instruction I then did
install.packages('mice','/home/[usr]/anaconda3/lib/R/library/',type = 'source')
It worked! I did the same thing for 'bigmemory'. No error message and I can use them both on Jupyter notebook now.
I use R version 3.0.3. I was not able to install library(xlsx). Error message:
Loading required package: rJava
Error : .onLoad failed in loadNamespace() for 'rJava', details:
call: inDL(x, as.logical(local), as.logical(now), ...)
error: unable to load shared object 'C:/Program Files/R/R-3.0.3/library/rJava/libs/x64/rJava.dll':
LoadLibrary failure: The specified module could not be found.
I then tried to install rjava on its own. Got the error message below:
library("rJava", lib.loc="C:/Program Files/R/R-3.0.3/library")
Error : .onLoad failed in loadNamespace() for 'rJava', details:
call: inDL(x, as.logical(local), as.logical(now), ...)
error: unable to load shared object 'C:/Program Files/R/R-3.0.3/library/rJava/libs/x64/rJava.dll':
LoadLibrary failure: The specified module could not be found.
Is there another way to load excel file in R?
Here are some possible solutions:
Install 64-bit version of Java. Here is the download link of Java.
Re-install rJava.
Manually set the directory of your Java location by setting it before loading the library
Sys.setenv(JAVA_HOME="C:\\Program Files\\Java\\jre7") # for 64-bit version
Sys.setenv(JAVA_HOME="C:\\Program Files (x86)\\Java\\jre7") # for 32-bit version
library(rJava)
Source: here
This problem is generally caused by x86 vs x64 bit differences between the R session and the install Java edition. By default Java installs the x86 version and you have to search for the x64 version. if you look at the version of Java you have installed and then open your R session to the same if your using R studio you can click on Tools.GlobalOptions and then select the version you need. ;-)
For mac user, installing Java for OS X 2014-001 works for me
https://support.apple.com/kb/DL1572?locale=en_US
For Windows 10 Pro users 64 bit OS, use
Sys.setenv(JAVA_HOME="C:\\Program Files\\Java\\jre1.8.0_144")
install.packages("openxlsx") try to install OPENXLSX instead of XLSX package. Now, the required library will work properly. library(openxlsx)
For MAC OS X follow these steps in order:
Use this command in the Terminal: sudo R CMD javareconf
Restart BaseR and RStudio...
in RStudio console: install.packages("xlConnect")
in RStudio console: library(xlConnect)
in RStudio console: library(xlsx)
Problem solved!