Develop Reference

rJava fails to install on server

I am trying to install rJava to conduct MaxEnt (Dismo package) on the servers of a super computer that run Linux. All the other packages have been successful, but rJava continues to give errors.
I have followed the answers from this thread including adding jre to my file path, using R CMD javareconf, and installing a new JDK and specifying that as the $JAVA_HOME. Unfortunately, I cannot use the apt-get function because of my role on the servers, although I believe this would be the best solution since it will correct my necessary file paths. However, perhaps I am missing something else that is causing the error.
This is the Java Version I am using:
- openjdk version "1.8.0_181"
- OpenJDK Runtime Environment (build 1.8.0_181-b13)
- OpenJDK 64-Bit Server VM (build 25.181-b13, mixed mode)
This is the error msg that is produced
checking whether ~/Core/java/1.8.0_121/bin/javah actually works... no
checking whether javah was replaced by javac -h... no
configure: error: one or more Java tools are missing.
*** JDK is incomplete! Please make sure you have a complete JDK. JRE is *not* sufficient.
configure: error: ./configure failed for jri
ERROR: configuration failed for package 'rJava'
* removing '/home/afila/R/x86_64-pc-linux-gnu-library/3.5/rJava'
The downloaded source packages are in
'/tmp/RtmpvYtNJY/downloaded_packages'

The issue I was having was indeed a permissions problem. Someone helped me resolve it by emulating the root system using proot. After that it was a matter of re-configuring the directory and R's access to it.
In Unix
mkdir ~/etc
cp -a $EBROOTR/lib64/R/etc/* ~/etc
proot -b
R CMD javareconf -e
In R
install.packages("rJava")
library(rJava)

rJava install error "JAVA_HOME cannot be determined from the Registry"

I am trying to load the rJava using the command:
library(rJava)
But I get the following error:
Error : .onLoad failed in loadNamespace() for 'rJava', details:
call: fun(libname, pkgname)
error: JAVA_HOME cannot be determined from the Registry
Error: package or namespace load failed for ‘rJava’
I tried reinstalling both the Java and the R program with the latest versions
but still get these errors..
May I know how I can resolve this? Thank you very much!

This error is often resolved by installing a Java version (i.e. 64-bit Java or 32-bit Java) that fits to the type of R version that you are using (i.e. 64-bit R or 32-bit R). This problem can easily effect Windows 7 users, since they might have installed a version of Java that is different than the version of R they are using.
http://www.r-statistics.com/2012/08/how-to-load-the-rjava-package-after-the-error-java_home-cannot-be-determined-from-the-registry/

Install 64 bit Java from https://java.com/en/download/manual.jsp.
Then in windows cmd run
setx PATH "C:\Program Files\Java\jre1.8.0_211\bin\server;%PATH%"
(make sure your path is correct).
Then in RStudio run
Sys.setenv(JAVA_HOME="")
Now, you should be able to run rJava!!

I got the same error resolved by installing same version of R and Java i.e. 64 bits and manually updating the path i.e. ,
Sys.setenv(JAVA_HOME='C:/Program Files/Java/jre1.8.0_121') # for 64-bit version

R for Windows installer installs by default both 32-bit and 64-bit files. Reinstalling R and unticking 32-bit part solved the problem for me.

Under Windows 10, first check your (running) R-Version:
R.version
If you see something like x86_64, a 64-bit version of Java is needed.
Simply downloading and installing the matching Java version (https://java.com/en/download/manual.jsp) solved the problem for me. No reinstall of R needed (as suggested by other users here). There also was no need to set the path explicitly.

As mentioned in the r-statistics link cited above, you have to manually download the 64-bit version of Java. If not, then the 32-bit version will be installed.
So, if you have a 64-bit operating system, then ensure that both R and Java are using the 64-bit installs. Otherwise, this problem will persist.

This has been killing me and I have tried multiple methods above, it doesn't work. After, I mix all solution to try and below process works for me.
Install Java for 64 bit
Run below code in windows command
setx PATH "C:\Program Files\Java\jre1.8.0_171\bin\server;%PATH%"
(please change the address acorrding to your dvm.dll real address)
Run below in R studio
Sys.setenv(JAVA_HOME="")
Then I finally can run
library(rJava)
library(xlsx)

I faced the same issue and was feeling very down as I couldnt get my analysis done.
This worked for me :
check your operating system. 64 bit or 32 bit.
https://helpx.adobe.com/x-productkb/global/determine-whether-computer-running-32.html
uninstall previous versions of Java.
delete rJAVA library from Doc>R>win-library. If you have more than 1 versions of R, make sure you delete rJAVA package from all of them.
install Java based on system requirement (64 bit or 32 bit).
and finally restart R before and after installing rJava package.

If R is 64-bit version make sure to install Java 64-bit version!
If R is x86-bit version make sure to install Java x86-bit version!

You can add INSTALL_opts=c("--no-multiarch") to your install_github() call:
devtools::install_github("mne-tools/mne-r", INSTALL_opts=c("--no-multiarch"))
For more info: https://github.com/mne-tools/mne-r/issues/5#issuecomment-489588267

Create a new directory in C: drive as "library"
set your libPath this directory. you need to type
.libPath("C:/library")
reinstall packages which requires java (xlsx, rJava, RJDemetra)
it will give error message again but it will work.

Error while loading rJava

I get an error when I'd like to load rJava. JDK is installed. (I run R on a CentOS VM (cloudera demo vm cdh3u4))
> library(rJava)
Error : .onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/home/cloudera/R/x86_64-redhat-linux-gnu-library/2.15/rJava/libs/rJava.so':
libjvm.so: cannot open shared object file: No such file or directory
Error: package/namespace load failed for ‘rJava’
Is there something wrong with LD_LIBRARY_PATH settings? If yes, how can I fix that?
I need rJava running that to install rhdfs later.
Some more information (if needed):
[cloudera#localhost ~]$ java -version
java version "1.6.0_31"
Java(TM) SE Runtime Environment (build 1.6.0_31-b04)
Java HotSpot(TM) 64-Bit Server VM (build 20.6-b01, mixed mode)

For Ubuntu, oracle-java (7/8) installed. It'll be at this location /usr/lib/jvm and sudo access is required.
Create the file /etc/ld.so.conf.d/java.conf with the following entries:
/usr/lib/jvm/java-8-oracle/jre/lib/amd64
/usr/lib/jvm/java-8-oracle/jre/lib/amd64/server
(Replace java-8-oracle with java-7-oracle or java-7-openjdk-amd64 depending on your java version)
Then:
sudo ldconfig
Restart RStudio and then install the rJava package.

Getting rJava to work depends heavily on your computers configuration. The following is working at least on a windows platform. You could try and check, if this will help you on your platform, too.
You have to use the same 32bit or 64bit version for both: R and JDK/JRE. A mixture of this will never work (at least for me).
If you use 64bit version make sure, that you do not set JAVA_HOME as a enviorment variable. If this variable is set, rJava will not work for whatever reason. You can check if your JAVA_HOME is set inside R with:
Sys.getenv("JAVA_HOME")
If you need to have JAVA_HOME set (e.g. you need it for maven or something else), you could deactivate it within your R-session with the following code before loading rJava:
if (Sys.getenv("JAVA_HOME")!="")
Sys.setenv(JAVA_HOME="")
library(rJava)
This should do the trick in most cases. Furthermore this will fix issue Using the rJava package on Win7 64 bit with R, too. I borrowed the idea of unsetting the enviorment variable from R: rJava package install failing.

How to install JPype on OS X Lion to use with Neo4j?

I am trying to use Neo4j for a project, and want to interface with it through Python since I'm a newbie to programming and don't know any Java. I'm following the installation instructions, but I'm stuck on
the first step, which is to install JPype.
I'm using OS X 10.7 (lion). I think my configuration is pretty standard
with Python 2.7.2 downloaded from the Python website and Java 1.6.0 downloaded from the Apple website.
When I run
% sudo python setup.py install
On the JPype installer, I get about a 100 lines of error code about various .h files, then it
terminates with the lines:
lipo: can't figure out the architecture type of: /var/tmp//
ccwOzLi9.out
error: command 'gcc-4.2' failed with exit status 1
I found a blog post about a gcc error with JPype, but I followed the instructions there to no avail. I also emailed the author of that post, and he told me had never actually used JPype, had been working in OS X 10.6, and didn't have any insight.
I also emailed the creator of JPype, who told me that he only uses Windows, and has no idea how to make the install work on OS X. But if we can solve this, I can point him to the answer and maybe he can add the solution to the JPype documentation and help lots of other people as well!
So, anyone know what I'm doing wrong? I would like to use Neo4j, but I
don't know Java so I'm at a complete loss for how to fix a compiler
error.
Based on reading every Google result available, my two running
theories are that:
I'm somehow using a 32-bit version of Python or of Java (though I
used standard official installations and can't figure out how to
switch to 64-bit or if that's even possible)
The JPype files can only be compiled using GCC 4.0 instead of 4.2.
But I can't find anything online about how to rollback to GCC 4.0 (or
if it comes shipped with 2011 MacBooks and there is some way to force
JPype to compile with that instead).
There is another similar question, but the solution there is to use a different adapter that goes through REST instead of hooking directly into Java. I will try that if I have to, but I would really rather use the recommended Neo4j method if it's possible.

I'm not a Python guy, but tried installing JPype on my machine:
% uname -a
Darwin fatty-i7.local.tld 11.2.0 Darwin Kernel Version 11.2.0: Tue Aug 9 20:54:00 PDT 2011; root:xnu-1699.24.8~1/RELEASE_X86_64 x86_64
% java -version
java version "1.6.0_29"
Java(TM) SE Runtime Environment (build 1.6.0_29-b11-402-11M3527)
Java HotSpot(TM) 64-Bit Server VM (build 20.4-b02-402, mixed mode)
On OSX Lion, the latest JDK appears to be located here:
/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/JavaVM.framework/
A little googling turned up this post: http://blog.y3xz.com/post/5037243230/installing-jpype-on-mac-os-x
I followed those instructions to modify setup.py, then ran sudo python setup.py install with no problems.
Does that help?

On my Lion, the "include" directory in the JDK was gone, so JPype couldn't find jni.h.
I updated setup.py in two places, one to set where to find jar libraries:
def setupMacOSX(self):
self.javaHome = '/System/Library/Frameworks/JavaVM.framework'
self.jdkInclude = ""
self.libraries = ["dl"]
self.libraryDir = [self.javaHome+"/Home/lib"]
self.macros = [('MACOSX',1)]
And one to set where to find jni.h:
def setupInclusion(self):
self.includeDirs = [
self.javaHome+"/Headers",
<other stuff>

For me,
self.javaHome = '/System/Library/Frameworks/JavaVM.framework/Versions/Current/'
worked.
$ uname -a Darwin 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64
$ java -version java version "1.6.0_33" Java(TM) SE Runtime Environment (build 1.6.0_33-b03-424-11M3720) Java HotSpot(TM) 64-Bit Server VM (build 20.8-b03-424, mixed mode)

Here are directions I put in my README to install JPype on OS X 10.7. Same idea as the answers here but different enough to warrant the submission.
The python interface to java (JPype) needs mods to the setup.py:
In summary, you need to make sure the JPype setup.py script can see your Java SDK "Headers" and "Home" directory
I had to install Java from Apple first since my default OS X installation did not come with Headers in the typical Java install path which I found by executing:
/usr/libexec/java_home
If you do happen to have a Headers dir, you probably do not need to reinstall Java and can set the path vars below based on your java HOME directory which is likely different from those in these directions
After I installed Java, I found the new installation in:
/Library/Java/JavaVirtualMachines/
My Home directory was:
/Library/Java/JavaVirtualMachines/1.6.0_37-b06-434.jdk/Contents/Home/
and my Header directory was:
/Library/Java/JavaVirtualMachines/1.6.0_37-b06-434.jdk/Contents/Headers/
1) The JPype script assumes that Headers is within the Home directory but it's not, so I changed the Home path var and created a new Content path var in the setup.py script - In setupMacOSX(self):
self.javaHome = '/Library/Java/JavaVirtualMachines/1.6.0_37-b06-434.jdk/Contents/Home/'
self.javaContents = '/Library/Java/JavaVirtualMachines/1.6.0_37-b06-434.jdk/Contents/'
2) In setupMacOSX(self), change self.libraryDir:
self.libraryDir = [self.javaContents + "/Libraries"]
Note that this step was mentioned as required but I did not have to do this for it to work so maybe try without it first
3) In setupInclusion, add paths to your "Home/include" dir and your "Headers" dir:
self.javaHome+"/include",
self.javaContents + "/Headers",
4) Running the installation should now work:
sudo python setup.py install

For everyone who is still trying to install Jpype but has meanwhile updated Mac OS: Andreas Kolleger's answer just works fine, but with XCode 4.3 the path changed to /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/JavaVM.framework/Versions/Current/
In ML it's MacOSX10.8.sdk. At least on my system. :)

For me, on Mountain Lion
self.javaHome = '/System/Library/Frameworks/JavaVM.framework/'
worked.
$uname -a
Darwin 12.0.0 Darwin Kernel Version 12.0.0: Sun Jun 24 23:00:16 PDT 2012; root:xnu-2050.7.9~1/RELEASE_X86_64 x86_64
$ java -version
java version "1.6.0_33"
Java(TM) SE Runtime Environment (build 1.6.0_33-b03-424-11M3720)
Java HotSpot(TM) 64-Bit Server VM (build 20.8-b03-424, mixed mode)

I did the same, but choosing
self.javaHome = '/Developer/SDKs/**MacOSX10.6.sdk**/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/'
instead
self.javaHome = '/Developer/SDKs/**MacOSX10.7.sdk**/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/'
realize that I use version 6 vs 7. With the 7 version I got the same errors that the beginning.

To make Will's answer a bit more specific: I had to modify the setupInclusion(self) method by adding the directory path he suggested, ie, '/System/Library/Frameworks/JavaVM.framework/Headers' on Mountain Lion (java version 1.6). With that the installation of JPype succeeded (though gave a bunch of warnings...)

Here's what worked for me - recommend you put the first line in your profile.
export JAVA_HOME=$(/usr/libexec/java_home)
cd $JAVA_HOME
sudo ln -s include Headers
sudo cp include/darwin/* include/
cd -
Note that instead of changing setup.py, I'm changing my JDK install. This has the advantage of fixing the issue for other projects.

For those trying to install on Mountain Lion, I had to further edit the setup.py file to include the header files here:
/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers

How do I set the default Java installation/runtime (Windows)?

I'm in the situation where I've installed the JDK, but I can't run applets in browsers (I may not have installed the JRE).
However, when I install the JRE, it clobbers my JDK as the default runtime. This breaks pretty much everything (Eclipse, Ant) - as they require a server JVM.
There's no JAVA_HOME environment variable these days - it just seems to use some registry magic (setting the system path is of no use either). Previously, I've just uninstalled the JRE after I've used it to restore the JDK. This time I want to fix it properly.
This also manifests itself with the jre autoupdater - once upon a time, I had a working setup with the JDK and JRE, but it updated and bust everything.

This is a bit of a pain on Windows. Here's what I do.
Install latest Sun JDK, e.g. 6u11, in path like c:\install\jdk\sun\6u11, then let the installer install public JRE in the default place (c:\program files\blah). This will setup your default JRE for the majority of things.
Install older JDKs as necessary, like 5u18 in c:\install\jdk\sun\5u18, but don't install the public JREs.
When in development, I have a little batch file that I use to setup a command prompt for each JDK version. Essentially just set JAVA_HOME=c:\jdk\sun\JDK_DESIRED and then set PATH=%JAVA_HOME%\bin;%PATH%. This will put the desired JDK first in the path and any secondary tools like Ant or Maven can use the JAVA_HOME variable.
The path is important because most public JRE installs put a linked executable at c:\WINDOWS\System32\java.exe, which usually overrides most other settings.

I have patched the behaviour of my eclipse startup shortcut in the properties dialogue
from
"E:\Program Files\eclipse\eclipse.exe"
to
"E:\Program Files\eclipse\eclipse.exe" -vm "E:\Program Files\Java\jdk1.6.0_30\bin"
as described in the Eclipse documentation
It is a patch only, as it depends on the shortcut to fix things...
The alternative is to set the parameter permanently in the eclipse initialisation file.

I just had that problem (Java 1.8 vs. Java 9 on Windows 7) and my findings are:
short version
default seems to be (because of Path entry)
c:\ProgramData\Oracle\Java\javapath\java -version
select the version you want (test, use tab completing in cmd, not sure what those numbers represent), I had 2 options, see longer version for details
c:\ProgramData\Oracle\Java\javapath_target_[tab]
remove junction/link and link to your version (the one ending with 181743567 in my case for Java 8)
rmdir javapath
mklink /D javapath javapath_target_181743567
longer version:
Reinstall Java 1.8 after Java 9 didn't work. The sequence of installations was jdk1.8.0_74, jdk-9.0.4 and attempt to make Java 8 default with jdk1.8.0_162...
After jdk1.8.0_162 installation I still have
java -version
java version "9.0.4"
Java(TM) SE Runtime Environment (build 9.0.4+11)
Java HotSpot(TM) 64-Bit Server VM (build 9.0.4+11, mixed mode)
What I see in path is
Path=...;C:\ProgramData\Oracle\Java\javapath;...
So I checked what is that and I found it is a junction (link)
c:\ProgramData\Oracle\Java>dir
Volume in drive C is OSDisk
Volume Serial Number is DA2F-C2CC
Directory of c:\ProgramData\Oracle\Java
2018-02-07 17:06 <DIR> .
2018-02-07 17:06 <DIR> ..
2018-02-08 17:08 <DIR> .oracle_jre_usage
2017-08-22 11:04 <DIR> installcache
2018-02-08 17:08 <DIR> installcache_x64
2018-02-07 17:06 <JUNCTION> javapath [C:\ProgramData\Oracle\Java\javapath_target_185258831]
2018-02-07 17:06 <DIR> javapath_target_181743567
2018-02-07 17:06 <DIR> javapath_target_185258831
Those hashes doesn't ring a bell, but when I checked
c:\ProgramData\Oracle\Java\javapath_target_181743567>.\java -version
java version "1.8.0_162"
Java(TM) SE Runtime Environment (build 1.8.0_162-b12)
Java HotSpot(TM) 64-Bit Server VM (build 25.162-b12, mixed mode)
c:\ProgramData\Oracle\Java\javapath_target_185258831>.\java -version
java version "9.0.4"
Java(TM) SE Runtime Environment (build 9.0.4+11)
Java HotSpot(TM) 64-Bit Server VM (build 9.0.4+11, mixed mode)
so to make Java 8 default again I had to delete the link as described here
rmdir javapath
and recreate with Java I wanted
mklink /D javapath javapath_target_181743567
tested:
c:\ProgramData\Oracle\Java>java -version
java version "1.8.0_162"
Java(TM) SE Runtime Environment (build 1.8.0_162-b12)
Java HotSpot(TM) 64-Bit Server VM (build 25.162-b12, mixed mode)
** update (Java 10) **
With Java 10 it is similar, only javapath is in c:\Program Files (x86)\Common Files\Oracle\Java\ which is strange as I installed 64-bit IMHO
.\java -version
java version "10.0.2" 2018-07-17
Java(TM) SE Runtime Environment 18.3 (build 10.0.2+13)
Java HotSpot(TM) 64-Bit Server VM 18.3 (build 10.0.2+13, mixed mode)

After many attempts, I found the junction approach more convenient. This is very similar on how this problem is solved in linux.
Basically it consists of having a link between c:\tools\java\default and the actual version of java you want to use as default in your system.
How to set it:
Download junction and make sure to put it in your PATH
environment variable
Set your environment this way:
- PATH pointing to ONLY to this jre c:\tools\java\default\bin
- JAVA_HOME pointing to `c:\tools\java\default
Store all your jre-s in one folder like (if you do that in your Program FIles folder you may encounter some
C:\tools\Java\JRE_1.6
C:\tools\Java\JRE_1.7
C:\tools\Java\JRE_1.8
Open a command prompt and cd to C:\tools\Java\
Execute junction default JRE_1.6
This will create a junction (which is more or less like a symbolic link in linux) between C:\tools\java\default and C:\tools\java\JRE_1.6
In this way you will always have your default java in c:\tools\java\default.
If you then need to change your default java to the 1.8 version you just need to execute
junction -d default
junction default JRE_1.8
Then you can have batch files to do that without command prompt like
set_jdk8.bat
set_jdk7.bat
As suggested from #СӏаџԁеМаятіи
EDIT: From windows vista, you can use mklink /J default JRE_1.8

I simply install all the versions of JDK I need and the latest installed becomes default, so I just reinstall the one I want to be default if necessary.

I have several JDK (1.4, 1.5, 1.6) installed in C:\Java with their JREs. Then I let Sun update the public JRE in C:\Program Files\Java.
Lately there is an improvement, installing in jre6. Previously, there was a different folder per new version (1.5.0_4, 1.5.0_5, etc.), which was taking lot of space

an alterable way to run an .jar app is create an .bat cmd for it.
for example, you have jre10 and jre8 installed on your pc,and jre10 is your default jre.
but your jar is specified to work with jre8,following cmd will work:
"C:\Program Files\Java\jre1.8.0_181\bin\java.exe" -jar JabRef-4.3.1.jar

Need to remove C:\Program Files (x86)\Common Files\Oracle\Java\javapath from environment and replace by JAVA_HOME which is works fine for me

Stacked by this issue and have resolved it in 2020, in Windows 10. I'm using Java 8 RE and 14.1 JDK and it worked well until Eclipse upgrade to version 2020-09. After that I can't run Eclipse because it needed to use Java 11 or newer and it found only 8 version. It was because of order of environment variables of "Path":
I suppose C:\Program Files (x86)\Common Files\Oracle\Java\javapath is path to link to installed JRE exe files (in my case Java 8) and the issue was resolved by move down this link after %JAVA_HOME%, what leads to Java 14.1/bin folder.
It seems that order of environment variables affects order of searched folders while executable file is requested.
Thanks for your comment or better explanation.