<p>I uninstalled <code>Java</code> the way it is written <a href="https://discussions.apple.com/thread/4772629" rel="nofollow noreferrer">here</a>:</p>

<blockquote>
  <ol>
  <li>Click on the Finder icon located in your dock</li>
  <li>Click on Applications tab on the sidebar</li>
  <li>In the Search box enter JavaAppletPlugin.plugin</li>
  <li>This will find the JavaAppletPlugin.plugin file</li>
  <li>Right click on JavaAppletPlugin.plugin and select Move to Trash</li>
  </ol>
</blockquote>

<p>Then installed the recommended latest version for mac on the official <code>Java</code> website and it fixed the issue.</p>

CC BY-SA 4.0
2018-07-16T23:21:36.050Z
2018-07-17T18:27:15.260Z
2018-07-17T18:27:15.260Z
Nikita Vlasenko
<p>I am trying to use the following <a href="https://www.bioconductor.org/packages/release/bioc/html/esATAC.html" rel="nofollow noreferrer"><code>ATACseq</code> pipeline</a>.</p>

<p>Unfortunately when I am importing it with <code>library(esATAC)</code>, it is giving me an error:</p>

<pre><code>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
</code></pre>

<p>There are threads that discuss similar problems <a href="https://www.r-statistics.com/2012/08/how-to-load-the-rjava-package-after-the-error-java_home-cannot-be-determined-from-the-registry/" rel="nofollow noreferrer">1</a> and <a href="https://stackoverflow.com/questions/37735108/r-error-onload-failed-in-loadnamespace-for-rjava">2</a>:</p>

<p>But I checked the Java version and it is the right one: <code>64bit</code>:</p>

<pre><code>d-172-25-60-75:~ nikitavlasenko$ java -version
java version "1.8.0_172"
Java(TM) SE Runtime Environment (build 1.8.0_172-b11)
Java HotSpot(TM) 64-Bit Server VM (build 25.172-b11, mixed mode)
</code></pre>

<p>I tried to do the following in <code>Rstudio</code>:</p>

<pre><code>Sys.setenv(JAVA_HOME = "/usr/bin/java")
library(rJava)
library(esATAC)
</code></pre>

<p>But <code>library(rJava)</code> fails. I am using macOS High Sierra 10.13.4. I am not sure what can I try further. Any suggestions would be greatly appreciated.</p>

CC BY-SA 4.0
2018-07-17T13:46:14.610Z
Fundamentally, `JAVA_HOME` needs to be set to the Java *home*, not to the Java binary. This is a folder path that ends in `Home`.
Konrad Rudolph
<atac-seq>
rJava issue when trying to use ATACseq pipeline
# rJava issue when trying to use ATACseq pipeline

(Asked by: username_0 on 2018-07-16)

I am trying to use the following ATACseq pipeline.
Unfortunately when I am importing it with library(esATAC), it is giving me an 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

There are threads that discuss similar problems 1 and 2:
But I checked the Java version and it is the right one: 64bit:
d-172-25-60-75:~ nikitavlasenko$ java -version
java version "1.8.0_172"
Java(TM) SE Runtime Environment (build 1.8.0_172-b11)
Java HotSpot(TM) 64-Bit Server VM (build 25.172-b11, mixed mode)

I tried to do the following in Rstudio:
Sys.setenv(JAVA_HOME = "/usr/bin/java")
library(rJava)
library(esATAC)

But library(rJava) fails. I am using macOS High Sierra 10.13.4. I am not sure what can I try further. Any suggestions would be greatly appreciated.

**Tags:** atac-seq
> **Comments:**
> **username_1**: Fundamentally, `JAVA_HOME` needs to be set to the Java *home*, not to the Java binary. This is a folder path that ends in `Home`.  

---

## 1 answers

### Answer by username_0 on 2018-07-16. Score: 0 | Accepted answer

I uninstalled `Java` the way it is written [here](https://discussions.apple.com/thread/4772629):

> 1. Click on the Finder icon located in your dock
> 2. Click on Applications tab on the sidebar
> 3. In the Search box enter JavaAppletPlugin.plugin
> 4. This will find the JavaAppletPlugin.plugin file
> 5. Right click on JavaAppletPlugin.plugin and select Move to Trash

Then installed the recommended latest version for mac on the official `Java` website and it fixed the issue.


---

