RJDBC issues: Error in .jfindClass(as.character(driverClass)[1]) : class not found
<p>I have been for a while reading about this issue, <a href="https://github.com/s-u/rJava/issues/47" rel="nofollow noreferrer">at github</a> and here at <a href="https://stackoverflow.com/questions/30738974/rjava-load-error-in-rstudio-r-after-upgrading-to-osx-yosemite">stackoverflow</a>. </p>

<p>However, I don't seem to find the right fix to my problem. </p>

<p>Here is the process of what I did: </p>

<p>a while ago I started using Spark and I had a Java related error which, based on <a href="https://stackoverflow.com/questions/12757558/installed-java-7-on-mac-os-x-but-terminal-is-still-using-version-6/14875241#14875241">this post</a> I solved by doing: </p>

<pre><code>sudo rm /usr/bin/java
sudo ln -s /Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/bin/java /usr/bin
</code></pre>

<p>Today, I am trying to connect to our Redshift database using: </p>

<pre><code>redshift.drv &lt;- JDBC('com.amazon.redshift.jdbc41.Driver',
                 '~/Amazon\ Redshift\ JDBC\ Driver/RedshiftJDBC41-1.1.10.1010.jar',
                identifier.quote="'")
</code></pre>

<p>which throws the following error:</p>

<pre><code>Error in .jfindClass(as.character(driverClass)[1]) : class not found
</code></pre>

<p>based on the answer at <a href="https://github.com/s-u/rJava/issues/47" rel="nofollow noreferrer">github</a> I run:</p>

<pre><code>$ R CMD javareconf 

Java interpreter : /usr/bin/java
Java version     : 1.8.0_66
Java home path   : /Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home
Unable to locate an executable at "/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/bin/javac" (-1)
Java compiler    : not functional
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
System Java on OS X

trying to compile and link a JNI program
detected JNI cpp flags    :
detected JNI linker flags :
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DPLATFORM_PKGTYPE='"mac.binary.mavericks"'    -fPIC  -Wall -mtune=core2 -g -O2  -c conftest.c -o conftest.o
conftest.c:1:10: fatal error: 'jni.h' file not found
#include &lt;jni.h&gt;
     ^
1 error generated.
make: *** [conftest.o] Error 1
Unable to compile a JNI program


JAVA_HOME        : /Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home
Java library path:
JNI cpp flags    :
JNI linker flags :
Updating Java configuration in /Library/Frameworks/R.framework/Resources
Done.
</code></pre>

<p>which 1st) throws this <code>conftest.c:1:10: fatal error: 'jni.h' file not found</code> error and 2nd) is not consistent with what R sees: </p>

<pre><code>&gt; J("java.lang.System")$getProperty("java.version")
[1] "1.6.0_65"
</code></pre>

<p>At this stage I have the "intuition" that the commands I run to be able to use Spark were not adequate, since it is clear I don't have a consistent environment. </p>

<p>Therefore, my question is:</p>

<p><strong>Does anyone know a fix to this set up? Something that allows R to see the 1.8.0_66 version (find the <code>'jni.h'</code> file, etc...)</strong> </p>

<p>I really don't ming having to re-do all the Java installation, I just want to have a clean, functional environment. </p>

<p>in case is of any help, this driver works perfectly:</p>

<pre><code>prod.drv &lt;- JDBC('com.microsoft.sqlserver.jdbc.SQLServerDriver',
             '~/sqljdbc_4.0/enu/sqljdbc4.jar',
             identifier.quote="'")
</code></pre>

<p>Thanks!</p>

<p><strong>EDIT:</strong> </p>

<p>I added: </p>

<pre><code>setenv JAVA_HOME `/usr/libexec/java_home -v 1.8`
</code></pre>

<p>to my <code>.tcshrc</code> file and run: </p>

<pre><code>R CMD javareconf JAVA_CPPFLAGS=/Library/Java/JavaVirtualMachines/jdk1.8.0_73.jdk/Contents/Home/include/jni.h
</code></pre>

<p>(if I don't pass the JAVA_CPPFLAGS explicitly it will not find it, obtaining the same error as before). </p>

<p>Now I get the following error: </p>

<pre><code>Java interpreter : /Library/Java/JavaVirtualMachines/jdk1.8.0_73.jdk/Contents/Home/jre/bin/java
Java version     : 1.8.0_73
Java home path   : /Library/Java/JavaVirtualMachines/jdk1.8.0_73.jdk/Contents/Home
Java compiler    : /Library/Java/JavaVirtualMachines/jdk1.8.0_73.jdk/Contents/Home/bin/javac
Java headers gen.: /Library/Java/JavaVirtualMachines/jdk1.8.0_73.jdk/Contents/Home/bin/javah
Java archive tool: /Library/Java/JavaVirtualMachines/jdk1.8.0_73.jdk/Contents/Home/bin/jar
System Java on OS X

trying to compile and link a JNI program
detected JNI cpp flags: /Library/Java/JavaVirtualMachines/jdk1.8.0_73.jdk/Contents/Home/include/jni.h
detected JNI linker flags : -framework JavaVM
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG /Library/Java/JavaVirtualMachines/jdk1.8.0_73.jdk/Contents/Home/include/jni.h -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DPLATFORM_PKGTYPE='"mac.binary.mavericks"'    -fPIC  -Wall -mtune=core2 -g -O2  -c conftest.c -o conftest.o
clang: error: cannot specify -o when generating multiple output files
make: *** [conftest.o] Error 1
Unable to compile a JNI program

JAVA_HOME        : /Library/Java/JavaVirtualMachines/jdk1.8.0_73.jdk/Contents/Home
Java library path:
JNI cpp flags    :
JNI linker flags :
Updating Java configuration in /Library/Frameworks/R.framework/Resources
Done.
</code></pre>

<p>so, any help would be highly appreciated :)</p>