Related
On a clean new machine with JDK 8 fresh installed, the freshly download Cytoscape .dmg file (v 3.7.2) opens but crashes before installing anything. The install GUI is very slow and doesn't proceed (I need to close it with "Force Quit" from the right-click menu).
The check script seems working fine:
Target Cytoscape version: 3.7.2
Your shell is zsh
Compatible OS version found: 10.15
- Pass: OS Version = 10.15.3
- Pass: Following Oracle JDK found:
/Library/Java/JavaVirtualMachines/jdk1.8.0_241.jdk
- Pass: Current Java Version = 1.8.0_241
- Pass: JAVA_HOME found: /Library/Java/JavaVirtualMachines/jdk1.8.0_*.jdk/Contents/Home
Sorry to hear you're having problems! Can you give us a bit more information? It sounds like the installer is trying to write files that it doesn't have access to (just a guess). I'm also running 10.15.3 and I'm not seeing the same problem, so something is definitely amiss. Three suggestions for you:
Submit a bug to the cytoscape bug list
Try downloading the tar ball (https://github.com/cytoscape/cytoscape/releases/download/3.7.2/cytoscape-3.7.2.tar.gz) and untar it in /Applications. Then try to run "cytoscape.sh" in that directory.
Upgrade to Java 11 and download Cytoscape 3.8-RC4 from https://cytoscape-builds.ucsd.edu/cytoscape-builds/Cytoscape-3.8.0/3.8.0-Release-Candidate-4/ to see if that works better.
-- scooter
Even though JRE 8 is installed on my MAC OS Yosemite 10.10.3,while running the Android present in tools in sdk - the error - " No Java Runtime present,requesting to install " gets displayed in terminal- how do i solve this issue?
I wanted to install Xamarin test recorder - after installing they
asked me to install Android sdk
SDK is downloaded in Library/Developer/Xamarin/android-sdk
Now when I run Android present in tools folder - I get the error -
No Java run time
I've installed JRE 8 with get the verified
java version from their site
Can someone please help!!
You have to install the full JDK, not only the JRE.
I had the same issue and solved by installing JDK.
Please use this link to download the latest JDK version 19.
After installing openjdk with brew and runnning brew info openjdk I got this
And from that I got this command here, and after running it I got Java working
sudo ln -sfn /usr/local/opt/openjdk/libexec/openjdk.jdk /Library/Java/JavaVirtualMachines/openjdk.jdk
2021 solution
TL;DR
brew install temurin
Details
On an M1 Mac/Apple Silicon (running Big Sur), I had already openjdk installed. As signaled in a previous answer by Mohammed, openjdk is keg-only with brew, and hence requires adding a symlink.
After following this, it solved the No Java Runtime present error, but rJava was complaining about missing libjvm.dylib and that existing libraries were for the wrong architecture:
.onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(jvm, FALSE)
error: unable to load shared object '/opt/homebrew/Cellar/openjdk/16.0.2/libexec/openjdk.jdk/Contents/Home/lib/server/libjvm.dylib':
dlopen(/opt/homebrew/Cellar/openjdk/16.0.2/libexec/openjdk.jdk/Contents/Home/lib/server/libjvm.dylib, 10):
no suitable image found. Did find:
/opt/homebrew/Cellar/openjdk/16.0.2/libexec/openjdk.jdk/Contents/Home/lib/server/libjvm.dylib:
mach-o, but wrong architecture
Installing Eclipse Temurin (previously AdoptOpenJDK) (and removing the previously created symlink in /Library/Java/JavaVirtualMachines/openjdk.jdk) immediately solved both issues seamlessly.
Just run brew install temurin and everything should be OK.
I didn't need the full JDK, I just needed to make JRE work and none of the other answers provided above worked for me.
Maybe it used to work, but now (1st Jul 2018) it isn't working. I just kept getting the error and the pop-up.
I eventually solved this issue by placing the following JAVA_HOME export in ~/.bash_profile:
export JAVA_HOME=/Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin/Contents/Home
Hope this helps someone.
I'm running Mac OS High Sierra.
I just had to do the following on Mac:
brew install openjdk
sudo ln -sfn /opt/homebrew/opt/openjdk/libexec/openjdk.jdk /Library/Java/JavaVirtualMachines/openjdk.jdk
export JAVA_HOME="/Library/Java/JavaVirtualMachines/openjdk.jdk/Contents/Home"
java --version
If you came across the error when tried to generate a jks file (keystore), so try adding
/Applications/Android\ Studio.app/Contents/jre/Contents/Home/bin/keytool
before running the command, like so:
/Applications/Android\ Studio.app/Contents/jre/Contents/Home/bin/keytool -genkey -v -keystore ~/key.jks -keyalg RSA -keysize 2048 -validity 10000 -alias key
Since it sounds like your JAVA_HOME variable is not set correctly, follow the instructions for setting that.
Setting JAVA_HOME environment variable on MAC OSX 10.9
I would imagine once you set this, it will stop complaining.
Maybe someone is still having the same issue. You can install openjdk using homebrew, and then add the new JDK bin directory to the front of your path:
cd ~
brew install openjdk
echo 'export PATH="/usr/local/opt/openjdk/bin:$PATH"' >> .bash_profile
source .bash_profile
Pre-Requisite:
I already had java11 installed on my machine using brew.
Step-1: brew info java11
output:
/opt/homebrew/Cellar/openjdk#11
USER1-MacBook-Pro JavaVirtualMachines % brew info java11
openjdk#11: stable 11.0.12 (bottled) [keg-only]
Development kit for the Java programming language
https://openjdk.java.net/
/opt/homebrew/Cellar/openjdk#11/11.0.12 (670 files, 273.0MB)
Poured from bottle on 2021-10-09 at 13:07:04
From: https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/openjdk#11.rb
License: GPL-2.0-only
==> Dependencies
Build: autoconf ✔
==> Requirements
Build: Xcode ✘
==> Caveats
For the system Java wrappers to find this JDK, symlink it with
sudo ln -sfn /opt/homebrew/opt/openjdk#11/libexec/openjdk.jdk /Library/Java/JavaVirtualMachines/openjdk-11.jdk
openjdk#11 is keg-only, which means it was not symlinked into /opt/homebrew,
because this is an alternate version of another formula.
If you need to have openjdk#11 first in your PATH, run:
echo 'export PATH="/opt/homebrew/opt/openjdk#11/bin:$PATH"' >> ~/.zshrc
For compilers to find openjdk#11 you may need to set:
export CPPFLAGS="-I/opt/homebrew/opt/openjdk#11/include"
==> Analytics
install: 44,188 (30 days), 149,578 (90 days), 433,845 (365 days)
install-on-request: 19,074 (30 days), 63,262 (90 days), 187,286 (365 days)
build-error: 0 (30 days)
Step-2: Append openJDK path to existing path.
echo 'export PATH="/opt/homebrew/opt/openjdk#11/bin:$PATH"' >> ~/.zshrc
Step-3: Source existing shell or open new terminal to validate changes
source ~/.zshrc
Step-4: Check path is added
which java
output: /opt/homebrew/opt/openjdk#11/bin/java
Step-5:
java --version
openjdk 11.0.12 2021-07-20
OpenJDK Runtime Environment Homebrew (build 11.0.12+0)
OpenJDK 64-Bit Server VM Homebrew (build 11.0.12+0, mixed mode)
working by following command
export JAVA_HOME="/Applications/Android Studio.app/Contents/jre/Contents/Home"
TL;DR
For JDK 11 try this:
To handle this problem in a clean way, I suggest to use brew and jenv.
For Java 11 follow this 2 steps, first :
JAVA_VERSION=11
brew reinstall jenv
brew reinstall openjdk#${JAVA_VERSION}
jenv add /usr/local/opt/openjdk#${JAVA_VERSION}/
jenv global ${JAVA_VERSION}
And add this at end of your shell config scripts ~/.bashrc or ~/.zshrc
export PATH="$HOME/.jenv/bin:$PATH"
eval "$(jenv init -)"
export JAVA_HOME="$HOME/.jenv/versions/`jenv version-name`"
Problem solved!
Then restart your shell and try to execute java -version
Note: If you have this problem, your current JDK version is not existent or misconfigured (or may be you have only JRE).
In 2022:
No need to download Java anymore, once Android Studio is installed.
Even though Java 11 is embedded with Android Studio now, on Mac sometimes this problem arises and the Java runtime is not found.
So, I have solved this problem by doing these two steps:
In Android Studio go to File > Project Structure. If, under the SDK entry, you can see there is no default SDK selected, but a text in red "No SDK", click on it and you will find an SDK / JDK list, select one of them. Thats it.
Make sure you run Android Studio from Application Folder.
For this copy the Android Studio launcher to the Application folder. Then in the Finder, go to the Application folder. Right-click on it. Click on "Show package contents", then navigate up to jre folder. Copy the folder and paste it into your home folder.
Now setup the path from the terminal: you can create a folder named java_jre, and the path must be set to jre/contents/Home :
Noors-Mac-mini:bin noorhossain$ export JAVA_HOME="/Users/noorhossain/java_jre/jre/Contents/Home"
// now checking the version :
Noors-Mac-mini:bin noorhossain$ java -version
openjdk version "11.0.11" 2021-04-20
OpenJDK Runtime Environment (build 11.0.11+0-b60-7772763)
OpenJDK 64-Bit Server VM (build 11.0.11+0-b60-7772763, mixed mode)
I solved the problem by installing oracle-sdk with brew.
brew install oracle-jdk --cask
In 2022, only if Android studio is installed:
Check if JDK is installed in Android studio. In Android Studio go to File > Project Structure. Under the SDK entry, if there is no default JDK selected, select from the list, or if there isn't any, add JDK and then apply to install.
After the JDK is installed in Android studio, you just need to add the JDK path directly from your Android Studio. Run the below command in the terminal and that's it.
echo 'export JAVA_HOME="/Applications/Android Studio.app/Contents/jre/Contents/Home"' >> ~/.zshrc
Now, check if it's working.
❯ java -version
openjdk version "11.0.11" 2021-04-20
OpenJDK Runtime Environment (build 11.0.11+0-b60-7772763)
OpenJDK 64-Bit Server VM (build 11.0.11+0-b60-7772763, mixed mode)
No need to install any package from brew or create any symlink. The Java is already embedded with the Android studio and we can use this directly for our system.
In newer versions of OS X (especially Yosemite, EL Capitan), Apple has removed Java support for security reasons.
To fix this you have to do the following.
Download Java for OS X 2015-001 from this link: https://support.apple.com/kb/dl1572?locale=en_US
Mount the disk image file and install Java 6 runtime for OS X.
After this you should not be seeing any of the below messages:
- Unable to find any JVMs matching version "(null)"
- No Java runtime present, try --request to install.
This should resolve the issue for the pop-up shown below:
Below is worked for me on macos mojave 10.14.6 version
I installed current jdk(https://www.oracle.com/java/technologies/javase-downloads.html)
Then do respectively;
vim .bash_profile
add "export JAVA_HOME=$(/usr/libexec/java_home)" to bash_profile
source .bash_profile
it is done. And you can check the version with java -version command.
If you are having this issue for the same reason that I am, I can tell you why it is happening. I just don't know how to fix it yet.
Here it is:
I am using JDK version 1.8 on MacOS Big Sur. I do not want to have to install a later version of the JDK because all my projects run on 1.8. But here's the thing.... On the command line
java -version
Returns this:
openjdk version "1.8.0_302"
OpenJDK Runtime Environment (build 1.8.0_302-bre_2021_08_14_21_34-b00)
OpenJDK 64-Bit Server VM (build 25.302-b00, mixed mode)
but a slightly different command (version prefixed with 2 dashes instead of 1)
java --version
returns this error:
Unrecognized option: --version
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
This is because Java 8 uses single dash version, all JDKs after use double dash.
So the machine, when looking for JAVA_HOME, is also using double dashes and getting the error.
just run this
sudo ln -sfn /usr/local/opt/openjdk/libexec/openjdk.jdk /Library/Java/JavaVirtualMachines/openjdk.jdk
I have Mojave 10.14.6 and the only thing that did work for me was:
setting JAVA_HOME to the following:
export JAVA_HOME=/Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin/Contents/Home
source .bash_profile (or wherever you keep your vars, in my case .zshrc)
Hope it helps! You can now type java --version and it should work
It's worth noting that with my current version of SQLDeveloper (21.2.1), there's another way to specify the JDK location. In my case, I was able to open up ~/.sqldeveloper/21.2.1/product.conf and set the JavaHome directive to the appropriate directory. I use jabba for JDK version management, and this path was something like ~/.jabba/jdk/amazon-corretto#1.8.292-10.1/Contents/Home. Needless to say, just setting that config value and restarting SQLDeveloper left me with a running copy again. This should work with any version of SQLDeveloper given the product.conf file exists inside your user's .sqldeveloper directory appropriate for the version you are using.
install JDK it will work ,
here is the jdk link to download .
link: https://www.oracle.com/technetwork/java/javase/downloads/jdk13-downloads-
5672538.html
I have been running Jira 6.1.5 on a Mac mini with OS X Mavericks and Java 7 for some time. This has been working just fine.
However, recently I updated the OS to Yosemite (10.10.3) and also installed Java 8. But now Jira refuses to start up.
If I execute:
sudo ./start-jira.sh
Jira appears to start as normally but then fails with:
Server startup logs are located in /Users/Michael/JIRA/logs/catalina.out
Neither the JAVA_HOME nor the JRE_HOME environment variable is defined
At least one of these environment variable is needed to run this program
I have tried to execute:
export JAVA_HOME='/usr/libexec/java_home -v 1.8'
but this doesn't seem to make any difference.
There are no logs in /Users/Michael/JIRA/logs/ at all.
Any help is appreciated :-)
I found a solution. I added:
export JAVA_HOME='/usr/libexec/java_home -v 1.7'
to the beginning of ~/JIRA/bin/start-jira.sh
I guess only Java 1.7 was registered. For some reason it couldn't accept -v 1.8.
Installed Java SE 1.7.0u10 from Oracle w/ their installer package
Downloaded and unpacked Eclipse Juno (4.2.1)
Double click Eclipse purple icon and get OS X alert prompt with error message:
To open "Eclipse," you need a Java SE 6 runtime. Would you like to
install one now?
(in terminal) which java - /usr/bin/java
ls -l /usr/bin/java - /usr/bin/java -> /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/java
(in Finder) Double click eclipse alias (included when unpacked download) - Terminal launches, /Applications/Eclipse/Eclipse.app/Contents/MacOS/eclipse ; exit ; and Exclipse launches without OS X alert prompt.
I've tried modifying the Eclipse app bundle plist to point the -vm key to /System/Library/Frameworks/JavaVM.frameworks/Versions/Current/Commands/java, but I feel like I probably shouldn't have to do this.`
I'd like to know how to get Eclipse to launch by just double clicking on the Application package. It's such a small thing to bug me... :o)
The best answer is to fix the Java 7 installation as shown here :
https://stackoverflow.com/a/19594116
Simple to do and I have confirmed it works on Mavericks. With this fix, you can launch your app from the launchpad as usual. If you upgrade your JDK, you will have to reapply the fix to the new installation.
I had JDK 7 installed and I solved this issue for eclipse Kepler by running eclipse from the terminal instead of the finder.
./eclipse
Just thought to share.
Update 1
For the sake of completeness, if you want to run it from Finder as well, you can wrap the ./eclipse command into a .command file and run it from Finder (so that you don't have to open a terminal)
The following lines should do the job (don't forget to replace "your-full-eclipse-path" with the eclipse path on your machine)
#!/bin/sh
/your-full-eclipse-path/eclipse
After that, give execute permission to the eclipse.command file you just created
chmod +x eclipse.command
I found the answer over on Ask Different
It's an ugly hack, but works perfectly.
posted on this page: Mountain Lion with Java 7 only
To trick OS X to accept Java 7 instead of proposing to install Java 6 a simple symlink is enough:
sudo mkdir /System/Library/Java/JavaVirtualMachines
sudo ln -s /Library/Java/JavaVirtualMachines/1.7.0.jdk /System/Library/Java/JavaVirtualMachines/1.6.0.jdk
Most Java Programs will run with this little hack without the need to install Java 6. OS X's Java Preferences (and maybe some others) will not as it seems to explicitly check the version of the JVM when it is started.
script above can fix my problem.
Hoping you are using 64-bit of Java SE 1.7.0 and so advising the following.
go to Eclipse->Preferences...->Java->Installed JREs
click Add...
Select Standard VM
paste /Library/Java/JavaVirtualMachines/1.7.0.jdk/Contents/Home into JRE home
Change the JRE name to something useful like Java SE 7
Click Finish
Check the check-box next to your newly created JRE.
You would need a restart.
For what it's worth, the Eclipse team seems to have worked around it by replacing their dlopen()-based method with a CFBundleCreate()-based one: https://bugs.eclipse.org/bugs/show_bug.cgi?id=411361
In case anybody has the same problem in their code that launches Java and does not want to resort to Apple-only APIs, I found an easier work-around: before dlopen()ing $JRE_HOME/lib/server/libjvm.dylib, make sure to open dlopen() $JRE_HOME/lib/jli/libjli.dylib. Then it won't ask to install Java 6.
Can you imagine that? You have to install a JDK 1.6 to get eclipse ran properly, even if you already have jdk 1.7 installed, and set the JAVA_HOME properly.
To resolve your issue, you just need to download the jdk1.6 from http://support.apple.com/kb/DL1572?viewlocale=en_US, and install it, later you will be able to run eclipse, and you can set the JAVA_HOME to JDK1.7, and you will be able to find the JDK1.7 from eclipse "Preferences".
All these hacks does not work on mac Mavericks,
But a simple and efficient solution is found here
it worked with me like a charm.
Note: a drawback of this solution is when you check your java version using "java -version" command, it will read Java 1.6
open /Library/Java/JavaVirtualMachines/jdkXXXXX.jdk/Contents/Info.plist
settting(<string>BundledApp</string> is usefull!):
<key>JVMCapabilities</key>
<array>
<string>JNI</string>
<string>BundledApp</string>
<string>WebStart</string>
<string>Applets</string>
<string>CommandLine</string>
</array>
I had the exact same message when setting up a new mac and trying to run eclipse 4.2.2 with only Java SE 7 installed (as part of JDK 7u17).
In order to be able to successfully launch Eclipse I had to let OSX download and install Apple's Java SE 6 runtime first before installing the latest JDK.
After installing the JDK, the command java -version correctly shows:
java version "1.7.0_17"
Java(TM) SE Runtime Environment (build 1.7.0_17-b02)
Java HotSpot(TM) 64-Bit Server VM (build 23.7-b01, mixed mode)
Trying to solve the problem the other way around didn't work -- i.e. installing JDK 7u17 first before installing Java SE 6 as suggested in the message.
I had the exactly same problem some days ago and I solved it today. Just installed this http://support.apple.com/kb/dl1572
And after that, when I opened the eclipse the OSX installed some java update and opening eclipse by Eclipse.app started working.
Hope it works with you too.
If you'd like to install Java 6 JDK only (no Java 7 JDK/JRE, no Java 6 JRE only), install the Apple OSX Java DMG (at time of writing, this was http://adcdownload.apple.com/Developer_Tools/java_for_os_x_2013003_developer_package/java_for_os_x_2013003_dp__11m4406.dmg).
You still won't be able to start Eclipse. Make a directory JavaVirtualMachines under /System/Library/Java. And then make an Alias of the java version folder at /Library/Java/JavaVirtualMachines and rename the alias 1.6.0.jdk and copy that alias to /System/Library/Java/JavaVirtualMachines/
After finished, you will have an Alias at /System/Library/Java/JavaVirtualMachines/1.6.0.jdk that points to the Java install directory at */Library/Java/JavaVirtualMachines/1.6.0_XX-XXX-XXX.jdk*
Install latest JDK from Sun, it installs into /Library/Java/JavaVirtualMachines/, e.g. /Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk
sudo mkdir /System/Library/Java/JavaVirtualMachines
sudo ln -s /Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/ /System/Library/Java/JavaVirtualMachines/1.6.0.jdk
========= this trick used to work on Mountain Lion, but not on Maverick 10.9 somehow ============
Tried this again on Maverick, it does not work anymore. I also tried to change eclipse app plist and eclipse.ini (by adding -vm or ), does not work either.
Some people suggested that this is caused by Eclipse binary prepared using Apple 1.6 appbundler instead of Oracle java7 appbundler: Application is using Java 6 from Apple instead of Java 7 from Oracle on Mac OS X?
For now, please just type the eclipse from command line, which works fine with JAVA_HOME set to Java 7 (/usr/libexec/java_home command will tell you)
How to Make Eclipse Run on OS X 10.9 Mavericks
Attempting to launch various Eclipse versions after the Mavericks upgrade pops up a dialog with this message:
To open "Eclipse.app" you need a Java SE 6 runtime. Would you like to install one now?
It turns out that Java 7 is disabled by default in OS X 10.9.
This is easily verified as follows:
$ java --version
No Java runtime present, requesting install.
The solution is to install the latest supported Java version from Apple support: Java for OS X 2013-005 (http://support.apple.com/kb/DL1572)
As of 10/15/13 this would be Java SE 6 1.6.0_65.
Post Date: Oct 15, 2013
File Size: 63.98 MB
After the install, Eclipse will run as expected from the Dock, the Finder, or the Terminal without any tricks, hacks, or work-arounds.
I wanted to run Eclipse itself with Java 7. As I have a couple of plugins that do not work without it. For me neither solution worked for 10.9, but I found a workaround. The main idea is that you start eclipse with java -jar launcher.jar and provide a couple of magic properties and then it starts. This guy provided the command line script in comments that works for me:
https://bugs.eclipse.org/bugs/show_bug.cgi?id=411361#c25
I found the same problem (Mac OS X 10.9.2, Java 1.7.0_53b13, Eclipse Kepler). The workaround was quite easy:
Find the executable in Finder (CMD+Click on Eclipse's icon in the Dock)
Remove the icon from the Dock
CTRL+Click on the executable in Finder
ALT+Open (to allow the execution of a non-signed application)
Eclipse opens normally and without any problem
Re-dragged the program onto the Dock
I had this problem and found that I did not have JDK installed on my Mac. Once I did that, Eclipse starts normally.
I had same problem.
First of all ; JDK(java development Kit) and JRE(Java Runtime Environment) are different things. It was confused by people
In order to install eclipse yo should install latest JDK . So
Visit
http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html
Download suitable version for your mac
You can check your version now ; it won't be 1.6 anymore
Try to install eclipse again , see it works.
Good luck!..
Trying to get Maven, Java, and OS X to play nice together - something I've done multiple times without issue on Linux and Windows machines. I assumed all I needed to do was download Maven, setup my environment variables and I'd be good. So here's a snippet from my .bash_profile...
export JAVA_HOME=/Library/Java/Home/
export M2_HOME=/usr/local/apache-maven/apache-maven-2.2.1
export PATH=$PATH:$M2_HOME/bin
The JAVA_HOME setting is what Apple recommends be used on this Q&A page. Yet after launching a terminal and running mvn --version, here's the output...
Apache Maven 2.2.1 (r801777; 2009-08-06 15:16:01-0400)
Java version: 1.6.0_17
Java home: /System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home
Default locale: en_US, platform encoding: MacRoman
OS name: "mac os x" version: "10.6.2" arch: "x86_64" Family: "mac"
Any idea why the JAVA_HOME I'm setting in my .bash_profile is being ignored by Maven? It's causing problems because things like rt.jar aren't found in the JAVA_HOME Maven is using. I can work around this by creating symbolic links and other hackery in the home Maven is using, but I'd rather have it work correctly since this will just blow up on me the next time Apple pushes a Java update. Thanks for any help...
The problem is that the symbolic link "CurrentJDK" inside the versions of JavaVm.framework points to the old jdk, so when i used the following commands to set the CurrentJDK to the latest one (1.7.0_45) it works
cd /System/Library/Frameworks/JavaVM.framework/Versions
sudo rm CurrentJDK
sudo ln -s /Library/Java/JavaVirtualMachines/jdk1.7.0_45.jdk/Contents CurrentJDK
reference:
http://java.dzone.com/articles/installing-jdk-7-mac-os-x
On Mac OS X, you should use /usr/libexec/java_home to determine the correct JAVA_HOME.
See What should I set JAVA_HOME to on OSX
On my Mac, /Library/Java/Home is a symlink (actually the start of a chain of symlinks) that ultimately points to /System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home. So I don't think maven is ignoring anything. It's just giving you the actual location.
I have the same setup and all works fine. UNSET the "JAVA_HOME" environment variable in your shell script. The Mac install takes care of that. You are setting it wrong anyways.
Unset it, source your file or startup shell and try again.
well the first thing I would check is whether mvn is a script. If it is you can see how it's sourcing the environment. If it isn't I would look for any config files typically named .mvnrc, or something in /etc. Of course it wouldn't hurt to RTFM!