I wonder if anyone can help me with Cytoscape start issue. It used to fucntiona perfectly but now it can no longer initiate. I reinstall the Cytoscape multiple times. When I ran the checker script (described on troubleshooting page) and "I receive Java is not reachable". See attached PICTURE 1 I reinstalled Java 11 but still has no luck. Here is my CytoscapeConfiguration folder looks like PICTURE 2. Thank you all in advance.
FYI
MacOS Mojave.
Cytoscape 3.9.0
Inside "JavaVirtualMachines" directory, there are:
adoptopenjdk-11.jdk
jdk-11.0.12.jdk
jdk-12.0.1.jdk
OK, so you have a number of java JDKs installed, but it's not clear which of these is active. The easiest way to determine that is to open up a terminal window and type "which java". That should give you a pointer to the actual java binary (it's /Library/Java/JavaVirtualMachines/adoptopenjdk-11.jdk/Contents/Home/bin/java on my Mac). If it doesn't come back with anything, then Java didn't get correctly installed. You might try explicitly setting your JAVA_HOME to the correct JDK (/Library/Java/JavaVirtualMachines/adoptopenjdk-11.jdk/Contents/Home) and seeing if that works.
-- scooter
Related
This morning I downloaded Cytoscape v3.8.0 and I can no longer successfully open the app.
Before this, I was using v3.7.4 (I believe?) and did not encounter any issues. I am working off a laptop with Windows 10.
After realizing that I could not open Cytoscape I went and downloaded the most recent version of Java but that did not appear to help.
I also tried downloading the Cytoscape troubleshooter for Windows, however, it only downloads as a .txt file and I cannot figure out how to use that to test my system.
If I try opening the app, it appears very quickly with "Cytoscape 3.8.0 - Initializing OSGi container..." before crashing.
Any help or insight would be greatly appreciated!
It's a little hard to diagnose your issues without a little more information, unfortunately. When you say you downloaded the latest Java -- which version did you actually download? If you open up a command (cmd) window and change directory to the Cytoscape install, can you try to run cytoscape.bat? What does it do, and what error messages are printed? If that doesn't work, in that same window, type "java -version" and let us know which version of Java is set to be the default. That will help us figure things out.
If you are on a Mac, a recent update has caused OpenCL based Cytoscape Apps to fail and prevents Cytoscape from launching.
This will be fixed in future updates, but you can fix your Mac installation immediately by disabling OpenCL by either of the two following methods:
Download the disable-opencl.dummy file to your CytoscapeConfiguration
directory (in your user home directory).
Or, you can create an empty dummy file by running this command in Terminal:
touch ~/CytoscapeConfiguration/disable-opencl.dummy
These fixes are described at Cytoscape.org.
I tried to download Java on my laptop (which has windows 10) but i keep getting a 1603 error. My computer used to have windows 8.1 and it did not work back then either
I appreciate any advice to solve or work around this problem
I have had this problem. I was able to fix it thanks to a co-worker. The problem started happening after I installed HP Unified Functional Testing (UFT, aka QTP). Installing this product changes the Windows environment variables used by Java. He told me the following: "So change the names of JAVA_OPTIONS, IBM_JAVA_OPTIONS, JAVA_TOOL_OPTIONS to something else (both in system and user variables) and delete any Java folder(in Program Files (x86) or Program Files) which gets installed despite the error. Restart the system and then try installing Java."
Actually, all I did was rename the environment variables and run the installer. This worked.
My answer is not related to win 10, but might help someone who is having similar problem in windows 7 machine and not able to install jre 32 bit version.
the work around to this is once you downloaded the jre, copy the path "C:\Program Files (x86)\Java\jre1.8.0_121\bin\javaw.exe" and paste it under java runtime environment settings which is found -Java Control panel>java>view
I think you downloaded the wrong version. If your laptop support x64 bit software you should download Java 1.8 x64 version.
Here is the link.
https://www.java.com/en/download/manual.jsp
I had this problem for a month now. I tried everything on my windows 8, but I couldn't get the latest java on it. When I tried to install java on an empty computer, the 64 bit version did not go through (error 1603) and I realized the problem didn't come from an old java install and I install 32 bit. it worked on the new computer with windows 7 and on my computer running 8.1.
note: I had deleted all the java versions before going through with it.
To fix java 1603 error you have to follow few simple steps.
First of all remove all old java version.
Then remove some windows update file which might be reason of this
error. Like KB2918614 update.
After that download and Install latest version of java and activate
java in browser. Now everything will be fine you can test the java
version on java website...
For explained and easy solution to java 1603 error follow this link: http://protechguides.com/java-error-code-1603-solved/
I encountered this error on Windows 8.1 and when I checked with Oracle web site, they said that is is not yet resolved, and under investigation. They also showed a link for off-line installation as an alternative arrangement. However, upon investigation of my system, i found out that the available space in C drive was only about 20 MB or so. I cleared my system and provided enough space. When I tried with the extra space, I didn't encounter any error. May be, you could try with a better free space...
First you should close the browser because if any webpage will use Java, it will cause conflict. Then do custom installation, i.e. install in some other folder other than default folder and point environment variable to newly installed Java location. It will resolve your issue.
Firstly I install JDK & JRE, it install correctly and works properly, but when I run Net-beans setup which is of 64 bit , after configuring process it shows an error and shows a message as title of Critical and displaying NUll Null message, I'm using window 8 with 64 bit (OS).
So how I Can come out from this problem?
Please help me my all friends on this issue........
Make sure you have installed JDK 64bit. during the setup jdk64 you may face with error when setup is trying install JRE, and it's normal, let just finish the setup.
I always have problems with windows too, you may just simply download the OS-independent package from netbeans.org. just extract and use it.
checking package(either zip or exe) hash is recommended, even a bit would mark the whole package incompatible.
You may also set the jre_home, java_home and jdk_home too before netbeans run.
For some reason my firefox browser stopped detecting java and now I can't run anything with java on it because it says that it's not installed, so I went to add/remove programs and tried to uninstall java but it just won't get removed.
http://rcupload.com/images/IDSnu.png
So when I try to uninstall it (Java(TM) 7 Update 5) a little window appears with a progress bar, after it completes it disappears but Java is still there..
this is the window that appears:
http://rcupload.com/images/HLUwZ.png
Here's what I tried to do:
1) Use CCleaner to uninstall it:
- I choose the program, press uninstall and it disappears, but when I refresh the list it will still be there. I also tried using the "remove entry" button in CCleaner and i just get a message saying "cannot delete msi installer'.
2) I tried using JavaRA:
- I ran it as administrator, clicked "remove older versions", and I got the message that Java JDK 1.7 was uninstalled and all the files, but now I see that there is no folder for it at "C:\program files (x86)\Java\" (there was one inside before, called something like jre-7) and the icon in the installed programs appears like a white box instead of looking the like the java logo.
3) I tried downloading java and installing it:
- I run it, it downloads and it gets to a screen where it asks me if I want to install a toolbar, I click next and I get this message:
http://rcupload.com/images/xiCIu.png
I also tried changing the destination folder. same result.
--
Resumed: I need to get rid of Java(TM) 7 Update 5 but the uninstaller seems not to work and files are missing.
Any help will be appreciated!
Thanks.
I was having the same exact problem, and solved it using Microsoft Fix it tool, here:
http://support.microsoft.com/mats/program_install_and_uninstall
Finally, a Microsoft troubleshooter that actually works !
I haven't experienced this before my self. Here's my guess. One may say this is a 'harsh' way to remove and cause system in-stability. But I don't see any other way with the given details.
Please don't continue if you don't understand every step. This is almost what the un-installer does behind the scenes. You will have to do them manually.
First Un-install Firefox.
It doesn't detect the Java version installed for some reason where the Java installer does. you'll have to re-install it later when everything is fine.
Delete (i mean, backup) your JRE folder in 'Program Files'
Open regedit, and find the key for Java Runtime under HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Uninstall and delete (export it first, just in case) the key. (You'll have to go through each key and see the DisplayName for them.)
This will remove the entry in Add/Remove programs and Windows will think there's no Java.
Remove Java path from your System's Environment variables.
This will cause some apps that check for Java to decide that there's no Java installed.
Run the un installer again (if it's still visible in Add/Remove Programs).
If Windows still has the reference to the uninstaller, this will cause it to update it self and remove any references because there's no registry entry, and no program files.
Reboot the machine.
This will flush any waiting changes, unregister stuff .etc.
Try installing Java again. (Installer should not detect that there's Java installed, because there's no Environment variables set, and no registry entries.)
Please try this at your own risk. This may cause issues in your system.
You may get a better answer if posted on superuser site.
Let us know the results.
I am a web developer, new to app development and Java/Android. I am about to follow some tutorials to get started learning but I'm running into a wall. The Android dev site says the recommended way to build Android apps is in Java using the Eclipse plug in. So I downloaded Eclipse Classic and unzipped it on to get this error:
"A Java Runtime Environment (JRE) or Java Development Kit (JDK) must be available in order to run Eclipse.
No Java virtual machine was found after searching the following locations:
/Users//Desktop/eclipse/Eclipse.app/Contents/MacOS/jre/bin/java
java in your current PATH"
Any idea what the issue is and how I can fix it? Again, newbie to java, jre, android, so I apologize if this question has already been asked. In my research I've discovered that most of the posts or solutions I've found are tough for me to follow. There's always a few unclear items that are probably prohibiting me from getting the answer I need. So I'm hoping someone can walk me through installing or configuring whatever I need to regarding Java so I can continue installing Eclipse and begin learning.
I should probably note that I'm on Mac OSX 10.6.6 Snow Leopard. Please let me know if you need any other info. Thanks so much in advance for any and all help!!!
Your Mac is telling the truth, it can't find a JRE or JDK - make sure one is in your PATH and then try again.
[edit]
At the command prompt:
whereis java
and got /usr/bin/java.
ls -l /usr/bin/java
showed a symlink to /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/java.
cd /System/Library/Frameworks/JavaVM.framework/Versions/
indicates that all my java's are located here.
So, as long as /usr/bin/java exists, it should be linked to your current jdk. If it's not, you're probably going to have to do a little googling to find out why.
Apple contends that all the java stuff is ready to go on your machine (as it was on mine). See here for more information.
[/edit]
Download a java jdk from Oracle.