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.
Related
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
I am trying to install the latest Java JRE for Windows 8.1:
http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html
And none of the installers work. Online/Offline/x86/x64
I double-click the installer, get the UAC popup, approve, and then it thinks for a second and then just does nothing. How can I troubleshoot this more?
Things I've Tried:
Disabling UAC
Disabling all anti-virus
Disabling Windows Firewall / Defender
Downloading older version of Java (still does nothing when run)
Running as Administrator
Launching from admin-command-line
Changing compatibility mode (all of vista -> windows 7)
Running in Safe Mode (same behavior)
Uninstalling all older Java installations (big mistake)
Monitoring Process List - the java installer pops up for a second and
disappears
Installing through the JDK - JDK installer also does nothing when launched
Event Viewer shows no errors
I can't find any logs or errors that might help narrow down what the issue could be.
Any help would be very much appreciated. If there are any additional tools I could check out to help with troubleshooting, or any logs people know of, I could use any help I could get.
Thank you!!
After hours of fiddling around, I think I finally have something working. It seems that there's some weirdness for any system that has ever upgraded their version of Windows (I went from 8 to 8.1) with some sort of MSI ID sort of thing. So, here's how I finally ended up:
HOW I FIXED:
1) The issue started after the Java 8 "51" installer. So the 51 still works, get it here:
http://www.oracle.com/technetwork/java/javase/downloads/java-archive-javase8-2177648.html
You want: jdk-8u51-windows-x64.exe (or i586)
Install older version
2) download latest Java .zip archive (like jre-8u91-windows-i586.tar.gz ) and unzip it in any location, preferably "c:\Program Files\Java"
3) Go to "C:\Program Files\Java" and rename jre1.8.0_51 to something else ("jre1.8.0_51_bak" maybe)
4) Copy the contents of the extracted .tar.gz contents into a new folder named "c:\program files\java\jre1.8.0_51" (or rename the directory)
So basically using the install directory for 51, but adding the latest Java files into the folder that the installation is pointing at.
Quick fix, for now, just to help anybody in a pinch. I'll update as I continue to sort it out and if there's any new information.
Good luck!
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.
So I've tried desperately to download JRE to end up with nothing.
Originally I thought I deleted something so I cleared my computer of all JRE files plus all java related files, deleted them and completely removed them. I even downloaded JavaRa and removed all files from there. I then re-started my computer and tried to re-download Java again but it didn't work. I then deleted that from the computer, re-started once more and downloaded the latest from JavaRa, and again nothing. I tried manually downloading from the website (Windows x86 Offline - jre-8u45-windows-i586.exe) and whenever I try to run it nothing happens, same with when I run with admin, nothing happens. I completely formatted my computer today and even then when I tried, nothing happened, I still had the same problem.
This is the actual text that appears whenever I try to download it:
The wizard was interrupted before Java 7 Update 67 could be completely installed. To complete installation at another time, please run setup again.
I've tried looking at so many help sites and Java help itself but nothing can help, please someone help. I can provide any additional information needed.
I run 32bit Windows Vista Home Premium.
how about this?
http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html
its jre for 32 bit windows
VisualVm hangs when started from either the downloaded visualvm.dmg or the zip. It gets to the Visual VM Calibration dialog and then stops. There are no messages in the dialog box nor does clicking the OK button do anything.
I can't find any log in either my home or the extracted zip folder when I run either.
From the command line I get
./visualvm
Unable to find any JVMs matching version "1.7.0_10+".
Found jdkhome=/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home
Any advice on how to diagnose the problem would be greatly appreciated.
It's telling you that you don't have a JDK/JRE with a version of 7 or higher. If you didn't install one, then it won't be there - download it from the oracle website, or install the Open JDK if you require version 7 or higher.
You should also be able to see error messages in the OS X console (but I doubt you'll get more detailed error messages than you already received)
Oracle link to install JRE 7
I've had the same issue, just resize the screen and you'll see the "I agree" button.
Or, add the "--laf Metal" arg to the startup of the application.
Hope it works for you, too!