Develop Reference

Cannot Start Cytoscape

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.

IntelliJ IDEA won't start on AMD Athlon XP 1500+ (Windows 7)

I have installed Windows 7 to test IntelliJ IDEA, and when I run it, the splash screen progress bar goes to 100%, shows up the initial window, and crashes.
My JDK version is 8u202. Strangely, I tested it in the past with Xubuntu, and it starts flawlessly without crashes, with OpenJDK 8u191.
I looked at error log and idea.log files, and the error log says EXCEPTION_ILLEGAL_INSTRUCTION, however idea.log reveals nothing.
I have made a bug report and asked a support question, but neither got a response.

IntelliJ IDEA is using a native library IdeaWin32.dll for some file system operations on Windows. This library is compiled with the default options using Visual Studio C compiler (cl.exe), therefore it may use SSE2 instructions which are not available on your CPU.
Workarounds (choose one):
Replace IdeaWin32.dll library in IDEA_HOME\bin with a version compiled without SSE2 instructions (with /arch:SSE option instead of /arch:SSE2) (attached to YouTrack ticket).
Disable the native file system library for Windows by adding -Didea.use.native.fs.for.win=false in the idea.vmoptions file
Unrelated to the original problem, but I'd recommend running IntelliJ IDEA under JetBrains Runtime instead of the Oracle JDK. Windows installer has an option to download and use the 32-bit version of JetBrains Runtime automatically or you can download and switch to it manually.

Oracle Sql developer error: could not install some modules

I have downloaded a fresh copy of sqldeveloper (sqldeveloper-4.1.3.20.78-no-jre) from the Oracle website. When I unzip it and lauch the GUI, I keep getting the following error message:
Warning - could not install some modules: Dynamic Module Config - No
module providing the capability org.netbeans.Netbinox could be found.
My system:
Windows 7 32 bit Hp Probook.
Jdk 1.6 , 1.7, 1.8 available in java/jdk
subdirectory.
Netbeans 8.0.2 installed

Finally got the way out after some dirty hours. Initially I extracted the sqldeveloper zip in a nested directory.
i.e: E://A/B/C/sqldeveloper.
starting sqldeveloper gui from the above directory threw erros.
Solution:
Go in C:\users**UserName**\AppData\Roaming : delete SQL Developer and sqldeveloper folders
Extract the Sql Developer zip in a new non nested directory. i.e: E://
Start it and should work now
Reference: https://community.oracle.com/thread/3870680?start=0&tstart=0

This is a very old post but I have had the same issue recently on version 22.2, and this might help.
WARNING: You may lose important settings with this solution.
Try deleting the system cache under C:\Users<your_user_name>\AppData\Roaming\SQL Developer\{whatever}
(or simply everything in that folder). This solved the problem for me, but obviously you do lose configuration settings, connections, and so on, ie, everything you've ever done in SQL Developer - so be careful.

In my case it was enough to change JDK pass to Java 8 in the
C:\Users\YourName\AppData\Roaming\sqldeveloper\19.2.1\product.conf file:
SetJavaHome C:\Program Files\Java\jdk1.8.0_202
I have Java 13 as default and although SQL developer complained at startup it worked OK with it until I started it and went away from the computer, so I missed the warning screen. After that it started to show the "could not install the modules" error.

For those that are working on a linux machine, for me worked just changing the jdk version that I'm currently using. I change went to the path usr/lib/jvm/ and look for the versions that my pc have. Then in ~/.sqldeveloper/"yourversion"/product.conf I changed the Java home to java-8-openjdk (It was using the 11 version)

In my case renaming/deleting only this folder was good enough:
C:\Users*username*\AppData\Roaming\SQL Developer\system22.2.0.173.2018
This way I could still import old connections after starting sqldeveloper again

Based on This I just deleted mypath\sqldeveloper\netbeans\platform\modules\org-netbeans-core-windows.jar and it works fine for me.

I found that I was getting this error after I reinstalled java while keeping an instance of sqldeveloper running.
After I ended the running instance, then I could start a new instance.

This is tricky, so when the could not install some modules board shows up, click the disable modules and continue, then immediately open the app again it should work :)))

The solution in my case was to unzip the SQL developer in a directory without special characters.
At first, I had exported it in a directory that included the hash (#) symbol.
I now have it in a nested directory again, without any special characters, and it works as expected.

Unable to install Java on Windows 10 (1603 Error)

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.

Android SDK suddenly stopped working

After a couple of months with no Android development, I ran the SDK Manager yesterday, and upgraded from r16 to r18. After that upgrade, everything stopped working. I downloaded a fresh copy of the SDK tools from Google. The Windows installer complains there's no Java installed (the solution here , which used to work before, doesn't work).
I downloaded the ZIP file instead and put it in the right place. Running SDK Manager.EXE does nothing (it just returns immediately to the command prompt). Running tools\android.bat displays an error complaining "Failed to convert path to a short DOS path: c:\windows\system32\java.exe", and then suggests I install Java.
I'm running Windows 7 64-bit, with Java 1.7 (64 bit) properly installed (Eclipse runs well, the Android tools r16 ran very well until yesterday). c:\windows\system32\java.exe exists and works as it should.
What am I doing wrong?
UPDATE: I found an old r16 setup around. I installed it and everything went back to normal.

I put this one aside for a while, but now I had to get it back running. I didn't want to install a 32-bit Java VM alongside the 64 bit one I have.
I found the culprit. in android_sdk\tools\lib there's a batch-file called find_java.bat. It calls find_java.exe -s to find a list of potential Java locations. Running the exe file like this returns the error I've been seeing:
Failed to convert path to short DOS path: c:\windows\system32\java.exe
-s stands for short. Running it without the -s causes find_java.exe to work, causing find_java.bat to work, causing everything else to work. So the fix was to edit find_java.bat, and remove the -s .
I honestly don't know what Google is thinking.

My fix was to remove /bin from my JAVA_HOME, as in C:\Java\jdk1.6.0_26\bin --> C:\Java\jdk1.6.0_26\
I'm running 64bit java on W7.
This google issue was helpful:
http://code.google.com/p/android/issues/detail?id=23648

This is just a guess, but I advise you to install JDK 6. It is said in the SDK requirements that you have to use it. I remember that I installed JDK 7 and I had some kind of trouble with it too.
Also it is safer to use the 32-bit version.

You need to also update the Eclipse plugins via Help > Install New Software.

I was able to fix same like problem by adding the jdk path to PATH variable in environment variables.