Peptide shaker failed to start

[GoogleCodeExporter]

> What steps will reproduce the problem?
I downloaded PeptideShaker-0.17.1, unzip and run.
It simply returned start up error. I can't successful run
the program.

> What is the expected output? What do you see instead?
I expect to see the program fire up without problem, just like I am using 
SearchGUI. Now I can't start up the program.

> What version of the product are you using? On what operating system?
I using using PeptideShaker-0.17.1, win 7 ultimate (fully updated).
I have java jre 7 installed, but I uninstalled it and download from oracle 
again, install it. Still I can't start up the program.
I can still run SearchGUI, nothing wrong. But I just can't startup
peptide shaker.

> Please provide any additional information below.
I attached my windows information, and the start-up log error
of the program. I checked the path of java in the log file, it's correct. I 
hopes these informaiton can help.

Thanks! Wish I can sort this out soon.

> If the reported issue resulted in the tool crashing, please
> also upload the file called PeptideShaker.log (found in the
> PeptideShaker-X.Y.Z\conf folder).

Original issue reported on code.google.com by jake...@gmail.com on 3 Jun 2012 at 8:24

Attachments:

• [Windows info.PNG](https://storage.googleapis.com/google-code-attachments/peptide-shaker/issue-14/comment-0/Windows info.PNG)
• startup.log

[GoogleCodeExporter]

Thank you for telling us about your startup issues.

I see that you have a 32-bit operating system even though you are running 
Windows 7. Please make sure that you have installed the 32-bit version of Java, 
as the 64-bit version will not run on a 32-bit system.

To check this click the Windows start button and in the 'Search programs and 
files' field type in 'cmd' and click enter. A command line window will then 
appear. Type in 'java -version' and click enter.

You should then get something like this:
java version "1.7.0_04"
Java(TM) SE Runtime Environment (build 1.7.0_04-b22)
Java HotSpot(TM) 64-Bit Server VM (build 23.0-b21, mixed mode)

If the information includes '64-Bit' in the last line you need to uninstall 
this version and install the 32-bit version. This can be done via the standard 
Windows uninstall feature.

Let us know if any of the above helps or not.

Original comment by harald.b...@gmail.com on 4 Jun 2012 at 12:06

[GoogleCodeExporter]

Sorry, the above test for Java version does not seem to be generic enough to 
work for all users. Instead try the following:

Click the Windows start button and in the 'Search programs and files' field 
type 'uninstall' and select the 'Uninstall a program' option. This will bring 
up a list of all the programs on your machine. Scroll down to find Java and see 
if it says 'Java (TM) Update 4' (or something similar) or 'Java (TM) Update 4 
(64-bit)'. Again, if you see '64-Bit' here you need to uninstall this version 
and install the 32-bit version.

Original comment by harald.b...@gmail.com on 4 Jun 2012 at 12:20

[GoogleCodeExporter]

After verifying that you have Java 32-bit installed, follow the point 'Memory 
Issues I' under the Troubleshooting section 
(http://code.google.com/p/peptide-shaker/#Troubleshooting).

On a 32-bit machine '-Xmx1500M' should be supported, while your current setting 
of '-Xmx1900M' is usually too high. Did you edit this file yourself by the way?

Original comment by harald.b...@gmail.com on 4 Jun 2012 at 1:08

[GoogleCodeExporter]

Hi,

I verified from your steps provide and checked my d/led java is 32 bit 
(jre-7u4-windows-i586.exe from 
http://www.oracle.com/technetwork/java/javase/downloads/jre-7u4-download-1591157
.html)

I changed to -xmx1500M, but still it won't start up. I attached the log file
for your reference.

It looks like to me that it's something to do with peptide shaker. SearchGUI is 
also a java program and I have no issue at all...

Original comment by jake...@gmail.com on 4 Jun 2012 at 5:10

Attachments:

• startup.log
• java.PNG

[GoogleCodeExporter]

Sorry I've forgotten to tell you that 1900M was my editing. I read through
troubleshooting after the program failed to start up and made that change 
accordingly.

Thanks!

Original comment by jake...@gmail.com on 4 Jun 2012 at 5:14

[GoogleCodeExporter]

SearchGUI is using 1024M. So if you try that I think it should work.

BTW, which error message did you get the first time you tried to run it? The 
memory limit should be set automatically to a limit your machine should be able 
to handle. This seems to have failed somehow.

Original comment by harald.b...@gmail.com on 4 Jun 2012 at 7:26

[GoogleCodeExporter]

The memory settings should be set automatically to the max setting your machine 
is able to handle during the first startup of PeptideShaker. This worked fine 
for Java 1.6 and for Java 1.7 64-bit, but not for Java 1.7 32-bit.

However, this bug has now been fixed and will be included in the next release.

Thanks for helping us detect this bug!

Original comment by harald.b...@gmail.com on 4 Jun 2012 at 2:09

• Changed state: Started

[GoogleCodeExporter]

PeptideShaker v0.17.2 has just been released, fixing the issue with the 
automatic setting of the upper memory limit on Java 1.7 32-bit.

Again, thanks for helping us detect this bug!

Original comment by harald.b...@gmail.com on 4 Jun 2012 at 2:40

• Changed state: Fixed

[GoogleCodeExporter]

I tested PeptideShaker 0.17.2. It works!
Thanks!

Keep up the good work!
:-)

Original comment by jake...@gmail.com on 4 Jun 2012 at 4:09