TIQAM on MAC

[RuthH]

I have problems to start TIQAM on the MAC. I downloaded the Mac
version of TIQAM from the web and wanted to start the software, but
for both, digester and viewer I get following error message:

!SESSION 2008-11-20 14:30:03.992
-----------------------------------------------
eclipse.buildId=unknown
java.version=1.5.0_13
java.vendor=Apple Inc.
BootLoader constants: OS=macosx, ARCH=x86, WS=carbon, NL=en_US
Framework arguments: -keyring /Users/Ruth/.eclipse_keyring -
showlocation
Command-line arguments: -os macosx -ws carbon -arch x86 -keyring /
Users/Ruth/.eclipse_keyring -consoleLog -showlocation

!ENTRY org.eclipse.osgi 4 0 2008-11-20 14:30:06.414
!MESSAGE Application error
!STACK 1
org.eclipse.core.runtime.CoreException: Plug-in proteinDigestor was
unable to load class proteinDigestor.Application.
at
org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.throwException
(RegistryStrategyOSGI.java:180)
at
org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.createExecutableExtension
(RegistryStrategyOSGI.java:164)
at
org.eclipse.core.internal.registry.ExtensionRegistry.createExecutableExtension
(ExtensionRegistry.java:788)
at
org.eclipse.core.internal.registry.ConfigurationElement.createExecutableExtension
(ConfigurationElement.java:243)
at
org.eclipse.core.internal.registry.ConfigurationElementHandle.createExecutableExtension
(ConfigurationElementHandle.java:51)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run
(EclipseAppHandle.java:165)
at
org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication
(EclipseAppLauncher.java:106)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start
(EclipseAppLauncher.java:76)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run
(EclipseStarter.java:363)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run
(EclipseStarter.java:176)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke
(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke
(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:508)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:447)
at org.eclipse.equinox.launcher.Main.run(Main.java:1173)
org.eclipse.core.runtime.CoreException[1]:
java.lang.UnsupportedClassVersionError: Bad version number in .class
file
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:675)
at
org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.defineClass
(DefaultClassLoader.java:161)
at org.eclipse.osgi.baseadaptor.loader.ClasspathManager.defineClass
(ClasspathManager.java:501)
at org.eclipse.osgi.baseadaptor.loader.ClasspathManager.findClassImpl
(ClasspathManager.java:471)
at
org.eclipse.osgi.baseadaptor.loader.ClasspathManager.findLocalClassImpl
(ClasspathManager.java:430)
at org.eclipse.osgi.baseadaptor.loader.ClasspathManager.findLocalClass
(ClasspathManager.java:413)
at
org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.findLocalClass
(DefaultClassLoader.java:189)
at
org.eclipse.osgi.framework.internal.core.BundleLoader.findLocalClass
(BundleLoader.java:340)
at
org.eclipse.osgi.framework.internal.core.BundleLoader.findClassInternal
(BundleLoader.java:408)
at org.eclipse.osgi.framework.internal.core.BundleLoader.findClass
(BundleLoader.java:369)
at org.eclipse.osgi.framework.internal.core.BundleLoader.findClass
(BundleLoader.java:357)
at org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.loadClass
(DefaultClassLoader.java:83)
at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
at org.eclipse.osgi.framework.internal.core.BundleLoader.loadClass
(BundleLoader.java:289)
at org.eclipse.osgi.framework.internal.core.BundleHost.loadClass
(BundleHost.java:227)
at org.eclipse.osgi.framework.internal.core.AbstractBundle.loadClass
(AbstractBundle.java:1269)
at
org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.createExecutableExtension
(RegistryStrategyOSGI.java:160)
at
org.eclipse.core.internal.registry.ExtensionRegistry.createExecutableExtension
(ExtensionRegistry.java:788)
at
org.eclipse.core.internal.registry.ConfigurationElement.createExecutableExtension
(ConfigurationElement.java:243)
at
org.eclipse.core.internal.registry.ConfigurationElementHandle.createExecutableExtension
(ConfigurationElementHandle.java:51)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run
(EclipseAppHandle.java:165)
at
org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication
(EclipseAppLauncher.java:106)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start
(EclipseAppLauncher.java:76)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run
(EclipseStarter.java:363)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run
(EclipseStarter.java:176)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke
(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke
(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:508)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:447)
at org.eclipse.equinox.launcher.Main.run(Main.java:1173)

Does anyone have experience with TIQAM on Mac and can make suggestions
how I could solve this problem?

Thanks a lot,

Ruth

[Mi-Youn Brusniak]

Dear Ruth,

We tested this with tiger macOS. TIQAM does not support leopard.
Is your OS tiger?

Mi-Youn

Mi-Youn Brusniak, Ph.D.
Computational Biology
Seattle Proteome Center
mbru...@systemsbiology.org
Tel: (206) 732-1327

[RuthH]

Dear Mi-Youn,

I am actually using Leopard. Would it be possible to adapt TIQUAM that
it could also support Leopard, since a lot of people are using
Leopard? That would be great. This is just an idea and I don't know
how much work it would be.

Ruth

On 20 Nov., 20:26, "Mi-Youn Brusniak" <mbrusn...@systemsbiology.org>
wrote:

> Dear Ruth,
>
> We tested this with tiger macOS. TIQAM does not support leopard.
> Is your OS tiger?
>
> Mi-Youn
>
> Mi-Youn Brusniak, Ph.D.
> Computational Biology
> Seattle Proteome Center

> mbrusn...@systemsbiology.org

[Simon Letarte]

Hi Ruth,

I am in the same boat as you, I use Leopard on my computer.
Unfortunately, there is an issue with the Java that ships with
Leopard. If I recall correctly, it is a 64 bits version and there is
no 32 bits java available for leopard. And changing TIQAM to use 64
bits java would be a lot of work. I run TIQAM using Windows emulation
under Parallels. It works fine.

Simon

>> (EclipseAppLauncher.java:106)
>> at
>> org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start
>> (EclipseAppLauncher.java:76)
>> at org.eclipse.core.runtime.adaptor.EclipseStarter.run
>> (EclipseStarter.java:363)
>> at org.eclipse.core.runtime.adaptor.EclipseStarter.run
>> (EclipseStarter.java:176)
>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
>> Method)
>> at sun.reflect.NativeMethodAccessorImpl.invoke
>> (NativeMethodAccessorImpl.java:39)
>> at sun.reflect.DelegatingMethodAccessorImpl.invoke
>> (DelegatingMethodAccessorImpl.java:25)
>> at java.lang.reflect.Method.invoke(Method.java:585)
>> at
>> org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:508)
>> at org.eclipse.equinox.launcher.Main.basicRun(Main.java:447)
>> at org.eclipse.equinox.launcher.Main.run(Main.java:1173)
>>
>> Does anyone have experience with TIQAM on Mac and can make
>> suggestions
>> how I could solve this problem?
>>
>> Thanks a lot,
>>
>> Ruth
>>
>>
> >

--
Simon Letarte, Ph. D.
Senior Research Scientist
Institute for Systems Biology
1441 North 34th Street
Seattle, WA 98103-8904

office: 206-732-1331
mobile: 206-859-0370
fax: 206-732-1299
slet...@systemsbiology.org

[RuthH]

Dear Simon,

thanks a lot for the suggestion. Now I installed it on the windows
partition and it works. Can you tell me where you save your SQL
datafiles? Since I have only some GB space left on my windows
parition, it would be much better to store the datafiles on the MAC,
even though the TIQAM is installed on windows. But when I tried to do
this, I got an error message. Have you tried this by chance before?

Thanks for your help,

Ruth

> sleta...@systemsbiology.org

[Simon Letarte]

Dear Ruth,

I am not sure which files you are talking about... I have installed
mySQL on the windows side. It is not that big. But maybe you have
files that are bigger than mine. I don't think it will work if you
put the sql on the mac side and tiqam on the windows side. Maybe
increase the size of your windows partition if you are running out of
space.

Simon