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problem with today's release?

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Kenneth Sloan-2
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problem with today's release?

Kenneth Sloan-2
I just accepted the latest update and am now having difficulties with locally written
plugins.  Here’s an example of the exception I get when trying to either run an installed
plugin or “compile-and-run” from source.

(Fiji Is Just) ImageJ 1.48v; Java 1.6.0_65 [64-bit]; Mac OS X 10.9.2; 46MB of 4783MB (<1%)
 
java.lang.NoClassDefFoundError: org/scijava/util/LineOutputStream
        at java.lang.ClassLoader.defineClass1(Native Method)
        at java.lang.ClassLoader.defineClassCond(ClassLoader.java:637)
        at java.lang.ClassLoader.defineClass(ClassLoader.java:621)
        at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
        at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
        at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
        at fiji.scripting.java.PlugInExecutor.<init>(PlugInExecutor.java:55)
        at fiji.scripting.java.PlugInExecutor.<init>(PlugInExecutor.java:50)
        at fiji.scripting.java.Refresh_Javas.runOutOfTreePlugin(Refresh_Javas.java:435)
        at fiji.scripting.java.Refresh_Javas.compileAndRun(Refresh_Javas.java:122)
        at fiji.scripting.java.Refresh_Javas.runScript(Refresh_Javas.java:71)
        at common.RefreshScripts.run(RefreshScripts.java:287)
        at fiji.scripting.java.Refresh_Javas.run(Refresh_Javas.java:61)
        at ij.IJ.runUserPlugIn(IJ.java:199)
        at ij.IJ.runPlugIn(IJ.java:163)
        at ij.IJ.runPlugIn(IJ.java:152)
        at fiji.Compile_and_Run.run(Compile_and_Run.java:25)
        at ij.IJ.runUserPlugIn(IJ.java:199)
        at ij.IJ.runPlugIn(IJ.java:163)
        at ij.Executer.runCommand(Executer.java:131)
        at ij.Executer.run(Executer.java:64)
        at java.lang.Thread.run(Thread.java:695)
Caused by: java.lang.ClassNotFoundException: org.scijava.util.LineOutputStream
        at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
        ... 27 more

--
Kenneth Sloan
[hidden email]

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Douglas Richardson
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Re: problem with today's release?

Douglas Richardson
Here's a quick fix I received from Johannes this morning:

Johannes Schindelin <[hidden email]> changed bug
742<http://fiji.sc/bugzilla/show_bug.cgi?id=742>
 What Removed Added  CC   [hidden email]

 *Comment # 1 <http://fiji.sc/bugzilla/show_bug.cgi?id=742#c1> on bug 742
<http://fiji.sc/bugzilla/show_bug.cgi?id=742> from Johannes Schindelin
<[hidden email]> *

This is caused by some version skew. To work around until the time when I can
fix it (I am transiting all day, so I cannot do it today), please
downloadhttps://oss.sonatype.org/service/local/artifact/maven/redirect?r=releases&g=org.scijava&a=scijava-common&v=2.18.1&e=jar
into your Fiji.app/jars/ directory and delete the scijava-common-2.9.0.jar that
is there already.

Sorry for the inconvenience.




On Thu, May 8, 2014 at 9:26 AM, Kenneth Sloan <[hidden email]>wrote:

> I just accepted the latest update and am now having difficulties with
> locally written
> plugins.  Here’s an example of the exception I get when trying to either
> run an installed
> plugin or “compile-and-run” from source.
>
> (Fiji Is Just) ImageJ 1.48v; Java 1.6.0_65 [64-bit]; Mac OS X 10.9.2; 46MB
> of 4783MB (<1%)
>
> java.lang.NoClassDefFoundError: org/scijava/util/LineOutputStream
>         at java.lang.ClassLoader.defineClass1(Native Method)
>         at java.lang.ClassLoader.defineClassCond(ClassLoader.java:637)
>         at java.lang.ClassLoader.defineClass(ClassLoader.java:621)
>         at
> java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
>         at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
>         at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
>         at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
>         at java.security.AccessController.doPrivileged(Native Method)
>         at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
>         at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
>         at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
>         at
> fiji.scripting.java.PlugInExecutor.<init>(PlugInExecutor.java:55)
>         at
> fiji.scripting.java.PlugInExecutor.<init>(PlugInExecutor.java:50)
>         at
> fiji.scripting.java.Refresh_Javas.runOutOfTreePlugin(Refresh_Javas.java:435)
>         at
> fiji.scripting.java.Refresh_Javas.compileAndRun(Refresh_Javas.java:122)
>         at
> fiji.scripting.java.Refresh_Javas.runScript(Refresh_Javas.java:71)
>         at common.RefreshScripts.run(RefreshScripts.java:287)
>         at fiji.scripting.java.Refresh_Javas.run(Refresh_Javas.java:61)
>         at ij.IJ.runUserPlugIn(IJ.java:199)
>         at ij.IJ.runPlugIn(IJ.java:163)
>         at ij.IJ.runPlugIn(IJ.java:152)
>         at fiji.Compile_and_Run.run(Compile_and_Run.java:25)
>         at ij.IJ.runUserPlugIn(IJ.java:199)
>         at ij.IJ.runPlugIn(IJ.java:163)
>         at ij.Executer.runCommand(Executer.java:131)
>         at ij.Executer.run(Executer.java:64)
>         at java.lang.Thread.run(Thread.java:695)
> Caused by: java.lang.ClassNotFoundException:
> org.scijava.util.LineOutputStream
>         at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
>         at java.security.AccessController.doPrivileged(Native Method)
>         at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
>         at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
>         at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
>         ... 27 more
>
> --
> Kenneth Sloan
> [hidden email]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
ctrueden
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Re: problem with today's release?

ctrueden
Hi all,

> I just accepted the latest update and am now having difficulties with
> locally written plugins.

I uploaded the fix; run Help > Update Fiji to get it. Please reply back if
you notice continued problems.

Regards,
Curtis


On Thu, May 8, 2014 at 8:51 AM, Douglas Richardson
<[hidden email]>wrote:

> Here's a quick fix I received from Johannes this morning:
>
> Johannes Schindelin <[hidden email]> changed bug
> 742<http://fiji.sc/bugzilla/show_bug.cgi?id=742>
>  What Removed Added  CC   [hidden email]
>
>  *Comment # 1 <http://fiji.sc/bugzilla/show_bug.cgi?id=742#c1> on bug 742
> <http://fiji.sc/bugzilla/show_bug.cgi?id=742> from Johannes Schindelin
> <[hidden email]> *
>
> This is caused by some version skew. To work around until the time when I
> can
> fix it (I am transiting all day, so I cannot do it today), please
> downloadhttps://
> oss.sonatype.org/service/local/artifact/maven/redirect?r=releases&g=org.scijava&a=scijava-common&v=2.18.1&e=jar
> into your Fiji.app/jars/ directory and delete the scijava-common-2.9.0.jar
> that
> is there already.
>
> Sorry for the inconvenience.
>
>
>
>
> On Thu, May 8, 2014 at 9:26 AM, Kenneth Sloan <[hidden email]
> >wrote:
>
> > I just accepted the latest update and am now having difficulties with
> > locally written
> > plugins.  Here’s an example of the exception I get when trying to either
> > run an installed
> > plugin or “compile-and-run” from source.
> >
> > (Fiji Is Just) ImageJ 1.48v; Java 1.6.0_65 [64-bit]; Mac OS X 10.9.2;
> 46MB
> > of 4783MB (<1%)
> >
> > java.lang.NoClassDefFoundError: org/scijava/util/LineOutputStream
> >         at java.lang.ClassLoader.defineClass1(Native Method)
> >         at java.lang.ClassLoader.defineClassCond(ClassLoader.java:637)
> >         at java.lang.ClassLoader.defineClass(ClassLoader.java:621)
> >         at
> > java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
> >         at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
> >         at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
> >         at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
> >         at java.security.AccessController.doPrivileged(Native Method)
> >         at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
> >         at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
> >         at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
> >         at
> > fiji.scripting.java.PlugInExecutor.<init>(PlugInExecutor.java:55)
> >         at
> > fiji.scripting.java.PlugInExecutor.<init>(PlugInExecutor.java:50)
> >         at
> >
> fiji.scripting.java.Refresh_Javas.runOutOfTreePlugin(Refresh_Javas.java:435)
> >         at
> > fiji.scripting.java.Refresh_Javas.compileAndRun(Refresh_Javas.java:122)
> >         at
> > fiji.scripting.java.Refresh_Javas.runScript(Refresh_Javas.java:71)
> >         at common.RefreshScripts.run(RefreshScripts.java:287)
> >         at fiji.scripting.java.Refresh_Javas.run(Refresh_Javas.java:61)
> >         at ij.IJ.runUserPlugIn(IJ.java:199)
> >         at ij.IJ.runPlugIn(IJ.java:163)
> >         at ij.IJ.runPlugIn(IJ.java:152)
> >         at fiji.Compile_and_Run.run(Compile_and_Run.java:25)
> >         at ij.IJ.runUserPlugIn(IJ.java:199)
> >         at ij.IJ.runPlugIn(IJ.java:163)
> >         at ij.Executer.runCommand(Executer.java:131)
> >         at ij.Executer.run(Executer.java:64)
> >         at java.lang.Thread.run(Thread.java:695)
> > Caused by: java.lang.ClassNotFoundException:
> > org.scijava.util.LineOutputStream
> >         at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
> >         at java.security.AccessController.doPrivileged(Native Method)
> >         at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
> >         at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
> >         at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
> >         ... 27 more
> >
> > --
> > Kenneth Sloan
> > [hidden email]
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Kenneth Sloan
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Re: problem with today's release?

Kenneth Sloan
Thanks for the quick action.  I'm away from the affected machine until late tonight.  Will test and report...when I can.

-Kenneth Sloan
(von meinem iPhone4S gesendet)

> On May 8, 2014, at 10:55, Curtis Rueden <[hidden email]> wrote:
>
> Hi all,
>
>> I just accepted the latest update and am now having difficulties with
>> locally written plugins.
>
> I uploaded the fix; run Help > Update Fiji to get it. Please reply back if
> you notice continued problems.
>
> Regards,
> Curtis
>
>
> On Thu, May 8, 2014 at 8:51 AM, Douglas Richardson
> <[hidden email]>wrote:
>
>> Here's a quick fix I received from Johannes this morning:
>>
>> Johannes Schindelin <[hidden email]> changed bug
>> 742<http://fiji.sc/bugzilla/show_bug.cgi?id=742>
>> What Removed Added  CC   [hidden email]
>>
>> *Comment # 1 <http://fiji.sc/bugzilla/show_bug.cgi?id=742#c1> on bug 742
>> <http://fiji.sc/bugzilla/show_bug.cgi?id=742> from Johannes Schindelin
>> <[hidden email]> *
>>
>> This is caused by some version skew. To work around until the time when I
>> can
>> fix it (I am transiting all day, so I cannot do it today), please
>> downloadhttps://
>> oss.sonatype.org/service/local/artifact/maven/redirect?r=releases&g=org.scijava&a=scijava-common&v=2.18.1&e=jar
>> into your Fiji.app/jars/ directory and delete the scijava-common-2.9.0.jar
>> that
>> is there already.
>>
>> Sorry for the inconvenience.
>>
>>
>>
>>
>> On Thu, May 8, 2014 at 9:26 AM, Kenneth Sloan <[hidden email]
>>> wrote:
>>
>>> I just accepted the latest update and am now having difficulties with
>>> locally written
>>> plugins.  Here’s an example of the exception I get when trying to either
>>> run an installed
>>> plugin or “compile-and-run” from source.
>>>
>>> (Fiji Is Just) ImageJ 1.48v; Java 1.6.0_65 [64-bit]; Mac OS X 10.9.2;
>> 46MB
>>> of 4783MB (<1%)
>>>
>>> java.lang.NoClassDefFoundError: org/scijava/util/LineOutputStream
>>>        at java.lang.ClassLoader.defineClass1(Native Method)
>>>        at java.lang.ClassLoader.defineClassCond(ClassLoader.java:637)
>>>        at java.lang.ClassLoader.defineClass(ClassLoader.java:621)
>>>        at
>>> java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
>>>        at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
>>>        at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
>>>        at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
>>>        at java.security.AccessController.doPrivileged(Native Method)
>>>        at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
>>>        at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
>>>        at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
>>>        at
>>> fiji.scripting.java.PlugInExecutor.<init>(PlugInExecutor.java:55)
>>>        at
>>> fiji.scripting.java.PlugInExecutor.<init>(PlugInExecutor.java:50)
>>>        at
>> fiji.scripting.java.Refresh_Javas.runOutOfTreePlugin(Refresh_Javas.java:435)
>>>        at
>>> fiji.scripting.java.Refresh_Javas.compileAndRun(Refresh_Javas.java:122)
>>>        at
>>> fiji.scripting.java.Refresh_Javas.runScript(Refresh_Javas.java:71)
>>>        at common.RefreshScripts.run(RefreshScripts.java:287)
>>>        at fiji.scripting.java.Refresh_Javas.run(Refresh_Javas.java:61)
>>>        at ij.IJ.runUserPlugIn(IJ.java:199)
>>>        at ij.IJ.runPlugIn(IJ.java:163)
>>>        at ij.IJ.runPlugIn(IJ.java:152)
>>>        at fiji.Compile_and_Run.run(Compile_and_Run.java:25)
>>>        at ij.IJ.runUserPlugIn(IJ.java:199)
>>>        at ij.IJ.runPlugIn(IJ.java:163)
>>>        at ij.Executer.runCommand(Executer.java:131)
>>>        at ij.Executer.run(Executer.java:64)
>>>        at java.lang.Thread.run(Thread.java:695)
>>> Caused by: java.lang.ClassNotFoundException:
>>> org.scijava.util.LineOutputStream
>>>        at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
>>>        at java.security.AccessController.doPrivileged(Native Method)
>>>        at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
>>>        at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
>>>        at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
>>>        ... 27 more
>>>
>>> --
>>> Kenneth Sloan
>>> [hidden email]
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Kenneth Sloan
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Re: problem with today's release?

Kenneth Sloan
appears to be fixed.  Thanks again!

--
Kenneth Sloan
[hidden email]


On May 8, 2014, at 11:13 , Kenneth Sloan <[hidden email]> wrote:

> Thanks for the quick action.  I'm away from the affected machine until late tonight.  Will test and report...when I can.
>
> -Kenneth Sloan
> (von meinem iPhone4S gesendet)
>
>> On May 8, 2014, at 10:55, Curtis Rueden <[hidden email]> wrote:
>>
>> Hi all,
>>
>>> I just accepted the latest update and am now having difficulties with
>>> locally written plugins.
>>
>> I uploaded the fix; run Help > Update Fiji to get it. Please reply back if
>> you notice continued problems.
>>
>> Regards,
>> Curtis
>>
>>
>> On Thu, May 8, 2014 at 8:51 AM, Douglas Richardson
>> <[hidden email]>wrote:
>>
>>> Here's a quick fix I received from Johannes this morning:
>>>
>>> Johannes Schindelin <[hidden email]> changed bug
>>> 742<http://fiji.sc/bugzilla/show_bug.cgi?id=742>
>>> What Removed Added  CC   [hidden email]
>>>
>>> *Comment # 1 <http://fiji.sc/bugzilla/show_bug.cgi?id=742#c1> on bug 742
>>> <http://fiji.sc/bugzilla/show_bug.cgi?id=742> from Johannes Schindelin
>>> <[hidden email]> *
>>>
>>> This is caused by some version skew. To work around until the time when I
>>> can
>>> fix it (I am transiting all day, so I cannot do it today), please
>>> downloadhttps://
>>> oss.sonatype.org/service/local/artifact/maven/redirect?r=releases&g=org.scijava&a=scijava-common&v=2.18.1&e=jar
>>> into your Fiji.app/jars/ directory and delete the scijava-common-2.9.0.jar
>>> that
>>> is there already.
>>>
>>> Sorry for the inconvenience.
>>>
>>>
>>>
>>>
>>> On Thu, May 8, 2014 at 9:26 AM, Kenneth Sloan <[hidden email]
>>>> wrote:
>>>
>>>> I just accepted the latest update and am now having difficulties with
>>>> locally written
>>>> plugins.  Here’s an example of the exception I get when trying to either
>>>> run an installed
>>>> plugin or “compile-and-run” from source.
>>>>
>>>> (Fiji Is Just) ImageJ 1.48v; Java 1.6.0_65 [64-bit]; Mac OS X 10.9.2;
>>> 46MB
>>>> of 4783MB (<1%)
>>>>
>>>> java.lang.NoClassDefFoundError: org/scijava/util/LineOutputStream
>>>>       at java.lang.ClassLoader.defineClass1(Native Method)
>>>>       at java.lang.ClassLoader.defineClassCond(ClassLoader.java:637)
>>>>       at java.lang.ClassLoader.defineClass(ClassLoader.java:621)
>>>>       at
>>>> java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
>>>>       at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
>>>>       at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
>>>>       at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
>>>>       at java.security.AccessController.doPrivileged(Native Method)
>>>>       at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
>>>>       at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
>>>>       at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
>>>>       at
>>>> fiji.scripting.java.PlugInExecutor.<init>(PlugInExecutor.java:55)
>>>>       at
>>>> fiji.scripting.java.PlugInExecutor.<init>(PlugInExecutor.java:50)
>>>>       at
>>> fiji.scripting.java.Refresh_Javas.runOutOfTreePlugin(Refresh_Javas.java:435)
>>>>       at
>>>> fiji.scripting.java.Refresh_Javas.compileAndRun(Refresh_Javas.java:122)
>>>>       at
>>>> fiji.scripting.java.Refresh_Javas.runScript(Refresh_Javas.java:71)
>>>>       at common.RefreshScripts.run(RefreshScripts.java:287)
>>>>       at fiji.scripting.java.Refresh_Javas.run(Refresh_Javas.java:61)
>>>>       at ij.IJ.runUserPlugIn(IJ.java:199)
>>>>       at ij.IJ.runPlugIn(IJ.java:163)
>>>>       at ij.IJ.runPlugIn(IJ.java:152)
>>>>       at fiji.Compile_and_Run.run(Compile_and_Run.java:25)
>>>>       at ij.IJ.runUserPlugIn(IJ.java:199)
>>>>       at ij.IJ.runPlugIn(IJ.java:163)
>>>>       at ij.Executer.runCommand(Executer.java:131)
>>>>       at ij.Executer.run(Executer.java:64)
>>>>       at java.lang.Thread.run(Thread.java:695)
>>>> Caused by: java.lang.ClassNotFoundException:
>>>> org.scijava.util.LineOutputStream
>>>>       at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
>>>>       at java.security.AccessController.doPrivileged(Native Method)
>>>>       at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
>>>>       at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
>>>>       at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
>>>>       ... 27 more
>>>>
>>>> --
>>>> Kenneth Sloan
>>>> [hidden email]
>>>>
>>>> --
>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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