Hi,
I’m trying to run the webstart version of Jalview under windows from the main link on the website (http://www.jalview.org/webstart/jalview.jnlp).
If I run with a fairly standard Java setup (Java 1.6.0_29 on XP) Jalview seems to work fine, but if I run with caching turned off (Java control panel → General tab → temporary internet files → settings) I get the following error:
com.sun.deploy.net.JARSigningException: Found unsigned entry in resource: http://www.jalview.org/webstart/castor-1.1-cycle-xml.jar
The simple answer would be to not turn caching off, but I’m running other applications that fail for different reasons when run with caching turned on…
Has anyone else encountered / solved this problem? I saw there was a related issue in the FAQ section of the website, but that’s to do with having an up to date jnlp file (I’m using the current one from the website, so I don’t think that’s the issue here).
Cheers,
Fred
Hi there, Fred.
Hi,
I'm trying to run the webstart version of Jalview under windows from the main link on the website (http://www.jalview.org/webstart/jalview.jnlp).
If I run with a fairly standard Java setup (Java 1.6.0_29 on XP) Jalview seems to work fine, but if I run with caching turned off (Java control panel -> General tab -> temporary internet files -> settings) I get the following error:
com.sun.deploy.net.JARSigningException: Found unsigned entry in resource: http://www.jalview.org/webstart/castor-1.1-cycle-xml.jar
wonderful. from what I can see, the version on the site is *definitely* signed with the same certificate as the rest of Jalview's libraries. However, it did expire on Boxing day - which normally means you are issued with a warning, rather than preventing Jalview from launching...
The simple answer would be to not turn caching off, but I'm running other applications that fail for different reasons when run with caching turned on...
Could you try to launch jalview again, after first clearing/uninstalling it from the web start cache ? (Right click on the corresponding entry in the list of java web start apps that are shown when you run 'javaws -viewer' from the run dialog box). This should delete any old files that are still hanging around.
Has anyone else encountered / solved this problem? I saw there was a related issue in the FAQ section of the website, but that's to do with having an up to date jnlp file (I'm using the current one from the website, so I don't think that's the issue here).
Web start is a remarkably fragile mechanism - if anyone can tell us what's going on here I'd also appreciate it!!
Jim.
···
On 10/01/2012 15:28, Fred Ludlow wrote:
HI Jim,
Could you try to launch jalview again, after first clearing/uninstalling it from the web start cache ? (Right click on the corresponding entry in the list of java web start apps that are shown when you run ‘javaws -viewer’ from the run dialog box). This should delete any old files that are still hanging around.
I’ve cleared the cache, unfortunately this doesn’t fix it, but see below
Has anyone else encountered / solved this problem? I saw there was a related issue in the FAQ section of the website, but that’s to do with having an up to date jnlp file (I’m using the current one from the website, so I don’t think that’s the issue here).
Web start is a remarkably fragile mechanism - if anyone can tell us what’s going on here I’d also appreciate it!!
I tried it on another machine, with Java 1.6.0_15 / Win XP, and it worked both with and without caching enabled. I then upgraded that machine to the latest version (1.6.0_30) and I have the same behaviour (works with caching turned on, fails with it turned off).
The best I could come up with on the web is this link:
http://blog.atlashost.eu/post/found-unsigned-entry-in-resource-java-web-start.html
The suggestion is that if any referenced jar file’s manifest file contains an entry for a directory it will cause problems when caching is turned off. castor-1.1-cycle-xml.jar does have entries like:
Name: org/exolab/castor
Sealed: false
So maybe removing those from the manifest file would fix it, though I’m not sure if that would also break something…
Fred
···
On 10 January 2012 15:47, Jim Procter <jprocter@compbio.dundee.ac.uk> wrote:
Hi Fred. This looks entirely plausible, and imho should be logged as a bug in webstart. I’ll see what I can do…
Jim
J. B. Procter Jalview/enfin Barton group
···
-----Original Message-----
From: Fred Ludlow fred.ludlow@gmail.com
To: Jim Procter jprocter@compbio.dundee.ac.uk
Cc: jalview-discuss@jalview.org
Sent: Wed, 11 Jan 2012 9:39
Subject: Re: [Jalview-discuss] Web start failing if caching turned off
HI Jim,
On 10 January 2012 15:47, Jim Procter <jprocter@compbio.dundee.ac.uk> wrote:
Could you try to launch jalview again, after first clearing/uninstalling it from the web start cache ? (Right click on the corresponding entry in the list of java web start apps that are shown when you run ‘javaws -viewer’ from the run dialog box). This should delete any old files that are still hanging around.
I’ve cleared the cache, unfortunately this doesn’t fix it, but see below
Has anyone else encountered / solved this problem? I saw there was a related issue in the FAQ section of the website, but that’s to do with having an up to date jnlp file (I’m using the current one from the website, so I don’t think that’s the issue here).
Web start is a remarkably fragile mechanism - if anyone can tell us what’s going on here I’d also appreciate it!!
I tried it on another machine, with Java 1.6.0_15 / Win XP, and it worked both with and without caching enabled. I then upgraded that machine to the latest version (1.6.0_30) and I have the same behaviour (works with caching turned on, fails with it turned off).
The best I could come up with on the web is this link:
http://blog.atlashost.eu/post/found-unsigned-entry-in-resource-java-web-start.html
The suggestion is that if any referenced jar file’s manifest file contains an entry for a directory it will cause problems when caching is turned off. castor-1.1-cycle-xml.jar does have entries like:
Name: org/exolab/castor
Sealed: false
So maybe removing those from the manifest file would fix it, though I’m not sure if that would also break something…
Fred
Awesome, works here too!
but (and there’s always a but…) I was trying to use the web start version so I could see if a different bug was fixed in the latest jalview before reporting it.
If I do the following steps:
Fetch Sequences → Uniprot P00325 (alcohol dehydrogenase)
Right click on sequence name → Structure → View all 9 structures
This gives me a jmol window with an error message at the top saying file not found, the filepath it gives is:
C:\Documents and Settings\username\Desktop\DOCUME~1usernameLOCALS~1Tempjalview… etc
so it looks like somewhere the temporary path is getting mangled
If I try and load the structures sequentially, the first one loads, but subsequent ones give a similar error in the console log:
FileManager opening C:\Documents and Settings\fludlow\Desktop\DOCUME~1fludlowLOCALS~1Tempjalview1776115461567806960.xml
file ERROR: java.io.FileNotFoundException: C:\Documents and Settings\fludlow\Desktop\DOCUME~1fludlowLOCALS~1Tempjalview1776115461567806960.xml (The system cannot find the file specified)
openFiles(2) 16 ms
eval ERROR: java.io.FileNotFoundException: C:\Documents and Settings\fludlow\Desktop\DOCUME~1fludlowLOCALS~1Tempjalview1776115461567806960.xml (The system cannot find the file specified)
···
load append “C:\DOCUME~1\fludlow\LOCALS~1\Temp\jalview3072553079554317356.xml” >> “C:DOCUME~1fludlowLOCALS~1Tempjalview1776115461567806960.xml” <<
(This is running the web-start version from the link you just sent with 1.6.0_29 on XP).
Thanks again for the very quick fix to the previous issue, and sorry to report another one (this is the last one I know about!)
Fred
On 11 January 2012 12:29, Jim Procter <foreveremain@gmail.com> wrote:
Hi Fred.
On 11/01/2012 09:39, Fred Ludlow wrote:
So maybe removing those from the manifest file would fix it, though I’m not sure if that would also break something…
Its working for me after cleaning up some of the older manifests. Have a go with this patched version of version 2.7 :
http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/release/webstart/jalview.jnlp
Jim.
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Jalview-discuss@jalview.org
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Hi Fred.
Awesome, works here too!
very glad to hear it!
but (and there's always a but...) I was trying to use the web start version so I could see if a different bug was fixed in the latest jalview before reporting it.
oh oh...
If I do the following steps:
Fetch Sequences -> Uniprot P00325 (alcohol dehydrogenase)
Right click on sequence name -> Structure -> View all 9 structures
This gives me a jmol window with an error message at the top saying file not found, the filepath it gives is:
C:\Documents and Settings\username\Desktop\DOCUME~1usernameLOCALS~1Tempjalview..... etc
so it looks like somewhere the temporary path is getting mangled
If I try and load the structures sequentially, the first one loads, but subsequent ones give a similar error in the console log:
FileManager opening C:\Documents and Settings\fludlow\Desktop\DOCUME~1fludlowLOCALS~1Tempjalview1776115461567806960.xml
file ERROR: java.io.FileNotFoundException: C:\Documents and Settings\fludlow\Desktop\DOCUME~1fludlowLOCALS~1Tempjalview1776115461567806960.xml (The system cannot find the file specified)
openFiles(2) 16 ms
eval ERROR: java.io.FileNotFoundException: C:\Documents and Settings\fludlow\Desktop\DOCUME~1fludlowLOCALS~1Tempjalview1776115461567806960.xml (The system cannot find the file specified)
----
load append "C:\DOCUME~1\fludlow\LOCALS~1\Temp\jalview3072553079554317356.xml" >> "C:DOCUME~1fludlowLOCALS~1Tempjalview1776115461567806960.xml" <<
(This is running the web-start version from the link you just sent with 1.6.0_29 on XP).
Thanks again for the very quick fix to the previous issue, and sorry to report another one (this is the last one I know about!)
It's always good to get bug reports - I'd much rather that I was told when things were failing!
Luckily enough, I had already hit this bug myself - http://issues.jalview.org/browse/JAL-1023
We encountered it during the last two Jalview courses of 2011. The root of the problem is that Jmol was upgraded, and it now behaves differently when working with file paths on windows. The problem also causes the linked structure highlighting to fail (since Jalview uses the filename as a unique ID when broadcasting mouseover events).
If you register, you can subscribe to the issue which will mean you'll get an email when I get around to fixing it!
Jim.
···
On 11/01/2012 13:22, Fred Ludlow wrote: