From gordonp at ucalgary.ca  Wed Sep  2 14:45:01 2009
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Wed, 02 Sep 2009 12:45:01 -0600
Subject: [MOBY-dev] Public CVS problems
Message-ID: <4A9EBD2D.2050908@ucalgary.ca>

Anyone know the status of the CVS mirroring issue?  The public version, 
and all the html pages in jMoby, haven't been updated for a couple weeks...

From markw at illuminae.com  Wed Sep  2 15:11:08 2009
From: markw at illuminae.com (Mark Wilkinson)
Date: Wed, 02 Sep 2009 12:11:08 -0700
Subject: [MOBY-dev] Public CVS problems
In-Reply-To: <4A9EBD2D.2050908@ucalgary.ca>
References: <4A9EBD2D.2050908@ucalgary.ca>
Message-ID: <op.uzm8wuhunbznux@dd0710001l.icapture.ubc.ca>

I've alerted open-bio roots

M



On Wed, 02 Sep 2009 11:45:01 -0700, Paul Gordon <gordonp at ucalgary.ca>  
wrote:

> Anyone know the status of the CVS mirroring issue?  The public version,  
> and all the html pages in jMoby, haven't been updated for a couple  
> weeks...
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


-- 
Mark D Wilkinson, PI Bioinformatics
Assistant Professor, Medical Genetics
The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
Providence Heart + Lung Institute
University of British Columbia - St. Paul's Hospital
Vancouver, BC, Canada

From martin.senger at gmail.com  Wed Sep  2 20:24:08 2009
From: martin.senger at gmail.com (Martin Senger)
Date: Thu, 3 Sep 2009 08:24:08 +0800
Subject: [MOBY-dev] Public CVS problems
In-Reply-To: <4A9EBD2D.2050908@ucalgary.ca>
References: <4A9EBD2D.2050908@ucalgary.ca>
Message-ID: <4d93f07c0909021724u37bec823mcde104331fc59e30@mail.gmail.com>

Anyone know the status of the CVS mirroring issue?  The public version, and
> all the html pages in jMoby, haven't been updated for a couple weeks...
>

I have discussed the issue with Eddie recently. Here is what I sent him:

According to my knowledge, the cronjob runs normally every three hours.
>
> But I see the problem: whenever an anonymous access updates the local CVS
> copy (as it does on the biomoby server in order to display the docs), the
> directory t2 is not created. It is also strange what is seen in the CVS
> viewer:
> http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/moby-live/Java/docs/taverna/?cvsroot=biomoby.
> Once you click here on the link "guide" you gen a strange message "NOTE:
> There are 38 files, but none match the current selection criteria."
>
> I do not know a cause of the problem (when the same directory is accessed
> by an SSH access, it works fine). If you do not see the solution, we may ask
> Chris.
>

This message was about one particular subdirectory (t2) that was not updated
properly. They may be others. I am cc-ing this also to Chris with the hope
that he can help.

Cheers,
Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From martin.senger at gmail.com  Mon Sep  7 08:47:22 2009
From: martin.senger at gmail.com (Martin Senger)
Date: Mon, 7 Sep 2009 20:47:22 +0800
Subject: [MOBY-dev] jMoby and Java 6
Message-ID: <4d93f07c0909070547w4eb7568bve06dc7e5b50008ea@mail.gmail.com>

Dmitry would like to submit some Java code to jMoby - but it needs Java 6.
So far, we have used Java 5. Should we move to Java 6 now? Any objections?
Or do you need some time to be able to update your code?

Cheers,
Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From pieter.neerincx at gmail.com  Mon Sep  7 09:05:01 2009
From: pieter.neerincx at gmail.com (Pieter Neerincx)
Date: Mon, 7 Sep 2009 15:05:01 +0200
Subject: [MOBY-dev] jMoby and Java 6
In-Reply-To: <4d93f07c0909070547w4eb7568bve06dc7e5b50008ea@mail.gmail.com>
References: <4d93f07c0909070547w4eb7568bve06dc7e5b50008ea@mail.gmail.com>
Message-ID: <661C0D68-2C82-479E-B125-0C57B065C9AD@gmail.com>

Hi Martin and Dmitry,

There is an issue for those on Mac OS X. Requiring Java 6 requires a  
recent Intel-based Mac, because Apple refused make a Java 6 VM for PPC- 
based Macs. There are still plenty PPC-based Macs in the wild, but for  
the latest version of Mac OS X "Snow Leopard" (released last week)  
Apple ditched support for PPC-based Macs. So, some might be  
disappointed, but I guess now that Apple ditched PPC support, the time  
is right for Moby to move on and ditch PPC support too...

Cheers,

Pi


On 7?Sep?2009, at 2:47 PM, Martin Senger wrote:

> Dmitry would like to submit some Java code to jMoby - but it needs  
> Java 6.
> So far, we have used Java 5. Should we move to Java 6 now? Any  
> objections?
> Or do you need some time to be able to update your code?
>
> Cheers,
> Martin
>
> -- 
> Martin Senger
> email: martin.senger at gmail.com,m.senger at cgiar.org
> skype: martinsenger
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev

-------------------------------------------------------------
Biomolecular Mass Spectrometry and Proteomics
Utrecht University

Visiting address:
H.R. Kruyt building room O607
Padualaan 8
3584 CH Utrecht
The Netherlands

Mail address:
P.O. box 80.082
3508 TB Utrecht
The Netherlands

phone: +31 (0)6-143 66 783
email: pieter.neerincx at gmail.com
skype: pieter.online
------------------------------------------------------------



From sneumann at ipb-halle.de  Mon Sep  7 09:03:34 2009
From: sneumann at ipb-halle.de (Steffen Neumann)
Date: Mon, 07 Sep 2009 15:03:34 +0200
Subject: [MOBY-dev] jMoby and Java 6
In-Reply-To: <4d93f07c0909070547w4eb7568bve06dc7e5b50008ea@mail.gmail.com>
References: <4d93f07c0909070547w4eb7568bve06dc7e5b50008ea@mail.gmail.com>
Message-ID: <1252328614.5755.704.camel@paddy>

On Mon, 2009-09-07 at 20:47 +0800, Martin Senger wrote:
> Dmitry would like to submit some Java code to jMoby - but it needs Java 6.
> So far, we have used Java 5. Should we move to Java 6 now? Any objections?

You will have to ask people with 32-bit Intel or any PowerPC Mac machine,
for which no Sun JDK 1.6 is available. I have no clue how many of these 
are out there in production or used by developers.

But any java 1.6 code should therefore work at least on SoyLatte,
which is available via the "Java Research License", see:

http://www.netbeans.org/kb/61/java/javafx-jdk6-on-32-bit-mac.html
"Java 6 Port for Mac OS X 10.4 and 10.5 (Intel)"

(Disclaimer: I am not sure whether the license collides with JRL.
 Ask your lawyer).

Yours,
Steffen



From gordonp at ucalgary.ca  Tue Sep  8 10:52:58 2009
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Tue, 08 Sep 2009 08:52:58 -0600
Subject: [MOBY-dev] jMoby and Java 6
In-Reply-To: <4d93f07c0909070547w4eb7568bve06dc7e5b50008ea@mail.gmail.com>
References: <4d93f07c0909070547w4eb7568bve06dc7e5b50008ea@mail.gmail.com>
Message-ID: <4AA66FCA.1020600@ucalgary.ca>

Java 6 sounds good to me...that's what I use to compile anyways.

Cheers,

-Paul


Martin Senger wrote:
> Dmitry would like to submit some Java code to jMoby - but it needs Java 6.
> So far, we have used Java 5. Should we move to Java 6 now? Any objections?
> Or do you need some time to be able to update your code?
>
> Cheers,
> Martin
>
>   

From martin.senger at gmail.com  Wed Sep 30 22:21:36 2009
From: martin.senger at gmail.com (Martin Senger)
Date: Thu, 1 Oct 2009 10:21:36 +0800
Subject: [MOBY-dev] jMoby does not compile
Message-ID: <4d93f07c0909301921x71a678f5sbb626013c946565c@mail.gmail.com>

Please correct the code asap - people cannot use jMoby when it does not
compile. Please be aware that we are still using Java 5. There was a
suggestion to switch to Java 6 but it was not yet broadly accepted. If this
is the case of not compiling, please make effort to bring the broader
consensus on this issue (you have my vote of support for Java 6).

The errors are:

compile:
    [javac] Compiling 476 source files to
/home/senger/moby-live/Java/build/classes
    [javac]
/home/senger/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf/MobyEndpointReference.java:18:
cannot find symbol
    [javac] symbol  : class W3CEndpointReferenceBuilder
    [javac] location: package javax.xml.ws.wsaddressing
    [javac] import javax.xml.ws.wsaddressing.W3CEndpointReferenceBuilder;
    [javac]                                  ^
    [javac]
/home/senger/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf/MobyEndpointReference.java:51:
cannot find symbol
    [javac] symbol  : class W3CEndpointReferenceBuilder
    [javac] location: class
org.inb.biomoby.shared.wsrf.MobyEndpointReference
    [javac]             W3CEndpointReferenceBuilder wsaBuilder = new
W3CEndpointReferenceBuilder();
    [javac]             ^
    [javac]
/home/senger/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf/MobyEndpointReference.java:51:
cannot find symbol
    [javac] symbol  : class W3CEndpointReferenceBuilder
    [javac] location: class
org.inb.biomoby.shared.wsrf.MobyEndpointReference
    [javac]             W3CEndpointReferenceBuilder wsaBuilder = new
W3CEndpointReferenceBuilder();
    [javac]                                                          ^
    [javac] Note:
/home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/PBERecorder.java
uses or overrides a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 3 errors


Thanks,
Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From gordonp at ucalgary.ca  Wed Sep  2 18:45:01 2009
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Wed, 02 Sep 2009 12:45:01 -0600
Subject: [MOBY-dev] Public CVS problems
Message-ID: <4A9EBD2D.2050908@ucalgary.ca>

Anyone know the status of the CVS mirroring issue?  The public version, 
and all the html pages in jMoby, haven't been updated for a couple weeks...


From markw at illuminae.com  Wed Sep  2 19:11:08 2009
From: markw at illuminae.com (Mark Wilkinson)
Date: Wed, 02 Sep 2009 12:11:08 -0700
Subject: [MOBY-dev] Public CVS problems
In-Reply-To: <4A9EBD2D.2050908@ucalgary.ca>
References: <4A9EBD2D.2050908@ucalgary.ca>
Message-ID: <op.uzm8wuhunbznux@dd0710001l.icapture.ubc.ca>

I've alerted open-bio roots

M



On Wed, 02 Sep 2009 11:45:01 -0700, Paul Gordon <gordonp at ucalgary.ca>  
wrote:

> Anyone know the status of the CVS mirroring issue?  The public version,  
> and all the html pages in jMoby, haven't been updated for a couple  
> weeks...
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


-- 
Mark D Wilkinson, PI Bioinformatics
Assistant Professor, Medical Genetics
The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
Providence Heart + Lung Institute
University of British Columbia - St. Paul's Hospital
Vancouver, BC, Canada


From martin.senger at gmail.com  Thu Sep  3 00:24:08 2009
From: martin.senger at gmail.com (Martin Senger)
Date: Thu, 3 Sep 2009 08:24:08 +0800
Subject: [MOBY-dev] Public CVS problems
In-Reply-To: <4A9EBD2D.2050908@ucalgary.ca>
References: <4A9EBD2D.2050908@ucalgary.ca>
Message-ID: <4d93f07c0909021724u37bec823mcde104331fc59e30@mail.gmail.com>

Anyone know the status of the CVS mirroring issue?  The public version, and
> all the html pages in jMoby, haven't been updated for a couple weeks...
>

I have discussed the issue with Eddie recently. Here is what I sent him:

According to my knowledge, the cronjob runs normally every three hours.
>
> But I see the problem: whenever an anonymous access updates the local CVS
> copy (as it does on the biomoby server in order to display the docs), the
> directory t2 is not created. It is also strange what is seen in the CVS
> viewer:
> http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/moby-live/Java/docs/taverna/?cvsroot=biomoby.
> Once you click here on the link "guide" you gen a strange message "NOTE:
> There are 38 files, but none match the current selection criteria."
>
> I do not know a cause of the problem (when the same directory is accessed
> by an SSH access, it works fine). If you do not see the solution, we may ask
> Chris.
>

This message was about one particular subdirectory (t2) that was not updated
properly. They may be others. I am cc-ing this also to Chris with the hope
that he can help.

Cheers,
Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From martin.senger at gmail.com  Mon Sep  7 12:47:22 2009
From: martin.senger at gmail.com (Martin Senger)
Date: Mon, 7 Sep 2009 20:47:22 +0800
Subject: [MOBY-dev] jMoby and Java 6
Message-ID: <4d93f07c0909070547w4eb7568bve06dc7e5b50008ea@mail.gmail.com>

Dmitry would like to submit some Java code to jMoby - but it needs Java 6.
So far, we have used Java 5. Should we move to Java 6 now? Any objections?
Or do you need some time to be able to update your code?

Cheers,
Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From pieter.neerincx at gmail.com  Mon Sep  7 13:05:01 2009
From: pieter.neerincx at gmail.com (Pieter Neerincx)
Date: Mon, 7 Sep 2009 15:05:01 +0200
Subject: [MOBY-dev] jMoby and Java 6
In-Reply-To: <4d93f07c0909070547w4eb7568bve06dc7e5b50008ea@mail.gmail.com>
References: <4d93f07c0909070547w4eb7568bve06dc7e5b50008ea@mail.gmail.com>
Message-ID: <661C0D68-2C82-479E-B125-0C57B065C9AD@gmail.com>

Hi Martin and Dmitry,

There is an issue for those on Mac OS X. Requiring Java 6 requires a  
recent Intel-based Mac, because Apple refused make a Java 6 VM for PPC- 
based Macs. There are still plenty PPC-based Macs in the wild, but for  
the latest version of Mac OS X "Snow Leopard" (released last week)  
Apple ditched support for PPC-based Macs. So, some might be  
disappointed, but I guess now that Apple ditched PPC support, the time  
is right for Moby to move on and ditch PPC support too...

Cheers,

Pi


On 7?Sep?2009, at 2:47 PM, Martin Senger wrote:

> Dmitry would like to submit some Java code to jMoby - but it needs  
> Java 6.
> So far, we have used Java 5. Should we move to Java 6 now? Any  
> objections?
> Or do you need some time to be able to update your code?
>
> Cheers,
> Martin
>
> -- 
> Martin Senger
> email: martin.senger at gmail.com,m.senger at cgiar.org
> skype: martinsenger
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev

-------------------------------------------------------------
Biomolecular Mass Spectrometry and Proteomics
Utrecht University

Visiting address:
H.R. Kruyt building room O607
Padualaan 8
3584 CH Utrecht
The Netherlands

Mail address:
P.O. box 80.082
3508 TB Utrecht
The Netherlands

phone: +31 (0)6-143 66 783
email: pieter.neerincx at gmail.com
skype: pieter.online
------------------------------------------------------------




From sneumann at ipb-halle.de  Mon Sep  7 13:03:34 2009
From: sneumann at ipb-halle.de (Steffen Neumann)
Date: Mon, 07 Sep 2009 15:03:34 +0200
Subject: [MOBY-dev] jMoby and Java 6
In-Reply-To: <4d93f07c0909070547w4eb7568bve06dc7e5b50008ea@mail.gmail.com>
References: <4d93f07c0909070547w4eb7568bve06dc7e5b50008ea@mail.gmail.com>
Message-ID: <1252328614.5755.704.camel@paddy>

On Mon, 2009-09-07 at 20:47 +0800, Martin Senger wrote:
> Dmitry would like to submit some Java code to jMoby - but it needs Java 6.
> So far, we have used Java 5. Should we move to Java 6 now? Any objections?

You will have to ask people with 32-bit Intel or any PowerPC Mac machine,
for which no Sun JDK 1.6 is available. I have no clue how many of these 
are out there in production or used by developers.

But any java 1.6 code should therefore work at least on SoyLatte,
which is available via the "Java Research License", see:

http://www.netbeans.org/kb/61/java/javafx-jdk6-on-32-bit-mac.html
"Java 6 Port for Mac OS X 10.4 and 10.5 (Intel)"

(Disclaimer: I am not sure whether the license collides with JRL.
 Ask your lawyer).

Yours,
Steffen




From gordonp at ucalgary.ca  Tue Sep  8 14:52:58 2009
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Tue, 08 Sep 2009 08:52:58 -0600
Subject: [MOBY-dev] jMoby and Java 6
In-Reply-To: <4d93f07c0909070547w4eb7568bve06dc7e5b50008ea@mail.gmail.com>
References: <4d93f07c0909070547w4eb7568bve06dc7e5b50008ea@mail.gmail.com>
Message-ID: <4AA66FCA.1020600@ucalgary.ca>

Java 6 sounds good to me...that's what I use to compile anyways.

Cheers,

-Paul


Martin Senger wrote:
> Dmitry would like to submit some Java code to jMoby - but it needs Java 6.
> So far, we have used Java 5. Should we move to Java 6 now? Any objections?
> Or do you need some time to be able to update your code?
>
> Cheers,
> Martin
>
>