From mwilkinson at mrl.ubc.ca Tue Apr 5 10:40:34 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue Apr 5 10:28:01 2005 Subject: [MOBY-dev] Apache2 & mod_perl 2 Message-ID: <1112712033.15804.3.camel@mobycentral.icapture.ubc.ca> Hi again, I'm still experiencing segfaults every hour or so on the server, even after a rebuild of Apache without expat, so I'm thinking of upgrading to Apache2 in hopes that it solves the problem. The last time I tried this there was a problem with Apache2 and mod_perl2 - does anyone know definitively if this has now been fixed? If I don't hear otherwise, I'll probably try this solution tomorrow, so any advice before I throw myself into the fray is appreciated :-) Cheers all! M -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From senger at ebi.ac.uk Tue Apr 5 10:45:54 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Tue Apr 5 10:39:44 2005 Subject: [MOBY-dev] Apache2 & mod_perl 2 In-Reply-To: <1112712033.15804.3.camel@mobycentral.icapture.ubc.ca> Message-ID: Mark, Why would you think that Apache & perl_mod is the cause of the current problems, considering that Moby Central was running without flaws many mnths before? What has changed before the current problems started? If you changed more things now - like having Apache2 - you could never be able to find what *really* was a problem... Just my 2c... Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From senger at ebi.ac.uk Tue Apr 5 10:45:54 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Tue Apr 5 10:39:46 2005 Subject: [MOBY-dev] Apache2 & mod_perl 2 In-Reply-To: <1112712033.15804.3.camel@mobycentral.icapture.ubc.ca> Message-ID: Mark, Why would you think that Apache & perl_mod is the cause of the current problems, considering that Moby Central was running without flaws many mnths before? What has changed before the current problems started? If you changed more things now - like having Apache2 - you could never be able to find what *really* was a problem... Just my 2c... Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From mwilkinson at mrl.ubc.ca Tue Apr 5 10:56:51 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue Apr 5 10:44:01 2005 Subject: [moby] Re: [MOBY-dev] Apache2 & mod_perl 2 In-Reply-To: References: Message-ID: <1112713011.15804.15.camel@mobycentral.icapture.ubc.ca> I don't think that Apache/mod_perl are the problem - I think the problem is with the (known) incompatibilities between Apache1 and EXPAT. This would make some sense, since we recently migrated from XML::DOM to XML::LibXML, and that seems to be when the worst of the symptoms started. The problem is that I have tried all the fixes for this problem that I could find through Google and none of them have worked so far, so I am left with no other option but to try upgrading in hopes that Apache2 has no incompatibilities (if that really is the problem...). The concern with doing so is that I know there were incompatibilities between Apache2 and mod_perl a year or so ago when I last tried this, so I am wondering if anyone knows if these have now been resolved. M On Tue, 2005-04-05 at 07:45, Martin Senger wrote: > Mark, > Why would you think that Apache & perl_mod is the cause of the current > problems, considering that Moby Central was running without flaws many > mnths before? What has changed before the current problems started? If you > changed more things now - like having Apache2 - you could never be able to > find what *really* was a problem... Just my 2c... > > Martin -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From mwilkinson at mrl.ubc.ca Tue Apr 5 10:56:51 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue Apr 5 10:44:22 2005 Subject: [moby] Re: [MOBY-dev] Apache2 & mod_perl 2 In-Reply-To: References: Message-ID: <1112713011.15804.15.camel@mobycentral.icapture.ubc.ca> I don't think that Apache/mod_perl are the problem - I think the problem is with the (known) incompatibilities between Apache1 and EXPAT. This would make some sense, since we recently migrated from XML::DOM to XML::LibXML, and that seems to be when the worst of the symptoms started. The problem is that I have tried all the fixes for this problem that I could find through Google and none of them have worked so far, so I am left with no other option but to try upgrading in hopes that Apache2 has no incompatibilities (if that really is the problem...). The concern with doing so is that I know there were incompatibilities between Apache2 and mod_perl a year or so ago when I last tried this, so I am wondering if anyone knows if these have now been resolved. M On Tue, 2005-04-05 at 07:45, Martin Senger wrote: > Mark, > Why would you think that Apache & perl_mod is the cause of the current > problems, considering that Moby Central was running without flaws many > mnths before? What has changed before the current problems started? If you > changed more things now - like having Apache2 - you could never be able to > find what *really* was a problem... Just my 2c... > > Martin -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From gordonp at ucalgary.ca Tue Apr 5 11:03:39 2005 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue Apr 5 10:57:24 2005 Subject: [MOBY-dev] Re: suggestions about the latest version In-Reply-To: <42529ECD.3070004@infobiogen.fr> References: <42529ECD.3070004@infobiogen.fr> Message-ID: <4252A8CB.4000704@ucalgary.ca> Hi Sophie, I'm cc'ing the list as this may be of some interest to other Java developers... Sophie Durand wrote: > Hi, > > Thanks to have modified so quickly on my demand ! > I have some remarks about the lastest version: > > In the MobyDataSimpleInstance.java file, for the equals method, I > would have compared values with > ourObject.equals(passedInObject) > instead of comparing the references that would generally be different. > This will use the equals method of BigInteger or BigDecimal depending > on the instance. Oops, this is what I meant to do! I even wrote that to you! I've fixed this now. > I've read the Java API for the comparable interface : > compareTo > Throws: > ClassCastException - if the specified object's type prevents it > from being compared to this Object. > Probably you should throw an Exception if the given object is not a > MobyDataSimpleInstance. I thought about this, but decided to allow any objects to be compared because I did not want to hard code in the list of acceptable child classes. This would mean if MobyDataX was added as a class, you'd have to remember to add X and other compatible classes to MobyDataSimple's equals() (to allow for the convenient comparison of java.lang.Integer and org.biomoby.shared.MobyDataInteger for example). If a child class wants to enforce a class equivalency, they can override the equals method. I've added the ClassCastException for this reason, but do not throw it in MobyDataSimpleInstance's method. Luckily you can say that you throw a ClassCastException, even if you don't, without the compiler complaining. > > In MobyDataFloat.java, there seems to be a problem in the clone > function : it returns an instance of MobyDataInt... Fixed... > Sophie From jmfernandez at cnb.uam.es Tue Apr 5 11:23:46 2005 From: jmfernandez at cnb.uam.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Tue Apr 5 11:19:44 2005 Subject: [moby] Re: [MOBY-dev] Apache2 & mod_perl 2 In-Reply-To: <1112713011.15804.15.camel@mobycentral.icapture.ubc.ca> References: <1112713011.15804.15.camel@mobycentral.icapture.ubc.ca> Message-ID: <4252AD82.8050205@cnb.uam.es> If the segfaults are more or less random, it could be an almost broken memory module, which makes jam with some of its bits when it gets hot. Are segfaults happening when the server is under heavy load? Or does they appear when about an hour has been spent doing almost "nothing"? If it is a software problem, a fresh, known stable installation should be the answer. Best Regards, Jos? Mar?a Mark Wilkinson wrote: > I don't think that Apache/mod_perl are the problem - I think the problem > is with the (known) incompatibilities between Apache1 and EXPAT. This > would make some sense, since we recently migrated from XML::DOM to > XML::LibXML, and that seems to be when the worst of the symptoms > started. > > The problem is that I have tried all the fixes for this problem that I > could find through Google and none of them have worked so far, so I am > left with no other option but to try upgrading in hopes that Apache2 has > no incompatibilities (if that really is the problem...). The concern > with doing so is that I know there were incompatibilities between > Apache2 and mod_perl a year or so ago when I last tried this, so I am > wondering if anyone knows if these have now been resolved. > > M > > > > On Tue, 2005-04-05 at 07:45, Martin Senger wrote: > >>Mark, >> Why would you think that Apache & perl_mod is the cause of the current >>problems, considering that Moby Central was running without flaws many >>mnths before? What has changed before the current problems started? If you >>changed more things now - like having Apache2 - you could never be able to >>find what *really* was a problem... Just my 2c... >> >> Martin -- Jos? Mar?a Fern?ndez Gonz?lez e-mail: jmfernandez@cnb.uam.es Tlfn: (+34) 91 585 54 50 Fax: (+34) 91 585 45 06 Grupo de Dise?o de Proteinas Protein Design Group Centro Nacional de Biotecnolog?a National Center of Biotechnology C.P.: 28049 Zip Code: 28049 C/. Darwin n? 3 (Campus Cantoblanco, U. Aut?noma), Madrid (Spain) From mwilkinson at mrl.ubc.ca Tue Apr 5 11:45:39 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue Apr 5 11:32:49 2005 Subject: [moby] Re: [MOBY-dev] Apache2 & mod_perl 2 In-Reply-To: <4252AD82.8050205@cnb.uam.es> References: <1112713011.15804.15.camel@mobycentral.icapture.ubc.ca> <4252AD82.8050205@cnb.uam.es> Message-ID: <1112715939.15804.20.camel@mobycentral.icapture.ubc.ca> Hi Jose (c.c. Jason) My first instinct was a memory problem as well, but I have asked the sysadmin to look into this and he doesn't think that is the case. The Google searches are split between those who say that the errors come from physical memory problems, and those who say that they are from Apache incompatibilities. I've chased down all of the Apache incompatibilities that I could find, and have done a completely fresh install of Apache and mod-perl over the weekend, but that hasn't helped. ...if it is a memory problem, it's a hard one to spot! :-) M On Tue, 2005-04-05 at 08:23, José María Fernández González wrote: > If the segfaults are more or less random, it could be an almost broken > memory module, which makes jam with some of its bits when it gets hot. > > Are segfaults happening when the server is under heavy load? Or does > they appear when about an hour has been spent doing almost "nothing"? > > If it is a software problem, a fresh, known stable installation should > be the answer. > > Best Regards, > José María > > Mark Wilkinson wrote: > > I don't think that Apache/mod_perl are the problem - I think the problem > > is with the (known) incompatibilities between Apache1 and EXPAT. This > > would make some sense, since we recently migrated from XML::DOM to > > XML::LibXML, and that seems to be when the worst of the symptoms > > started. > > > > The problem is that I have tried all the fixes for this problem that I > > could find through Google and none of them have worked so far, so I am > > left with no other option but to try upgrading in hopes that Apache2 has > > no incompatibilities (if that really is the problem...). The concern > > with doing so is that I know there were incompatibilities between > > Apache2 and mod_perl a year or so ago when I last tried this, so I am > > wondering if anyone knows if these have now been resolved. > > > > M > > > > > > > > On Tue, 2005-04-05 at 07:45, Martin Senger wrote: > > > >>Mark, > >> Why would you think that Apache & perl_mod is the cause of the current > >>problems, considering that Moby Central was running without flaws many > >>mnths before? What has changed before the current problems started? If you > >>changed more things now - like having Apache2 - you could never be able to > >>find what *really* was a problem... Just my 2c... > >> > >> Martin -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From mwilkinson at mrl.ubc.ca Tue Apr 5 12:48:27 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue Apr 5 12:35:49 2005 Subject: [moby] Re: [MOBY-dev] Apache2 & mod_perl 2 In-Reply-To: <4252AD82.8050205@cnb.uam.es> References: <1112713011.15804.15.camel@mobycentral.icapture.ubc.ca> <4252AD82.8050205@cnb.uam.es> Message-ID: <1112719706.15804.97.camel@mobycentral.icapture.ubc.ca> On Tue, 2005-04-05 at 08:23, José María Fernández González wrote: > Are segfaults happening when the server is under heavy load? Or does > they appear when about an hour has been spent doing almost "nothing"? The segfaults are random. From a fresh startup at 11:40 under light load I got a segfault at 11:49, 11:54, 12:32 and 12:33 Not pretty :-) M -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From jmfernandez at cnb.uam.es Tue Apr 5 14:58:49 2005 From: jmfernandez at cnb.uam.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Tue Apr 5 14:52:38 2005 Subject: [moby] Re: [MOBY-dev] Apache2 & mod_perl 2 In-Reply-To: <1112719706.15804.97.camel@mobycentral.icapture.ubc.ca> References: <11 12713011.15804.15.camel@mobycentral.icapture.ubc.ca><4252AD82.8050205@cnb.u am.es> <1112719706.15804.97.camel@mobycentral.icapture.ubc.ca> Message-ID: <4252DFE9.5060802@cnb.uam.es> D'oh! It smells like a hardware problem! Perhaps it is not related to memory modules, but the power supply. If it is dying, it could be giving bad voltage levels under light load (computing+disk), and they could be good enough for a memory check task (only computing). Most of motherboard BIOS can tell you about power supply voltages they are receiving. Have luck! Jos? Mar?a Mark Wilkinson wrote: > On Tue, 2005-04-05 at 08:23, Jos?? Mar??a Fern??ndez Gonz??lez wrote: > > >>Are segfaults happening when the server is under heavy load? Or does >>they appear when about an hour has been spent doing almost "nothing"? > > > The segfaults are random. From a fresh startup at 11:40 under light > load I got a segfault at 11:49, 11:54, 12:32 and 12:33 > > Not pretty :-) > > M > > -- Jos? Mar?a Fern?ndez Gonz?lez e-mail: jmfernandez@cnb.uam.es Tlfn: (+34) 91 585 54 50 Fax: (+34) 91 585 45 06 Grupo de Dise?o de Proteinas Protein Design Group Centro Nacional de Biotecnolog?a National Center of Biotechnology C.P.: 28049 Zip Code: 28049 C/. Darwin n? 3 (Campus Cantoblanco, U. Aut?noma), Madrid (Spain) -------------- next part -------------- A non-text attachment was scrubbed... Name: homer_doh.png Type: image/png Size: 15301 bytes Desc: not available Url : http://biomoby.org/pipermail/moby-dev/attachments/20050405/91654c0a/homer_doh-0001.png From senger at ebi.ac.uk Tue Apr 5 15:46:18 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Tue Apr 5 15:40:23 2005 Subject: [moby] Re: [MOBY-dev] Apache2 & mod_perl 2 In-Reply-To: <4252DFE9.5060802@cnb.uam.es> Message-ID: > D'oh! It smells like a hardware problem! > Mark, why not just to try another computer for a while? Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From senger at ebi.ac.uk Thu Apr 7 17:27:06 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Thu Apr 7 17:21:28 2005 Subject: [MOBY-dev] jMoby compilation problems In-Reply-To: <42123912.362bff4b.58cb.30c8@smtp.gmail.com> Message-ID: Dear Java developers, Today I found (with a great help and support from Eddie) that there are classes in the current jMoby module that cannot be compiled. Which is - according to my opinion - completely wrong. And stressfully frustrating. Please let me repeat that I believe that the rule number one for shared Java development is that you commit code only when it compiles. It does not need to run correctly - especially if you just started to develop it - but it *must* compile - otherwise other developers are stuck and cannot do anything. If your code cannot compile from serious reasons (for example you are using Java 1.5, and we other have not yet commited to it), do not commit your code, or create your own CVS branche. If you have any third-party libraries that you wish to be added, send them to me, and I will put them into a central place where the jMoby Ant take sthem from. As a summary, this is what you should always do before you commit: ./build-dev.sh clean compile And if you are using some new third-party classes in 'lib' (which you should not, but let's assume that you just tested your new code with a new library that you still may have in 'lib') do before committing this: ./build-dev.sh cleanall ./build.sh Thank for your attention. Eddie - as far as I know - is now trying to clean the code of someone else. So if you think that it is your code that does not compile, please hurry to help him. Thanks you. Cheers, martin PS. Mark, could we have scheduled a short session about Java developing in Vancouver - to discuss the similar things and rules that I mentioned above. I know that Eddie is also working on documenting such principles, so it would be good to have some time to present it, discuss and hopefully accept it. Thanks. M. -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From mwilkinson at mrl.ubc.ca Thu Apr 7 19:03:57 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Thu Apr 7 18:50:34 2005 Subject: [moby] [MOBY-dev] jMoby compilation problems In-Reply-To: References: Message-ID: <1112915037.25115.18.camel@mobycentral.icapture.ubc.ca> Hi Martin, There have been a variety of requests for what we should talk about at the Vancouver meeting. I suspect that the best way to meet everyone's interests is for us to have a couple of hours each morning where we discuss things as a whole, and then break into smaller BoF groups to discuss specific issues. There are enough of us at this meeting (yay MOBY!) that we can probably accomplish more by breaking into smaller task-specific groups anyway. Damian/Gary do you have specific goals for the meeting? Does the BoF idea suit you? Let's start working-up an outline for the two days. Cheers all! M On Thu, 2005-04-07 at 14:27, Martin Senger wrote: > PS. Mark, could we have scheduled a short session about Java developing in > Vancouver - to discuss the similar things and rules that I mentioned > above. I know that Eddie is also working on documenting such principles, > so it would be good to have some time to present it, discuss and > hopefully accept it. Thanks. M. -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From gss at ncgr.org Thu Apr 7 19:06:10 2005 From: gss at ncgr.org (Gary Schiltz) Date: Thu Apr 7 18:59:51 2005 Subject: [moby] [MOBY-dev] jMoby compilation problems In-Reply-To: <1112915037.25115.18.camel@mobycentral.icapture.ubc.ca> References: <1112915037.25115.18.camel@mobycentral.icapture.ubc.ca> Message-ID: <4255BCE2.6050200@ncgr.org> Damian should feel free to chime in, but I'd be fine with giving a quick update on Semantic MOBY activities to all, and then host a task-specific BoF as Mark suggests. // Gary Mark Wilkinson wrote: >Hi Martin, > >There have been a variety of requests for what we should talk about at >the Vancouver meeting. I suspect that the best way to meet everyone's >interests is for us to have a couple of hours each morning where we >discuss things as a whole, and then break into smaller BoF groups to >discuss specific issues. There are enough of us at this meeting (yay >MOBY!) that we can probably accomplish more by breaking into smaller >task-specific groups anyway. > >Damian/Gary do you have specific goals for the meeting? Does the BoF >idea suit you? > >Let's start working-up an outline for the two days. > >Cheers all! > >M > >On Thu, 2005-04-07 at 14:27, Martin Senger wrote: > > >>PS. Mark, could we have scheduled a short session about Java developing in >>Vancouver - to discuss the similar things and rules that I mentioned >>above. I know that Eddie is also working on documenting such principles, >>so it would be good to have some time to present it, discuss and >>hopefully accept it. Thanks. M. >> From senger at ebi.ac.uk Thu Apr 7 19:16:40 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Thu Apr 7 19:11:22 2005 Subject: [moby] [MOBY-dev] jMoby compilation problems In-Reply-To: <1112915037.25115.18.camel@mobycentral.icapture.ubc.ca> Message-ID: Well, generally I do not like BoFs. Because then I am always in a BoF where I am involved most - and I am loosing overview what is happenning elsewhwere. Of course, there is no other way if there are many topics and many participants. But perhaps we could try to tell everybody about everything (the speakers can promise not to repeat much what we all know already) - and only then to split into BoFs. And perhaps to make not many BoFs in the same time (ideal would be just two). Cheers, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From gordonp at ucalgary.ca Fri Apr 8 10:18:35 2005 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri Apr 8 10:12:28 2005 Subject: [moby] [MOBY-dev] jMoby compilation problems In-Reply-To: References: Message-ID: <425692BB.9000007@ucalgary.ca> I always like software demos. Just my CAN$0.02 worth, but as this is a developers meeting, it might make sense to (in this order): Day 1: 1) have general updates from the leaders on S-MOBY and MOBY-S on language-neutral subjects (e.g. usage stats, publications, changes to the architecture, support software status, etc.) 2) have a series of (a) software or (b) canned programming demos from interested parties to show off (a) what people are doing with the system as it stands today or (b) how easy/hard it is to code, inspiring others to improve their APIs Lunch 3) have discussions amongst everyone on S-MOBY and MOBY-S language-neutral subjects (e.g. namespace usage, potential changes to the architecture, how to improve robustness, etc.) 4) Bird of a Feather meetings to resolve language specific API issues, plus how to possibly implement improvements discussed in (3). This will likely continue to be discussed into the evening until too many "wobbly pops" are consumed. Day 2: 1) Flesh out changes to the central, platform neutral APIs/architectures based on contemplation and discussion from yesterday. 2) Updates from all BoFs to the group on what they discussed 3) Discussed future directions, "action items" (forgive the management speak) and how they can be coordinated Lunch 4) Birds of a Feather meetings to either do a mini-hackathon, discuss futher, and/or document API changes Martin Senger wrote: >Well, generally I do not like BoFs. Because then I am always in a BoF >where I am involved most - and I am loosing overview what is happenning >elsewhwere. Of course, there is no other way if there are many topics and >many participants. But perhaps we could try to tell everybody about >everything (the speakers can promise not to repeat much what we all know >already) - and only then to split into BoFs. And perhaps to make not many >BoFs in the same time (ideal would be just two). > >Cheers, >Martin > > > From gordonp at ucalgary.ca Fri Apr 15 17:26:39 2005 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri Apr 15 17:20:18 2005 Subject: [MOBY-dev] Uncompilable class in CVS? Message-ID: <4260318F.9030707@ucalgary.ca> Hi everyone, The following class: org/biomoby/registry/rdfagent/verifier/ServiceDescrParser.java appears to be uncompilable because it references an undeclared class or variable called "MRes". Anyone else have this issue? I did a "cvs update -dP " to no avail... From edward.kawas at gmail.com Sat Apr 16 10:21:20 2005 From: edward.kawas at gmail.com (Eddie Kawas) Date: Sat Apr 16 10:16:47 2005 Subject: [MOBY-dev] Uncompilable class in CVS? In-Reply-To: <4260318F.9030707@ucalgary.ca> Message-ID: <42611f63.78dc2c21.0fca.ffff806b@mx.gmail.com> Fixed. I guess when the package was updated, the file was missing. Eddie > -----Original Message----- > From: moby-dev-bounces@portal.open-bio.org [mailto:moby- > dev-bounces@portal.open-bio.org] On Behalf Of Paul Gordon > Sent: Friday, April 15, 2005 2:27 PM > To: Core developer announcements > Subject: [MOBY-dev] Uncompilable class in CVS? > > Hi everyone, > > The following class: > > org/biomoby/registry/rdfagent/verifier/ServiceDescrParser. > java > > appears to be uncompilable because it references an > undeclared class or > variable called "MRes". Anyone else have this issue? I > did a "cvs > update -dP " to no avail... > _______________________________________________ > MOBY-dev mailing list > MOBY-dev@biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev From dlondon at ebi.ac.uk Tue Apr 19 05:16:30 2005 From: dlondon at ebi.ac.uk (Darin London) Date: Tue Apr 19 07:08:34 2005 Subject: [MOBY-dev] Re: BOSC 2005 In-Reply-To: <20050120175859.GA7254@parrot.ebi.ac.uk> References: <20050120175859.GA7254@parrot.ebi.ac.uk> Message-ID: <20050419091628.GN17377@parrot.ebi.ac.uk> {Please pass the word!} SECOND CALL FOR SPEAKERS The 6th annual Bioinformatics Open Source Conference (BOSC'2005) is organized by the not-for-profit Open Bioinformatics Foundation. The meeting will take place June 23-24, 2005 in Detroit, Michigan, USA, and is one of several Special Interest Group (SIG) meetings occurring in conjunction with the 13th International Conference on Intelligent Systems for Molecular Biology. see http://www.iscb.org/ismb2005 for more information. Because of the power of many Open Source bioinformatics packages in use by the Research Community today, it is not too presumptuous to say that the work of the Open Source Bioinformatics Community represents the cutting edge of Bioinformatics in general. This has been repeatedly demonstrated by the quality of presentations at previous BOSC conferences. This year, at BOSC 2005, we want to continue this tradition of excellence, while presenting this message to a wider part of the Research Community. Please, pass this message on to anyone you know that is interested in Bioinformatics software. BOSC PROGRAM & CONTACT INFO * Web: http://www.open-bio.org/bosc2005/ * Online Registration: https://www.cteusa.com/iscb4/ * Email: bosc@open-bio.org FEES * Corporate : $195 ($245 after May 16th) * Academic : $170 ($220 after May 16th) * Student : $145 ($195 after May 16th) SPEAKERS & ABSTRACTS WANTED The program committee is currently seeking abstracts for talks at BOSC 2005. BOSC is a great opportunity for you to tell the community about your use, development, or philosophy of open source software development in bioinformatics. The committee will select several submitted abstracts for 25-minute talks and others for shorter "lightning" talks. Accepted abstracts will be published on the BOSC web site. If you are interested in speaking at BOSC 2005, please send us before April 26, 2005: * an abstract (no more than a few paragraphs) * a URL for the project page, if applicable * information about the open source license used for your software or your release plans. Abstracts will be accepted for submission until April 26, 2005. Abstracts chosen for presentation will be announced May 12, 2005 (before the ISMB Early Registration Deadline). LIGHTNING-TALK SPEAKERS WANTED! The program committee is currently seeking speakers for the lightning talks at BOSC 2005. Lightning talks are quick - only five minutes long - and a great opportunity for you to give people a quick summary of your open source project, code, idea, or vision of the future. If you are interested in giving a lightning talk at BOSC 2005, please send us: * a brief title and summary (one or two lines) * a URL for the project page, if applicable * information about the open source license used for your software or your release plans. We will accept entries on-line until BOSC starts, but space for demos and lightning talks is limited.
Message-ID: Dear jMoby developers, Eddie and me, we have updated Ant's build.xml file in order to be able to add to jMoby also Java sources that needs to be compiled with the latest Java 1.5 - but still let the others work with Java 1.4 as usual. Here is how to do it (please comment if you need any more assistance, or if you disagree with our approach): * First to say is that it was put there as a workaround for those who really needs to use 1.5. Any new class that needs 1.5 must be exlicitely named in the build.xml file. Which is not too suitable if you have many such classes. So when you start to use Java 1.5. in greater scale we need to re-factor it. Let me know. * Having said that please note that nothing prevents you to use Java 1.5 to compile all classes. That should work fine (with perhaps few semantic warnings which I am sure the authors, including me, will take care of sooner or later). The previous (and the next) bullets are for those *adding* sources that can be compiled *only* with Java 1.5 (an example is the Eddie's class org.biomoby.shared.MobyObjectDecompositionImpl.java). * If you are using regular javac compiler you do not need to do anything special. The Ant will sniff around and find what java version you are using and depending on the result it will compile always all classes not mentioned as specific for 1.5, and then - only if you have java 1.5 - it compiles additionally those new bastards. Which means that when you are using java 1.4, the new (Eddie's) classes will not compiled so you will not be able to use them. But that's obvious - you cannot shop with the old Deutches Marks anymore without having new Euros, can you? * If you are using jikes (which I strongly recommend because it is much much faster compiler, but that's another story) and have Java 1.4 on your path, again nothing needs to be done. However, if you are using jikes (latest version is 1.22) *and* have java 1.5 on your path, jikes will try to compile also the new (Eddie's) classes and fails. I do not exactly why (let me know if you know). So for this case you need to instruct Ant that - eventhough the java 1.5 is available - you do not want it. Do it with by setting property java.latest.version to false. Either (recommended) put the line: java.latest.version = false in your build.property files, or use it on the Ant's command line: ./build-dev.sh -Djava.latest.version=false compile With regard, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From ywong at infobiogen.fr Wed Apr 20 04:53:38 2005 From: ywong at infobiogen.fr (Yan Wong) Date: Wed Apr 20 04:47:21 2005 Subject: [MOBY-dev] Updates on the bioMoby Python API Message-ID: <42661892.9030809@infobiogen.fr> Hi, I've put two classes SQLDispatcher and SQLInvocator in the API in order to ease the build of DB based webservices An example can be found in the tutorials directory Cheers Yan From mwilkinson at mrl.ubc.ca Tue Apr 5 10:40:34 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue, 05 Apr 2005 07:40:34 -0700 Subject: [MOBY-dev] Apache2 & mod_perl 2 Message-ID: <1112712033.15804.3.camel@mobycentral.icapture.ubc.ca> Hi again, I'm still experiencing segfaults every hour or so on the server, even after a rebuild of Apache without expat, so I'm thinking of upgrading to Apache2 in hopes that it solves the problem. The last time I tried this there was a problem with Apache2 and mod_perl2 - does anyone know definitively if this has now been fixed? If I don't hear otherwise, I'll probably try this solution tomorrow, so any advice before I throw myself into the fray is appreciated :-) Cheers all! M -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From senger at ebi.ac.uk Tue Apr 5 10:45:54 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 5 Apr 2005 15:45:54 +0100 (BST) Subject: [MOBY-dev] Apache2 & mod_perl 2 In-Reply-To: <1112712033.15804.3.camel@mobycentral.icapture.ubc.ca> Message-ID: Mark, Why would you think that Apache & perl_mod is the cause of the current problems, considering that Moby Central was running without flaws many mnths before? What has changed before the current problems started? If you changed more things now - like having Apache2 - you could never be able to find what *really* was a problem... Just my 2c... Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From senger at ebi.ac.uk Tue Apr 5 10:45:54 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 5 Apr 2005 15:45:54 +0100 (BST) Subject: [MOBY-dev] Apache2 & mod_perl 2 In-Reply-To: <1112712033.15804.3.camel@mobycentral.icapture.ubc.ca> Message-ID: Mark, Why would you think that Apache & perl_mod is the cause of the current problems, considering that Moby Central was running without flaws many mnths before? What has changed before the current problems started? If you changed more things now - like having Apache2 - you could never be able to find what *really* was a problem... Just my 2c... Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From mwilkinson at mrl.ubc.ca Tue Apr 5 10:56:51 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue, 05 Apr 2005 07:56:51 -0700 Subject: [moby] Re: [MOBY-dev] Apache2 & mod_perl 2 In-Reply-To: References: Message-ID: <1112713011.15804.15.camel@mobycentral.icapture.ubc.ca> I don't think that Apache/mod_perl are the problem - I think the problem is with the (known) incompatibilities between Apache1 and EXPAT. This would make some sense, since we recently migrated from XML::DOM to XML::LibXML, and that seems to be when the worst of the symptoms started. The problem is that I have tried all the fixes for this problem that I could find through Google and none of them have worked so far, so I am left with no other option but to try upgrading in hopes that Apache2 has no incompatibilities (if that really is the problem...). The concern with doing so is that I know there were incompatibilities between Apache2 and mod_perl a year or so ago when I last tried this, so I am wondering if anyone knows if these have now been resolved. M On Tue, 2005-04-05 at 07:45, Martin Senger wrote: > Mark, > Why would you think that Apache & perl_mod is the cause of the current > problems, considering that Moby Central was running without flaws many > mnths before? What has changed before the current problems started? If you > changed more things now - like having Apache2 - you could never be able to > find what *really* was a problem... Just my 2c... > > Martin -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From mwilkinson at mrl.ubc.ca Tue Apr 5 10:56:51 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue, 05 Apr 2005 07:56:51 -0700 Subject: [moby] Re: [MOBY-dev] Apache2 & mod_perl 2 In-Reply-To: References: Message-ID: <1112713011.15804.15.camel@mobycentral.icapture.ubc.ca> I don't think that Apache/mod_perl are the problem - I think the problem is with the (known) incompatibilities between Apache1 and EXPAT. This would make some sense, since we recently migrated from XML::DOM to XML::LibXML, and that seems to be when the worst of the symptoms started. The problem is that I have tried all the fixes for this problem that I could find through Google and none of them have worked so far, so I am left with no other option but to try upgrading in hopes that Apache2 has no incompatibilities (if that really is the problem...). The concern with doing so is that I know there were incompatibilities between Apache2 and mod_perl a year or so ago when I last tried this, so I am wondering if anyone knows if these have now been resolved. M On Tue, 2005-04-05 at 07:45, Martin Senger wrote: > Mark, > Why would you think that Apache & perl_mod is the cause of the current > problems, considering that Moby Central was running without flaws many > mnths before? What has changed before the current problems started? If you > changed more things now - like having Apache2 - you could never be able to > find what *really* was a problem... Just my 2c... > > Martin -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From gordonp at ucalgary.ca Tue Apr 5 11:03:39 2005 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 05 Apr 2005 09:03:39 -0600 Subject: [MOBY-dev] Re: suggestions about the latest version In-Reply-To: <42529ECD.3070004@infobiogen.fr> References: <42529ECD.3070004@infobiogen.fr> Message-ID: <4252A8CB.4000704@ucalgary.ca> Hi Sophie, I'm cc'ing the list as this may be of some interest to other Java developers... Sophie Durand wrote: > Hi, > > Thanks to have modified so quickly on my demand ! > I have some remarks about the lastest version: > > In the MobyDataSimpleInstance.java file, for the equals method, I > would have compared values with > ourObject.equals(passedInObject) > instead of comparing the references that would generally be different. > This will use the equals method of BigInteger or BigDecimal depending > on the instance. Oops, this is what I meant to do! I even wrote that to you! I've fixed this now. > I've read the Java API for the comparable interface : > compareTo > Throws: > ClassCastException - if the specified object's type prevents it > from being compared to this Object. > Probably you should throw an Exception if the given object is not a > MobyDataSimpleInstance. I thought about this, but decided to allow any objects to be compared because I did not want to hard code in the list of acceptable child classes. This would mean if MobyDataX was added as a class, you'd have to remember to add X and other compatible classes to MobyDataSimple's equals() (to allow for the convenient comparison of java.lang.Integer and org.biomoby.shared.MobyDataInteger for example). If a child class wants to enforce a class equivalency, they can override the equals method. I've added the ClassCastException for this reason, but do not throw it in MobyDataSimpleInstance's method. Luckily you can say that you throw a ClassCastException, even if you don't, without the compiler complaining. > > In MobyDataFloat.java, there seems to be a problem in the clone > function : it returns an instance of MobyDataInt... Fixed... > Sophie From jmfernandez at cnb.uam.es Tue Apr 5 11:23:46 2005 From: jmfernandez at cnb.uam.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Tue, 05 Apr 2005 17:23:46 +0200 Subject: [moby] Re: [MOBY-dev] Apache2 & mod_perl 2 In-Reply-To: <1112713011.15804.15.camel@mobycentral.icapture.ubc.ca> References: <1112713011.15804.15.camel@mobycentral.icapture.ubc.ca> Message-ID: <4252AD82.8050205@cnb.uam.es> If the segfaults are more or less random, it could be an almost broken memory module, which makes jam with some of its bits when it gets hot. Are segfaults happening when the server is under heavy load? Or does they appear when about an hour has been spent doing almost "nothing"? If it is a software problem, a fresh, known stable installation should be the answer. Best Regards, Jos? Mar?a Mark Wilkinson wrote: > I don't think that Apache/mod_perl are the problem - I think the problem > is with the (known) incompatibilities between Apache1 and EXPAT. This > would make some sense, since we recently migrated from XML::DOM to > XML::LibXML, and that seems to be when the worst of the symptoms > started. > > The problem is that I have tried all the fixes for this problem that I > could find through Google and none of them have worked so far, so I am > left with no other option but to try upgrading in hopes that Apache2 has > no incompatibilities (if that really is the problem...). The concern > with doing so is that I know there were incompatibilities between > Apache2 and mod_perl a year or so ago when I last tried this, so I am > wondering if anyone knows if these have now been resolved. > > M > > > > On Tue, 2005-04-05 at 07:45, Martin Senger wrote: > >>Mark, >> Why would you think that Apache & perl_mod is the cause of the current >>problems, considering that Moby Central was running without flaws many >>mnths before? What has changed before the current problems started? If you >>changed more things now - like having Apache2 - you could never be able to >>find what *really* was a problem... Just my 2c... >> >> Martin -- Jos? Mar?a Fern?ndez Gonz?lez e-mail: jmfernandez at cnb.uam.es Tlfn: (+34) 91 585 54 50 Fax: (+34) 91 585 45 06 Grupo de Dise?o de Proteinas Protein Design Group Centro Nacional de Biotecnolog?a National Center of Biotechnology C.P.: 28049 Zip Code: 28049 C/. Darwin n? 3 (Campus Cantoblanco, U. Aut?noma), Madrid (Spain) From mwilkinson at mrl.ubc.ca Tue Apr 5 11:45:39 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue, 05 Apr 2005 08:45:39 -0700 Subject: [moby] Re: [MOBY-dev] Apache2 & mod_perl 2 In-Reply-To: <4252AD82.8050205@cnb.uam.es> References: <1112713011.15804.15.camel@mobycentral.icapture.ubc.ca> <4252AD82.8050205@cnb.uam.es> Message-ID: <1112715939.15804.20.camel@mobycentral.icapture.ubc.ca> Hi Jose (c.c. Jason) My first instinct was a memory problem as well, but I have asked the sysadmin to look into this and he doesn't think that is the case. The Google searches are split between those who say that the errors come from physical memory problems, and those who say that they are from Apache incompatibilities. I've chased down all of the Apache incompatibilities that I could find, and have done a completely fresh install of Apache and mod-perl over the weekend, but that hasn't helped. ...if it is a memory problem, it's a hard one to spot! :-) M On Tue, 2005-04-05 at 08:23, José María Fernández González wrote: > If the segfaults are more or less random, it could be an almost broken > memory module, which makes jam with some of its bits when it gets hot. > > Are segfaults happening when the server is under heavy load? Or does > they appear when about an hour has been spent doing almost "nothing"? > > If it is a software problem, a fresh, known stable installation should > be the answer. > > Best Regards, > José María > > Mark Wilkinson wrote: > > I don't think that Apache/mod_perl are the problem - I think the problem > > is with the (known) incompatibilities between Apache1 and EXPAT. This > > would make some sense, since we recently migrated from XML::DOM to > > XML::LibXML, and that seems to be when the worst of the symptoms > > started. > > > > The problem is that I have tried all the fixes for this problem that I > > could find through Google and none of them have worked so far, so I am > > left with no other option but to try upgrading in hopes that Apache2 has > > no incompatibilities (if that really is the problem...). The concern > > with doing so is that I know there were incompatibilities between > > Apache2 and mod_perl a year or so ago when I last tried this, so I am > > wondering if anyone knows if these have now been resolved. > > > > M > > > > > > > > On Tue, 2005-04-05 at 07:45, Martin Senger wrote: > > > >>Mark, > >> Why would you think that Apache & perl_mod is the cause of the current > >>problems, considering that Moby Central was running without flaws many > >>mnths before? What has changed before the current problems started? If you > >>changed more things now - like having Apache2 - you could never be able to > >>find what *really* was a problem... Just my 2c... > >> > >> Martin -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From mwilkinson at mrl.ubc.ca Tue Apr 5 12:48:27 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue, 05 Apr 2005 09:48:27 -0700 Subject: [moby] Re: [MOBY-dev] Apache2 & mod_perl 2 In-Reply-To: <4252AD82.8050205@cnb.uam.es> References: <1112713011.15804.15.camel@mobycentral.icapture.ubc.ca> <4252AD82.8050205@cnb.uam.es> Message-ID: <1112719706.15804.97.camel@mobycentral.icapture.ubc.ca> On Tue, 2005-04-05 at 08:23, José María Fernández González wrote: > Are segfaults happening when the server is under heavy load? Or does > they appear when about an hour has been spent doing almost "nothing"? The segfaults are random. From a fresh startup at 11:40 under light load I got a segfault at 11:49, 11:54, 12:32 and 12:33 Not pretty :-) M -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From jmfernandez at cnb.uam.es Tue Apr 5 14:58:49 2005 From: jmfernandez at cnb.uam.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Tue, 05 Apr 2005 20:58:49 +0200 Subject: [moby] Re: [MOBY-dev] Apache2 & mod_perl 2 In-Reply-To: <1112719706.15804.97.camel@mobycentral.icapture.ubc.ca> References: <11 12713011.15804.15.camel@mobycentral.icapture.ubc.ca><4252AD82.8050205@cnb.u am.es> <1112719706.15804.97.camel@mobycentral.icapture.ubc.ca> Message-ID: <4252DFE9.5060802@cnb.uam.es> D'oh! It smells like a hardware problem! Perhaps it is not related to memory modules, but the power supply. If it is dying, it could be giving bad voltage levels under light load (computing+disk), and they could be good enough for a memory check task (only computing). Most of motherboard BIOS can tell you about power supply voltages they are receiving. Have luck! Jos? Mar?a Mark Wilkinson wrote: > On Tue, 2005-04-05 at 08:23, Jos?? Mar??a Fern??ndez Gonz??lez wrote: > > >>Are segfaults happening when the server is under heavy load? Or does >>they appear when about an hour has been spent doing almost "nothing"? > > > The segfaults are random. From a fresh startup at 11:40 under light > load I got a segfault at 11:49, 11:54, 12:32 and 12:33 > > Not pretty :-) > > M > > -- Jos? Mar?a Fern?ndez Gonz?lez e-mail: jmfernandez at cnb.uam.es Tlfn: (+34) 91 585 54 50 Fax: (+34) 91 585 45 06 Grupo de Dise?o de Proteinas Protein Design Group Centro Nacional de Biotecnolog?a National Center of Biotechnology C.P.: 28049 Zip Code: 28049 C/. Darwin n? 3 (Campus Cantoblanco, U. Aut?noma), Madrid (Spain) -------------- next part -------------- A non-text attachment was scrubbed... Name: homer_doh.png Type: image/png Size: 15301 bytes Desc: not available Url : http://www.biomoby.org/pipermail/moby-dev/attachments/20050405/91654c0a/homer_doh-0002.png From senger at ebi.ac.uk Tue Apr 5 15:46:18 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 5 Apr 2005 20:46:18 +0100 (BST) Subject: [moby] Re: [MOBY-dev] Apache2 & mod_perl 2 In-Reply-To: <4252DFE9.5060802@cnb.uam.es> Message-ID: > D'oh! It smells like a hardware problem! > Mark, why not just to try another computer for a while? Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From senger at ebi.ac.uk Thu Apr 7 17:27:06 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Thu, 7 Apr 2005 22:27:06 +0100 (BST) Subject: [MOBY-dev] jMoby compilation problems In-Reply-To: <42123912.362bff4b.58cb.30c8@smtp.gmail.com> Message-ID: Dear Java developers, Today I found (with a great help and support from Eddie) that there are classes in the current jMoby module that cannot be compiled. Which is - according to my opinion - completely wrong. And stressfully frustrating. Please let me repeat that I believe that the rule number one for shared Java development is that you commit code only when it compiles. It does not need to run correctly - especially if you just started to develop it - but it *must* compile - otherwise other developers are stuck and cannot do anything. If your code cannot compile from serious reasons (for example you are using Java 1.5, and we other have not yet commited to it), do not commit your code, or create your own CVS branche. If you have any third-party libraries that you wish to be added, send them to me, and I will put them into a central place where the jMoby Ant take sthem from. As a summary, this is what you should always do before you commit: ./build-dev.sh clean compile And if you are using some new third-party classes in 'lib' (which you should not, but let's assume that you just tested your new code with a new library that you still may have in 'lib') do before committing this: ./build-dev.sh cleanall ./build.sh Thank for your attention. Eddie - as far as I know - is now trying to clean the code of someone else. So if you think that it is your code that does not compile, please hurry to help him. Thanks you. Cheers, martin PS. Mark, could we have scheduled a short session about Java developing in Vancouver - to discuss the similar things and rules that I mentioned above. I know that Eddie is also working on documenting such principles, so it would be good to have some time to present it, discuss and hopefully accept it. Thanks. M. -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From mwilkinson at mrl.ubc.ca Thu Apr 7 19:03:57 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Thu, 07 Apr 2005 16:03:57 -0700 Subject: [moby] [MOBY-dev] jMoby compilation problems In-Reply-To: References: Message-ID: <1112915037.25115.18.camel@mobycentral.icapture.ubc.ca> Hi Martin, There have been a variety of requests for what we should talk about at the Vancouver meeting. I suspect that the best way to meet everyone's interests is for us to have a couple of hours each morning where we discuss things as a whole, and then break into smaller BoF groups to discuss specific issues. There are enough of us at this meeting (yay MOBY!) that we can probably accomplish more by breaking into smaller task-specific groups anyway. Damian/Gary do you have specific goals for the meeting? Does the BoF idea suit you? Let's start working-up an outline for the two days. Cheers all! M On Thu, 2005-04-07 at 14:27, Martin Senger wrote: > PS. Mark, could we have scheduled a short session about Java developing in > Vancouver - to discuss the similar things and rules that I mentioned > above. I know that Eddie is also working on documenting such principles, > so it would be good to have some time to present it, discuss and > hopefully accept it. Thanks. M. -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From gss at ncgr.org Thu Apr 7 19:06:10 2005 From: gss at ncgr.org (Gary Schiltz) Date: Thu, 07 Apr 2005 17:06:10 -0600 Subject: [moby] [MOBY-dev] jMoby compilation problems In-Reply-To: <1112915037.25115.18.camel@mobycentral.icapture.ubc.ca> References: <1112915037.25115.18.camel@mobycentral.icapture.ubc.ca> Message-ID: <4255BCE2.6050200@ncgr.org> Damian should feel free to chime in, but I'd be fine with giving a quick update on Semantic MOBY activities to all, and then host a task-specific BoF as Mark suggests. // Gary Mark Wilkinson wrote: >Hi Martin, > >There have been a variety of requests for what we should talk about at >the Vancouver meeting. I suspect that the best way to meet everyone's >interests is for us to have a couple of hours each morning where we >discuss things as a whole, and then break into smaller BoF groups to >discuss specific issues. There are enough of us at this meeting (yay >MOBY!) that we can probably accomplish more by breaking into smaller >task-specific groups anyway. > >Damian/Gary do you have specific goals for the meeting? Does the BoF >idea suit you? > >Let's start working-up an outline for the two days. > >Cheers all! > >M > >On Thu, 2005-04-07 at 14:27, Martin Senger wrote: > > >>PS. Mark, could we have scheduled a short session about Java developing in >>Vancouver - to discuss the similar things and rules that I mentioned >>above. I know that Eddie is also working on documenting such principles, >>so it would be good to have some time to present it, discuss and >>hopefully accept it. Thanks. M. >> From senger at ebi.ac.uk Thu Apr 7 19:16:40 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Fri, 8 Apr 2005 00:16:40 +0100 (BST) Subject: [moby] [MOBY-dev] jMoby compilation problems In-Reply-To: <1112915037.25115.18.camel@mobycentral.icapture.ubc.ca> Message-ID: Well, generally I do not like BoFs. Because then I am always in a BoF where I am involved most - and I am loosing overview what is happenning elsewhwere. Of course, there is no other way if there are many topics and many participants. But perhaps we could try to tell everybody about everything (the speakers can promise not to repeat much what we all know already) - and only then to split into BoFs. And perhaps to make not many BoFs in the same time (ideal would be just two). Cheers, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From gordonp at ucalgary.ca Fri Apr 8 10:18:35 2005 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 08 Apr 2005 08:18:35 -0600 Subject: [moby] [MOBY-dev] jMoby compilation problems In-Reply-To: References: Message-ID: <425692BB.9000007@ucalgary.ca> I always like software demos. Just my CAN$0.02 worth, but as this is a developers meeting, it might make sense to (in this order): Day 1: 1) have general updates from the leaders on S-MOBY and MOBY-S on language-neutral subjects (e.g. usage stats, publications, changes to the architecture, support software status, etc.) 2) have a series of (a) software or (b) canned programming demos from interested parties to show off (a) what people are doing with the system as it stands today or (b) how easy/hard it is to code, inspiring others to improve their APIs Lunch 3) have discussions amongst everyone on S-MOBY and MOBY-S language-neutral subjects (e.g. namespace usage, potential changes to the architecture, how to improve robustness, etc.) 4) Bird of a Feather meetings to resolve language specific API issues, plus how to possibly implement improvements discussed in (3). This will likely continue to be discussed into the evening until too many "wobbly pops" are consumed. Day 2: 1) Flesh out changes to the central, platform neutral APIs/architectures based on contemplation and discussion from yesterday. 2) Updates from all BoFs to the group on what they discussed 3) Discussed future directions, "action items" (forgive the management speak) and how they can be coordinated Lunch 4) Birds of a Feather meetings to either do a mini-hackathon, discuss futher, and/or document API changes Martin Senger wrote: >Well, generally I do not like BoFs. Because then I am always in a BoF >where I am involved most - and I am loosing overview what is happenning >elsewhwere. Of course, there is no other way if there are many topics and >many participants. But perhaps we could try to tell everybody about >everything (the speakers can promise not to repeat much what we all know >already) - and only then to split into BoFs. And perhaps to make not many >BoFs in the same time (ideal would be just two). > >Cheers, >Martin > > > From gordonp at ucalgary.ca Fri Apr 15 17:26:39 2005 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 15 Apr 2005 15:26:39 -0600 Subject: [MOBY-dev] Uncompilable class in CVS? Message-ID: <4260318F.9030707@ucalgary.ca> Hi everyone, The following class: org/biomoby/registry/rdfagent/verifier/ServiceDescrParser.java appears to be uncompilable because it references an undeclared class or variable called "MRes". Anyone else have this issue? I did a "cvs update -dP " to no avail... From edward.kawas at gmail.com Sat Apr 16 10:21:20 2005 From: edward.kawas at gmail.com (Eddie Kawas) Date: Sat, 16 Apr 2005 07:21:20 -0700 Subject: [MOBY-dev] Uncompilable class in CVS? In-Reply-To: <4260318F.9030707@ucalgary.ca> Message-ID: <42611f63.78dc2c21.0fca.ffff806b@mx.gmail.com> Fixed. I guess when the package was updated, the file was missing. Eddie > -----Original Message----- > From: moby-dev-bounces at portal.open-bio.org [mailto:moby- > dev-bounces at portal.open-bio.org] On Behalf Of Paul Gordon > Sent: Friday, April 15, 2005 2:27 PM > To: Core developer announcements > Subject: [MOBY-dev] Uncompilable class in CVS? > > Hi everyone, > > The following class: > > org/biomoby/registry/rdfagent/verifier/ServiceDescrParser. > java > > appears to be uncompilable because it references an > undeclared class or > variable called "MRes". Anyone else have this issue? I > did a "cvs > update -dP " to no avail... > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev From dlondon at ebi.ac.uk Tue Apr 19 05:16:30 2005 From: dlondon at ebi.ac.uk (Darin London) Date: Tue, 19 Apr 2005 10:16:30 +0100 Subject: [MOBY-dev] Re: BOSC 2005 In-Reply-To: <20050120175859.GA7254@parrot.ebi.ac.uk> References: <20050120175859.GA7254@parrot.ebi.ac.uk> Message-ID: <20050419091628.GN17377@parrot.ebi.ac.uk> {Please pass the word!} SECOND CALL FOR SPEAKERS The 6th annual Bioinformatics Open Source Conference (BOSC'2005) is organized by the not-for-profit Open Bioinformatics Foundation. The meeting will take place June 23-24, 2005 in Detroit, Michigan, USA, and is one of several Special Interest Group (SIG) meetings occurring in conjunction with the 13th International Conference on Intelligent Systems for Molecular Biology. see http://www.iscb.org/ismb2005 for more information. Because of the power of many Open Source bioinformatics packages in use by the Research Community today, it is not too presumptuous to say that the work of the Open Source Bioinformatics Community represents the cutting edge of Bioinformatics in general. This has been repeatedly demonstrated by the quality of presentations at previous BOSC conferences. This year, at BOSC 2005, we want to continue this tradition of excellence, while presenting this message to a wider part of the Research Community. Please, pass this message on to anyone you know that is interested in Bioinformatics software. BOSC PROGRAM & CONTACT INFO * Web: http://www.open-bio.org/bosc2005/ * Online Registration: https://www.cteusa.com/iscb4/ * Email: bosc at open-bio.org FEES * Corporate : $195 ($245 after May 16th) * Academic : $170 ($220 after May 16th) * Student : $145 ($195 after May 16th) SPEAKERS & ABSTRACTS WANTED The program committee is currently seeking abstracts for talks at BOSC 2005. BOSC is a great opportunity for you to tell the community about your use, development, or philosophy of open source software development in bioinformatics. The committee will select several submitted abstracts for 25-minute talks and others for shorter "lightning" talks. Accepted abstracts will be published on the BOSC web site. If you are interested in speaking at BOSC 2005, please send us before April 26, 2005: * an abstract (no more than a few paragraphs) * a URL for the project page, if applicable * information about the open source license used for your software or your release plans. Abstracts will be accepted for submission until April 26, 2005. Abstracts chosen for presentation will be announced May 12, 2005 (before the ISMB Early Registration Deadline). LIGHTNING-TALK SPEAKERS WANTED! The program committee is currently seeking speakers for the lightning talks at BOSC 2005. Lightning talks are quick - only five minutes long - and a great opportunity for you to give people a quick summary of your open source project, code, idea, or vision of the future. If you are interested in giving a lightning talk at BOSC 2005, please send us: * a brief title and summary (one or two lines) * a URL for the project page, if applicable * information about the open source license used for your software or your release plans. We will accept entries on-line until BOSC starts, but space for demos and lightning talks is limited.
Message-ID: Dear jMoby developers, Eddie and me, we have updated Ant's build.xml file in order to be able to add to jMoby also Java sources that needs to be compiled with the latest Java 1.5 - but still let the others work with Java 1.4 as usual. Here is how to do it (please comment if you need any more assistance, or if you disagree with our approach): * First to say is that it was put there as a workaround for those who really needs to use 1.5. Any new class that needs 1.5 must be exlicitely named in the build.xml file. Which is not too suitable if you have many such classes. So when you start to use Java 1.5. in greater scale we need to re-factor it. Let me know. * Having said that please note that nothing prevents you to use Java 1.5 to compile all classes. That should work fine (with perhaps few semantic warnings which I am sure the authors, including me, will take care of sooner or later). The previous (and the next) bullets are for those *adding* sources that can be compiled *only* with Java 1.5 (an example is the Eddie's class org.biomoby.shared.MobyObjectDecompositionImpl.java). * If you are using regular javac compiler you do not need to do anything special. The Ant will sniff around and find what java version you are using and depending on the result it will compile always all classes not mentioned as specific for 1.5, and then - only if you have java 1.5 - it compiles additionally those new bastards. Which means that when you are using java 1.4, the new (Eddie's) classes will not compiled so you will not be able to use them. But that's obvious - you cannot shop with the old Deutches Marks anymore without having new Euros, can you? * If you are using jikes (which I strongly recommend because it is much much faster compiler, but that's another story) and have Java 1.4 on your path, again nothing needs to be done. However, if you are using jikes (latest version is 1.22) *and* have java 1.5 on your path, jikes will try to compile also the new (Eddie's) classes and fails. I do not exactly why (let me know if you know). So for this case you need to instruct Ant that - eventhough the java 1.5 is available - you do not want it. Do it with by setting property java.latest.version to false. Either (recommended) put the line: java.latest.version = false in your build.property files, or use it on the Ant's command line: ./build-dev.sh -Djava.latest.version=false compile With regard, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From ywong at infobiogen.fr Wed Apr 20 04:53:38 2005 From: ywong at infobiogen.fr (Yan Wong) Date: Wed, 20 Apr 2005 10:53:38 +0200 Subject: [MOBY-dev] Updates on the bioMoby Python API Message-ID: <42661892.9030809@infobiogen.fr> Hi, I've put two classes SQLDispatcher and SQLInvocator in the API in order to ease the build of DB based webservices An example can be found in the tutorials directory Cheers Yan From smontgom at bcgsc.bc.ca Fri Apr 1 00:01:26 2005 From: smontgom at bcgsc.bc.ca (Stephen Montgomery) Date: Thu, 31 Mar 2005 16:01:26 -0800 Subject: [MOBY-dev] moby data and parameters Message-ID: <424C8F56.7080701@bcgsc.bc.ca> hi - does anyone have an example of a xml input where more than one dna sequence is coming down the wire. is this a collection? also, for a registered return data type we want to attach some parameters (corresponding to the application that is going to be run). is there a java example out there of doing this? all the best, stephen ps ben and i had an awesome crash coding session yesterday. set-up the plan, built the supports, now we just need to execute the vision. rock on. From mwilkinson at mrl.ubc.ca Tue Apr 5 14:40:34 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue, 05 Apr 2005 07:40:34 -0700 Subject: [MOBY-dev] Apache2 & mod_perl 2 Message-ID: <1112712033.15804.3.camel@mobycentral.icapture.ubc.ca> Hi again, I'm still experiencing segfaults every hour or so on the server, even after a rebuild of Apache without expat, so I'm thinking of upgrading to Apache2 in hopes that it solves the problem. The last time I tried this there was a problem with Apache2 and mod_perl2 - does anyone know definitively if this has now been fixed? If I don't hear otherwise, I'll probably try this solution tomorrow, so any advice before I throw myself into the fray is appreciated :-) Cheers all! M -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From senger at ebi.ac.uk Tue Apr 5 14:45:54 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 5 Apr 2005 15:45:54 +0100 (BST) Subject: [MOBY-dev] Apache2 & mod_perl 2 In-Reply-To: <1112712033.15804.3.camel@mobycentral.icapture.ubc.ca> Message-ID: Mark, Why would you think that Apache & perl_mod is the cause of the current problems, considering that Moby Central was running without flaws many mnths before? What has changed before the current problems started? If you changed more things now - like having Apache2 - you could never be able to find what *really* was a problem... Just my 2c... Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From senger at ebi.ac.uk Tue Apr 5 14:45:54 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 5 Apr 2005 15:45:54 +0100 (BST) Subject: [MOBY-dev] Apache2 & mod_perl 2 In-Reply-To: <1112712033.15804.3.camel@mobycentral.icapture.ubc.ca> Message-ID: Mark, Why would you think that Apache & perl_mod is the cause of the current problems, considering that Moby Central was running without flaws many mnths before? What has changed before the current problems started? If you changed more things now - like having Apache2 - you could never be able to find what *really* was a problem... Just my 2c... Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From mwilkinson at mrl.ubc.ca Tue Apr 5 14:56:51 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue, 05 Apr 2005 07:56:51 -0700 Subject: [moby] Re: [MOBY-dev] Apache2 & mod_perl 2 In-Reply-To: References: Message-ID: <1112713011.15804.15.camel@mobycentral.icapture.ubc.ca> I don't think that Apache/mod_perl are the problem - I think the problem is with the (known) incompatibilities between Apache1 and EXPAT. This would make some sense, since we recently migrated from XML::DOM to XML::LibXML, and that seems to be when the worst of the symptoms started. The problem is that I have tried all the fixes for this problem that I could find through Google and none of them have worked so far, so I am left with no other option but to try upgrading in hopes that Apache2 has no incompatibilities (if that really is the problem...). The concern with doing so is that I know there were incompatibilities between Apache2 and mod_perl a year or so ago when I last tried this, so I am wondering if anyone knows if these have now been resolved. M On Tue, 2005-04-05 at 07:45, Martin Senger wrote: > Mark, > Why would you think that Apache & perl_mod is the cause of the current > problems, considering that Moby Central was running without flaws many > mnths before? What has changed before the current problems started? If you > changed more things now - like having Apache2 - you could never be able to > find what *really* was a problem... Just my 2c... > > Martin -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From mwilkinson at mrl.ubc.ca Tue Apr 5 14:56:51 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue, 05 Apr 2005 07:56:51 -0700 Subject: [moby] Re: [MOBY-dev] Apache2 & mod_perl 2 In-Reply-To: References: Message-ID: <1112713011.15804.15.camel@mobycentral.icapture.ubc.ca> I don't think that Apache/mod_perl are the problem - I think the problem is with the (known) incompatibilities between Apache1 and EXPAT. This would make some sense, since we recently migrated from XML::DOM to XML::LibXML, and that seems to be when the worst of the symptoms started. The problem is that I have tried all the fixes for this problem that I could find through Google and none of them have worked so far, so I am left with no other option but to try upgrading in hopes that Apache2 has no incompatibilities (if that really is the problem...). The concern with doing so is that I know there were incompatibilities between Apache2 and mod_perl a year or so ago when I last tried this, so I am wondering if anyone knows if these have now been resolved. M On Tue, 2005-04-05 at 07:45, Martin Senger wrote: > Mark, > Why would you think that Apache & perl_mod is the cause of the current > problems, considering that Moby Central was running without flaws many > mnths before? What has changed before the current problems started? If you > changed more things now - like having Apache2 - you could never be able to > find what *really* was a problem... Just my 2c... > > Martin -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From gordonp at ucalgary.ca Tue Apr 5 15:03:39 2005 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 05 Apr 2005 09:03:39 -0600 Subject: [MOBY-dev] Re: suggestions about the latest version In-Reply-To: <42529ECD.3070004@infobiogen.fr> References: <42529ECD.3070004@infobiogen.fr> Message-ID: <4252A8CB.4000704@ucalgary.ca> Hi Sophie, I'm cc'ing the list as this may be of some interest to other Java developers... Sophie Durand wrote: > Hi, > > Thanks to have modified so quickly on my demand ! > I have some remarks about the lastest version: > > In the MobyDataSimpleInstance.java file, for the equals method, I > would have compared values with > ourObject.equals(passedInObject) > instead of comparing the references that would generally be different. > This will use the equals method of BigInteger or BigDecimal depending > on the instance. Oops, this is what I meant to do! I even wrote that to you! I've fixed this now. > I've read the Java API for the comparable interface : > compareTo > Throws: > ClassCastException - if the specified object's type prevents it > from being compared to this Object. > Probably you should throw an Exception if the given object is not a > MobyDataSimpleInstance. I thought about this, but decided to allow any objects to be compared because I did not want to hard code in the list of acceptable child classes. This would mean if MobyDataX was added as a class, you'd have to remember to add X and other compatible classes to MobyDataSimple's equals() (to allow for the convenient comparison of java.lang.Integer and org.biomoby.shared.MobyDataInteger for example). If a child class wants to enforce a class equivalency, they can override the equals method. I've added the ClassCastException for this reason, but do not throw it in MobyDataSimpleInstance's method. Luckily you can say that you throw a ClassCastException, even if you don't, without the compiler complaining. > > In MobyDataFloat.java, there seems to be a problem in the clone > function : it returns an instance of MobyDataInt... Fixed... > Sophie From jmfernandez at cnb.uam.es Tue Apr 5 15:23:46 2005 From: jmfernandez at cnb.uam.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Tue, 05 Apr 2005 17:23:46 +0200 Subject: [moby] Re: [MOBY-dev] Apache2 & mod_perl 2 In-Reply-To: <1112713011.15804.15.camel@mobycentral.icapture.ubc.ca> References: <1112713011.15804.15.camel@mobycentral.icapture.ubc.ca> Message-ID: <4252AD82.8050205@cnb.uam.es> If the segfaults are more or less random, it could be an almost broken memory module, which makes jam with some of its bits when it gets hot. Are segfaults happening when the server is under heavy load? Or does they appear when about an hour has been spent doing almost "nothing"? If it is a software problem, a fresh, known stable installation should be the answer. Best Regards, Jos? Mar?a Mark Wilkinson wrote: > I don't think that Apache/mod_perl are the problem - I think the problem > is with the (known) incompatibilities between Apache1 and EXPAT. This > would make some sense, since we recently migrated from XML::DOM to > XML::LibXML, and that seems to be when the worst of the symptoms > started. > > The problem is that I have tried all the fixes for this problem that I > could find through Google and none of them have worked so far, so I am > left with no other option but to try upgrading in hopes that Apache2 has > no incompatibilities (if that really is the problem...). The concern > with doing so is that I know there were incompatibilities between > Apache2 and mod_perl a year or so ago when I last tried this, so I am > wondering if anyone knows if these have now been resolved. > > M > > > > On Tue, 2005-04-05 at 07:45, Martin Senger wrote: > >>Mark, >> Why would you think that Apache & perl_mod is the cause of the current >>problems, considering that Moby Central was running without flaws many >>mnths before? What has changed before the current problems started? If you >>changed more things now - like having Apache2 - you could never be able to >>find what *really* was a problem... Just my 2c... >> >> Martin -- Jos? Mar?a Fern?ndez Gonz?lez e-mail: jmfernandez at cnb.uam.es Tlfn: (+34) 91 585 54 50 Fax: (+34) 91 585 45 06 Grupo de Dise?o de Proteinas Protein Design Group Centro Nacional de Biotecnolog?a National Center of Biotechnology C.P.: 28049 Zip Code: 28049 C/. Darwin n? 3 (Campus Cantoblanco, U. Aut?noma), Madrid (Spain) From mwilkinson at mrl.ubc.ca Tue Apr 5 15:45:39 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue, 05 Apr 2005 08:45:39 -0700 Subject: [moby] Re: [MOBY-dev] Apache2 & mod_perl 2 In-Reply-To: <4252AD82.8050205@cnb.uam.es> References: <1112713011.15804.15.camel@mobycentral.icapture.ubc.ca> <4252AD82.8050205@cnb.uam.es> Message-ID: <1112715939.15804.20.camel@mobycentral.icapture.ubc.ca> Hi Jose (c.c. Jason) My first instinct was a memory problem as well, but I have asked the sysadmin to look into this and he doesn't think that is the case. The Google searches are split between those who say that the errors come from physical memory problems, and those who say that they are from Apache incompatibilities. I've chased down all of the Apache incompatibilities that I could find, and have done a completely fresh install of Apache and mod-perl over the weekend, but that hasn't helped. ...if it is a memory problem, it's a hard one to spot! :-) M On Tue, 2005-04-05 at 08:23, Jos?? Mar??a Fern??ndez Gonz??lez wrote: > If the segfaults are more or less random, it could be an almost broken > memory module, which makes jam with some of its bits when it gets hot. > > Are segfaults happening when the server is under heavy load? Or does > they appear when about an hour has been spent doing almost "nothing"? > > If it is a software problem, a fresh, known stable installation should > be the answer. > > Best Regards, > Jos?? Mar??a > > Mark Wilkinson wrote: > > I don't think that Apache/mod_perl are the problem - I think the problem > > is with the (known) incompatibilities between Apache1 and EXPAT. This > > would make some sense, since we recently migrated from XML::DOM to > > XML::LibXML, and that seems to be when the worst of the symptoms > > started. > > > > The problem is that I have tried all the fixes for this problem that I > > could find through Google and none of them have worked so far, so I am > > left with no other option but to try upgrading in hopes that Apache2 has > > no incompatibilities (if that really is the problem...). The concern > > with doing so is that I know there were incompatibilities between > > Apache2 and mod_perl a year or so ago when I last tried this, so I am > > wondering if anyone knows if these have now been resolved. > > > > M > > > > > > > > On Tue, 2005-04-05 at 07:45, Martin Senger wrote: > > > >>Mark, > >> Why would you think that Apache & perl_mod is the cause of the current > >>problems, considering that Moby Central was running without flaws many > >>mnths before? What has changed before the current problems started? If you > >>changed more things now - like having Apache2 - you could never be able to > >>find what *really* was a problem... Just my 2c... > >> > >> Martin -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From mwilkinson at mrl.ubc.ca Tue Apr 5 16:48:27 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue, 05 Apr 2005 09:48:27 -0700 Subject: [moby] Re: [MOBY-dev] Apache2 & mod_perl 2 In-Reply-To: <4252AD82.8050205@cnb.uam.es> References: <1112713011.15804.15.camel@mobycentral.icapture.ubc.ca> <4252AD82.8050205@cnb.uam.es> Message-ID: <1112719706.15804.97.camel@mobycentral.icapture.ubc.ca> On Tue, 2005-04-05 at 08:23, Jos?? Mar??a Fern??ndez Gonz??lez wrote: > Are segfaults happening when the server is under heavy load? Or does > they appear when about an hour has been spent doing almost "nothing"? The segfaults are random. From a fresh startup at 11:40 under light load I got a segfault at 11:49, 11:54, 12:32 and 12:33 Not pretty :-) M -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From jmfernandez at cnb.uam.es Tue Apr 5 18:58:49 2005 From: jmfernandez at cnb.uam.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Tue, 05 Apr 2005 20:58:49 +0200 Subject: [moby] Re: [MOBY-dev] Apache2 & mod_perl 2 In-Reply-To: <1112719706.15804.97.camel@mobycentral.icapture.ubc.ca> References: <11 12713011.15804.15.camel@mobycentral.icapture.ubc.ca><4252AD82.8050205@cnb.u am.es> <1112719706.15804.97.camel@mobycentral.icapture.ubc.ca> Message-ID: <4252DFE9.5060802@cnb.uam.es> D'oh! It smells like a hardware problem! Perhaps it is not related to memory modules, but the power supply. If it is dying, it could be giving bad voltage levels under light load (computing+disk), and they could be good enough for a memory check task (only computing). Most of motherboard BIOS can tell you about power supply voltages they are receiving. Have luck! Jos? Mar?a Mark Wilkinson wrote: > On Tue, 2005-04-05 at 08:23, Jos?? Mar??a Fern??ndez Gonz??lez wrote: > > >>Are segfaults happening when the server is under heavy load? Or does >>they appear when about an hour has been spent doing almost "nothing"? > > > The segfaults are random. From a fresh startup at 11:40 under light > load I got a segfault at 11:49, 11:54, 12:32 and 12:33 > > Not pretty :-) > > M > > -- Jos? Mar?a Fern?ndez Gonz?lez e-mail: jmfernandez at cnb.uam.es Tlfn: (+34) 91 585 54 50 Fax: (+34) 91 585 45 06 Grupo de Dise?o de Proteinas Protein Design Group Centro Nacional de Biotecnolog?a National Center of Biotechnology C.P.: 28049 Zip Code: 28049 C/. Darwin n? 3 (Campus Cantoblanco, U. Aut?noma), Madrid (Spain) -------------- next part -------------- A non-text attachment was scrubbed... Name: homer_doh.png Type: image/png Size: 15301 bytes Desc: not available URL: From senger at ebi.ac.uk Tue Apr 5 19:46:18 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 5 Apr 2005 20:46:18 +0100 (BST) Subject: [moby] Re: [MOBY-dev] Apache2 & mod_perl 2 In-Reply-To: <4252DFE9.5060802@cnb.uam.es> Message-ID: > D'oh! It smells like a hardware problem! > Mark, why not just to try another computer for a while? Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From senger at ebi.ac.uk Thu Apr 7 21:27:06 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Thu, 7 Apr 2005 22:27:06 +0100 (BST) Subject: [MOBY-dev] jMoby compilation problems In-Reply-To: <42123912.362bff4b.58cb.30c8@smtp.gmail.com> Message-ID: Dear Java developers, Today I found (with a great help and support from Eddie) that there are classes in the current jMoby module that cannot be compiled. Which is - according to my opinion - completely wrong. And stressfully frustrating. Please let me repeat that I believe that the rule number one for shared Java development is that you commit code only when it compiles. It does not need to run correctly - especially if you just started to develop it - but it *must* compile - otherwise other developers are stuck and cannot do anything. If your code cannot compile from serious reasons (for example you are using Java 1.5, and we other have not yet commited to it), do not commit your code, or create your own CVS branche. If you have any third-party libraries that you wish to be added, send them to me, and I will put them into a central place where the jMoby Ant take sthem from. As a summary, this is what you should always do before you commit: ./build-dev.sh clean compile And if you are using some new third-party classes in 'lib' (which you should not, but let's assume that you just tested your new code with a new library that you still may have in 'lib') do before committing this: ./build-dev.sh cleanall ./build.sh Thank for your attention. Eddie - as far as I know - is now trying to clean the code of someone else. So if you think that it is your code that does not compile, please hurry to help him. Thanks you. Cheers, martin PS. Mark, could we have scheduled a short session about Java developing in Vancouver - to discuss the similar things and rules that I mentioned above. I know that Eddie is also working on documenting such principles, so it would be good to have some time to present it, discuss and hopefully accept it. Thanks. M. -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From mwilkinson at mrl.ubc.ca Thu Apr 7 23:03:57 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Thu, 07 Apr 2005 16:03:57 -0700 Subject: [moby] [MOBY-dev] jMoby compilation problems In-Reply-To: References: Message-ID: <1112915037.25115.18.camel@mobycentral.icapture.ubc.ca> Hi Martin, There have been a variety of requests for what we should talk about at the Vancouver meeting. I suspect that the best way to meet everyone's interests is for us to have a couple of hours each morning where we discuss things as a whole, and then break into smaller BoF groups to discuss specific issues. There are enough of us at this meeting (yay MOBY!) that we can probably accomplish more by breaking into smaller task-specific groups anyway. Damian/Gary do you have specific goals for the meeting? Does the BoF idea suit you? Let's start working-up an outline for the two days. Cheers all! M On Thu, 2005-04-07 at 14:27, Martin Senger wrote: > PS. Mark, could we have scheduled a short session about Java developing in > Vancouver - to discuss the similar things and rules that I mentioned > above. I know that Eddie is also working on documenting such principles, > so it would be good to have some time to present it, discuss and > hopefully accept it. Thanks. M. -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From gss at ncgr.org Thu Apr 7 23:06:10 2005 From: gss at ncgr.org (Gary Schiltz) Date: Thu, 07 Apr 2005 17:06:10 -0600 Subject: [moby] [MOBY-dev] jMoby compilation problems In-Reply-To: <1112915037.25115.18.camel@mobycentral.icapture.ubc.ca> References: <1112915037.25115.18.camel@mobycentral.icapture.ubc.ca> Message-ID: <4255BCE2.6050200@ncgr.org> Damian should feel free to chime in, but I'd be fine with giving a quick update on Semantic MOBY activities to all, and then host a task-specific BoF as Mark suggests. // Gary Mark Wilkinson wrote: >Hi Martin, > >There have been a variety of requests for what we should talk about at >the Vancouver meeting. I suspect that the best way to meet everyone's >interests is for us to have a couple of hours each morning where we >discuss things as a whole, and then break into smaller BoF groups to >discuss specific issues. There are enough of us at this meeting (yay >MOBY!) that we can probably accomplish more by breaking into smaller >task-specific groups anyway. > >Damian/Gary do you have specific goals for the meeting? Does the BoF >idea suit you? > >Let's start working-up an outline for the two days. > >Cheers all! > >M > >On Thu, 2005-04-07 at 14:27, Martin Senger wrote: > > >>PS. Mark, could we have scheduled a short session about Java developing in >>Vancouver - to discuss the similar things and rules that I mentioned >>above. I know that Eddie is also working on documenting such principles, >>so it would be good to have some time to present it, discuss and >>hopefully accept it. Thanks. M. >> From senger at ebi.ac.uk Thu Apr 7 23:16:40 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Fri, 8 Apr 2005 00:16:40 +0100 (BST) Subject: [moby] [MOBY-dev] jMoby compilation problems In-Reply-To: <1112915037.25115.18.camel@mobycentral.icapture.ubc.ca> Message-ID: Well, generally I do not like BoFs. Because then I am always in a BoF where I am involved most - and I am loosing overview what is happenning elsewhwere. Of course, there is no other way if there are many topics and many participants. But perhaps we could try to tell everybody about everything (the speakers can promise not to repeat much what we all know already) - and only then to split into BoFs. And perhaps to make not many BoFs in the same time (ideal would be just two). Cheers, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From gordonp at ucalgary.ca Fri Apr 8 14:18:35 2005 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 08 Apr 2005 08:18:35 -0600 Subject: [moby] [MOBY-dev] jMoby compilation problems In-Reply-To: References: Message-ID: <425692BB.9000007@ucalgary.ca> I always like software demos. Just my CAN$0.02 worth, but as this is a developers meeting, it might make sense to (in this order): Day 1: 1) have general updates from the leaders on S-MOBY and MOBY-S on language-neutral subjects (e.g. usage stats, publications, changes to the architecture, support software status, etc.) 2) have a series of (a) software or (b) canned programming demos from interested parties to show off (a) what people are doing with the system as it stands today or (b) how easy/hard it is to code, inspiring others to improve their APIs Lunch 3) have discussions amongst everyone on S-MOBY and MOBY-S language-neutral subjects (e.g. namespace usage, potential changes to the architecture, how to improve robustness, etc.) 4) Bird of a Feather meetings to resolve language specific API issues, plus how to possibly implement improvements discussed in (3). This will likely continue to be discussed into the evening until too many "wobbly pops" are consumed. Day 2: 1) Flesh out changes to the central, platform neutral APIs/architectures based on contemplation and discussion from yesterday. 2) Updates from all BoFs to the group on what they discussed 3) Discussed future directions, "action items" (forgive the management speak) and how they can be coordinated Lunch 4) Birds of a Feather meetings to either do a mini-hackathon, discuss futher, and/or document API changes Martin Senger wrote: >Well, generally I do not like BoFs. Because then I am always in a BoF >where I am involved most - and I am loosing overview what is happenning >elsewhwere. Of course, there is no other way if there are many topics and >many participants. But perhaps we could try to tell everybody about >everything (the speakers can promise not to repeat much what we all know >already) - and only then to split into BoFs. And perhaps to make not many >BoFs in the same time (ideal would be just two). > >Cheers, >Martin > > > From gordonp at ucalgary.ca Fri Apr 15 21:26:39 2005 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 15 Apr 2005 15:26:39 -0600 Subject: [MOBY-dev] Uncompilable class in CVS? Message-ID: <4260318F.9030707@ucalgary.ca> Hi everyone, The following class: org/biomoby/registry/rdfagent/verifier/ServiceDescrParser.java appears to be uncompilable because it references an undeclared class or variable called "MRes". Anyone else have this issue? I did a "cvs update -dP " to no avail... From edward.kawas at gmail.com Sat Apr 16 14:21:20 2005 From: edward.kawas at gmail.com (Eddie Kawas) Date: Sat, 16 Apr 2005 07:21:20 -0700 Subject: [MOBY-dev] Uncompilable class in CVS? In-Reply-To: <4260318F.9030707@ucalgary.ca> Message-ID: <42611f63.78dc2c21.0fca.ffff806b@mx.gmail.com> Fixed. I guess when the package was updated, the file was missing. Eddie > -----Original Message----- > From: moby-dev-bounces at portal.open-bio.org [mailto:moby- > dev-bounces at portal.open-bio.org] On Behalf Of Paul Gordon > Sent: Friday, April 15, 2005 2:27 PM > To: Core developer announcements > Subject: [MOBY-dev] Uncompilable class in CVS? > > Hi everyone, > > The following class: > > org/biomoby/registry/rdfagent/verifier/ServiceDescrParser. > java > > appears to be uncompilable because it references an > undeclared class or > variable called "MRes". Anyone else have this issue? I > did a "cvs > update -dP " to no avail... > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev From dlondon at ebi.ac.uk Tue Apr 19 09:16:30 2005 From: dlondon at ebi.ac.uk (Darin London) Date: Tue, 19 Apr 2005 10:16:30 +0100 Subject: [MOBY-dev] Re: BOSC 2005 In-Reply-To: <20050120175859.GA7254@parrot.ebi.ac.uk> References: <20050120175859.GA7254@parrot.ebi.ac.uk> Message-ID: <20050419091628.GN17377@parrot.ebi.ac.uk> {Please pass the word!} SECOND CALL FOR SPEAKERS The 6th annual Bioinformatics Open Source Conference (BOSC'2005) is organized by the not-for-profit Open Bioinformatics Foundation. The meeting will take place June 23-24, 2005 in Detroit, Michigan, USA, and is one of several Special Interest Group (SIG) meetings occurring in conjunction with the 13th International Conference on Intelligent Systems for Molecular Biology. see http://www.iscb.org/ismb2005 for more information. Because of the power of many Open Source bioinformatics packages in use by the Research Community today, it is not too presumptuous to say that the work of the Open Source Bioinformatics Community represents the cutting edge of Bioinformatics in general. This has been repeatedly demonstrated by the quality of presentations at previous BOSC conferences. This year, at BOSC 2005, we want to continue this tradition of excellence, while presenting this message to a wider part of the Research Community. Please, pass this message on to anyone you know that is interested in Bioinformatics software. BOSC PROGRAM & CONTACT INFO * Web: http://www.open-bio.org/bosc2005/ * Online Registration: https://www.cteusa.com/iscb4/ * Email: bosc at open-bio.org FEES * Corporate : $195 ($245 after May 16th) * Academic : $170 ($220 after May 16th) * Student : $145 ($195 after May 16th) SPEAKERS & ABSTRACTS WANTED The program committee is currently seeking abstracts for talks at BOSC 2005. BOSC is a great opportunity for you to tell the community about your use, development, or philosophy of open source software development in bioinformatics. The committee will select several submitted abstracts for 25-minute talks and others for shorter "lightning" talks. Accepted abstracts will be published on the BOSC web site. If you are interested in speaking at BOSC 2005, please send us before April 26, 2005: * an abstract (no more than a few paragraphs) * a URL for the project page, if applicable * information about the open source license used for your software or your release plans. Abstracts will be accepted for submission until April 26, 2005. Abstracts chosen for presentation will be announced May 12, 2005 (before the ISMB Early Registration Deadline). LIGHTNING-TALK SPEAKERS WANTED! The program committee is currently seeking speakers for the lightning talks at BOSC 2005. Lightning talks are quick - only five minutes long - and a great opportunity for you to give people a quick summary of your open source project, code, idea, or vision of the future. If you are interested in giving a lightning talk at BOSC 2005, please send us: * a brief title and summary (one or two lines) * a URL for the project page, if applicable * information about the open source license used for your software or your release plans. We will accept entries on-line until BOSC starts, but space for demos and lightning talks is limited.
From senger at ebi.ac.uk Tue Apr 19 13:34:09 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 19 Apr 2005 14:34:09 +0100 (BST) Subject: [MOBY-dev] jMoby - java 1.5 In-Reply-To: Message-ID: Dear jMoby developers, Eddie and me, we have updated Ant's build.xml file in order to be able to add to jMoby also Java sources that needs to be compiled with the latest Java 1.5 - but still let the others work with Java 1.4 as usual. Here is how to do it (please comment if you need any more assistance, or if you disagree with our approach): * First to say is that it was put there as a workaround for those who really needs to use 1.5. Any new class that needs 1.5 must be exlicitely named in the build.xml file. Which is not too suitable if you have many such classes. So when you start to use Java 1.5. in greater scale we need to re-factor it. Let me know. * Having said that please note that nothing prevents you to use Java 1.5 to compile all classes. That should work fine (with perhaps few semantic warnings which I am sure the authors, including me, will take care of sooner or later). The previous (and the next) bullets are for those *adding* sources that can be compiled *only* with Java 1.5 (an example is the Eddie's class org.biomoby.shared.MobyObjectDecompositionImpl.java). * If you are using regular javac compiler you do not need to do anything special. The Ant will sniff around and find what java version you are using and depending on the result it will compile always all classes not mentioned as specific for 1.5, and then - only if you have java 1.5 - it compiles additionally those new bastards. Which means that when you are using java 1.4, the new (Eddie's) classes will not compiled so you will not be able to use them. But that's obvious - you cannot shop with the old Deutches Marks anymore without having new Euros, can you? * If you are using jikes (which I strongly recommend because it is much much faster compiler, but that's another story) and have Java 1.4 on your path, again nothing needs to be done. However, if you are using jikes (latest version is 1.22) *and* have java 1.5 on your path, jikes will try to compile also the new (Eddie's) classes and fails. I do not exactly why (let me know if you know). So for this case you need to instruct Ant that - eventhough the java 1.5 is available - you do not want it. Do it with by setting property java.latest.version to false. Either (recommended) put the line: java.latest.version = false in your build.property files, or use it on the Ant's command line: ./build-dev.sh -Djava.latest.version=false compile With regard, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From ywong at infobiogen.fr Wed Apr 20 08:53:38 2005 From: ywong at infobiogen.fr (Yan Wong) Date: Wed, 20 Apr 2005 10:53:38 +0200 Subject: [MOBY-dev] Updates on the bioMoby Python API Message-ID: <42661892.9030809@infobiogen.fr> Hi, I've put two classes SQLDispatcher and SQLInvocator in the API in order to ease the build of DB based webservices An example can be found in the tutorials directory Cheers Yan