From ap3 at sanger.ac.uk Sun Sep 2 06:02:47 2007 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Sun, 2 Sep 2007 11:02:47 +0100 Subject: [Biojava-dev] cruisecontrol In-Reply-To: <93b45ca50708281716x3c2cadc9me9cb0b00b52647a2@mail.gmail.com> References: <93b45ca50708281716x3c2cadc9me9cb0b00b52647a2@mail.gmail.com> Message-ID: Hi, CruiseControl is now running at http://www.spice-3d.org/cruise/ it does: * trigger a new build 20 minutes after a new commit to CVS * run the junit tests * build the javadocs * provide the latest biojava.jar for download * send a notification email if something goes wrong (and only then) to this list This basically works with a chain of ant scripts that are triggered by CruiseControl, so it is easy to add other functionality / exchange CVS with subversion, etc. Andreas On 29 Aug 2007, at 01:16, Mark Schreiber wrote: > Sounds good. > > Thomas had a script running off his home machine a while ago for > nightly builds which I have missed since he stopped running it. > > Notifications of failed tests would be good too. > > - Mark > > On 8/28/07, Andreas Prlic wrote: >> Hi biojava - devs, >> >> would you be interested in getting CruiseControl running for BioJava? >> >> It would allow us to >> >> * provide nightly builds of biojava, >> * run unit test in regular intervals, >> * get a notification email sent to biojava-dev if the CVS does not >> build >> >> http://cruisecontrol.sourceforge.net/ >> >> If there is interest for this I will set it up, >> >> Andreas >> >> --------------------------------------------------------------------- >> -- >> >> Andreas Prlic Wellcome Trust Sanger Institute >> Hinxton, Cambridge CB10 1SA, UK >> +44 (0) 1223 49 6891 >> >> --------------------------------------------------------------------- >> -- >> >> >> >> -- >> The Wellcome Trust Sanger Institute is operated by Genome Research >> Limited, a charity registered in England with number 1021457 and a >> company registered in England with number 2742969, whose registered >> office is 215 Euston Road, London, NW1 2BE. >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> ----------------------------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK +44 (0) 1223 49 6891 ----------------------------------------------------------------------- -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From holland at ebi.ac.uk Mon Sep 3 03:42:10 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Mon, 03 Sep 2007 08:42:10 +0100 Subject: [Biojava-dev] cruisecontrol In-Reply-To: References: <93b45ca50708281716x3c2cadc9me9cb0b00b52647a2@mail.gmail.com> Message-ID: <46DBBAD2.3040900@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 that's really cool. is there any way of integrating it into the open-bio servers that the rest of BioJava lives on? Andreas Prlic wrote: > Hi, > > CruiseControl is now running at > > http://www.spice-3d.org/cruise/ > > it does: > * trigger a new build 20 minutes after a new commit to CVS > * run the junit tests > * build the javadocs > * provide the latest biojava.jar for download > * send a notification email if something goes wrong (and only then) > to this list > > This basically works with a chain of ant scripts that are triggered > by CruiseControl, > so it is easy to add other functionality / exchange CVS with > subversion, etc. > > Andreas > > > > On 29 Aug 2007, at 01:16, Mark Schreiber wrote: > >> Sounds good. >> >> Thomas had a script running off his home machine a while ago for >> nightly builds which I have missed since he stopped running it. >> >> Notifications of failed tests would be good too. >> >> - Mark >> >> On 8/28/07, Andreas Prlic wrote: >>> Hi biojava - devs, >>> >>> would you be interested in getting CruiseControl running for BioJava? >>> >>> It would allow us to >>> >>> * provide nightly builds of biojava, >>> * run unit test in regular intervals, >>> * get a notification email sent to biojava-dev if the CVS does not >>> build >>> >>> http://cruisecontrol.sourceforge.net/ >>> >>> If there is interest for this I will set it up, >>> >>> Andreas >>> >>> --------------------------------------------------------------------- >>> -- >>> >>> Andreas Prlic Wellcome Trust Sanger Institute >>> Hinxton, Cambridge CB10 1SA, UK >>> +44 (0) 1223 49 6891 >>> >>> --------------------------------------------------------------------- >>> -- >>> >>> >>> >>> -- >>> The Wellcome Trust Sanger Institute is operated by Genome Research >>> Limited, a charity registered in England with number 1021457 and a >>> company registered in England with number 2742969, whose registered >>> office is 215 Euston Road, London, NW1 2BE. >>> _______________________________________________ >>> biojava-dev mailing list >>> biojava-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >>> > > ----------------------------------------------------------------------- > > Andreas Prlic Wellcome Trust Sanger Institute > Hinxton, Cambridge CB10 1SA, UK > +44 (0) 1223 49 6891 > > ----------------------------------------------------------------------- > > > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFG27rS4C5LeMEKA/QRAvpaAJ0f7bC3OeMoqGUGPiQ2zX9YTfq/2ACcCKWu qo+/SvcrG0a5Ycf9H1XmSsY= =CR4f -----END PGP SIGNATURE----- From ap3 at sanger.ac.uk Mon Sep 3 09:15:35 2007 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Mon, 3 Sep 2007 14:15:35 +0100 Subject: [Biojava-dev] cruisecontrol In-Reply-To: <46DBBAD2.3040900@ebi.ac.uk> References: <93b45ca50708281716x3c2cadc9me9cb0b00b52647a2@mail.gmail.com> <46DBBAD2.3040900@ebi.ac.uk> Message-ID: <948C3625-6C4B-4D9B-A739-980579CC12D9@sanger.ac.uk> > is there any way of integrating it into the open-bio servers that the > rest of BioJava lives on? the simples way is to link to it, Another possibility is to run it directly on the open-bio servers, but I do not have any admin permissions to set this up. Andreas ----------------------------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK +44 (0) 1223 49 6891 ----------------------------------------------------------------------- -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From bugzilla-daemon at portal.open-bio.org Thu Sep 6 10:11:26 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 6 Sep 2007 10:11:26 -0400 Subject: [Biojava-dev] [Bug 2330] DP/ Profile HMM bug In-Reply-To: Message-ID: <200709061411.l86EBQbm011955@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2330 mark.schreiber at novartis.com changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #1 from mark.schreiber at novartis.com 2007-09-06 10:11 EST ------- Added change listener to LinearAlphabetIndex so that it rebuilds as Symbols are added and removed from the Alphabet. Interesting SimpleAlphabet was not emitting a ChangeEvent when removing Symbols, this is fixed now. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Sat Sep 8 19:02:38 2007 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Sat, 8 Sep 2007 19:02:38 -0400 Subject: [Biojava-dev] [Bug 2359] New: SingleDP deserialization fails Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2359 Summary: SingleDP deserialization fails Product: BioJava Version: 1.5 Platform: PC OS/Version: Linux Status: NEW Severity: major Priority: P2 Component: dist/dp AssignedTo: biojava-dev at biojava.org ReportedBy: daniel.rohrbach at web.de it isn't possible to load an instance of SingleDP via serialization. SingleDP which is serializable inherits from DP which is not serializable . Loading the Object works well. I used biojava 1.5 latest build 9/8/07 2:22 AM but the same exception occurs in all 1.5 the reason for the bug is that SingleDP extends DP which is not serializable. In that case it must implement a no args constructor but it doesn't! Because of that the same should occur for PairwiseDP the stack trace: java.io.InvalidClassException: org.biojava.bio.dp.onehead.SingleDP; org.biojava.bio.dp.onehead.SingleDP; no valid constructor at java.io.ObjectStreamClass.checkDeserialize(ObjectStreamClass.java:713) at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1733) at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1329) at java.io.ObjectInputStream.readObject(ObjectInputStream.java:351) at biojavabugs.SingleDBBug.main(SingleDBBug.java:92) Caused by: java.io.InvalidClassException: org.biojava.bio.dp.onehead.SingleDP; no valid constructor at java.io.ObjectStreamClass.(ObjectStreamClass.java:471) at java.io.ObjectStreamClass.lookup(ObjectStreamClass.java:310) and the code i used to cause the bug: //create the HMM ProfileHMM hmm = new ProfileHMM(ProteinTools.getAlphabet(), 12, DistributionFactory.DEFAULT, DistributionFactory.DEFAULT, "biojava profile hmm"); //create an SingleDP object which we want to save and load DP dp = (SingleDP) DPFactory.DEFAULT.createDP(hmm); try { // // saving // // the filename File load = new File("/home/dani/Desktop/dp"); FilePermission fp = new FilePermission(load.getAbsolutePath(), "write"); if(!load.createNewFile()) { throw new IOException("file '" + load.getAbsolutePath() + "' could not be created!"); } FileOutputStream fos = new FileOutputStream(load); ObjectOutputStream oos = new ObjectOutputStream(fos); //store object to disk oos.writeObject(dp); oos.close(); // // loading // // try to load the SingleDP object fp = new FilePermission( load.getAbsolutePath(), "read"); FileInputStream fis = new FileInputStream(load); ObjectInputStream ois = new ObjectInputStream(fis); Vector