From martin.senger at gmail.com Wed Sep 1 04:29:05 2010 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 1 Sep 2010 11:29:05 +0300 Subject: [MOBY-dev] =?iso-8859-1?q?Fwd=3A_Security_Settings_Violations/Vio?= =?iso-8859-1?q?lation_des_r=E8gles_de_s=E9curit=E9s?= In-Reply-To: <4C7E0369.3060400@cirad.fr> References: <201008311451.o7VEpFkm031707@bessin.cirad.fr> <4C7E0369.3060400@cirad.fr> Message-ID: > Having a look at the Moby Dashboard, we couldn't find a registry that > contains both types GCP_SimpleIdentifierWithTypeOperatorAndCount and > GCP_GenomicFeatureVariant. Even stranger, GCP_GenomicFeatureVariant is > missing from IRRI registry whereas it contains a service named > GetTropgeneAlleleV2 (in tropgenedb.cirad.fr) that actually uses that > datatype as output... > A simple answer is that, probably, the IRRI registry is not in the best shape. From the beginning, and by its nature (I would say) the BioMoby project had two (at least) parts: one part are services and one part are the registries of services. And these two parts do not need necessarily be synchronized. One can run a service that is not registered, at all. But some software clients expect this synchronization to happen - and the software using the jar file you are looking for (a jar file with Java classes represented known BioMoby data types) is one of them. The best way out is to update IRRI (or whatever) registry by the missing data types, I would suggest. Martin -- Martin Senger email: martin.senger at gmail.com,martin.senger at kaust.edu.sa skype: martinsenger From py at pingoured.fr Thu Sep 9 10:56:16 2010 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Thu, 09 Sep 2010 16:56:16 +0200 Subject: [MOBY-dev] CVS time out Message-ID: <1284044176.3506.91.camel@lab.localdomain> Dear all, I running into: $ cvs update cvs [update aborted]: connect to [cvs.open-bio.org]:2401 failed: Connection timed out Am I the only one ? Thanks, Pierre From edward.kawas at gmail.com Thu Sep 9 11:04:48 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 9 Sep 2010 08:04:48 -0700 Subject: [MOBY-dev] CVS time out In-Reply-To: <1284044176.3506.91.camel@lab.localdomain> References: <1284044176.3506.91.camel@lab.localdomain> Message-ID: <001001cb5030$59a578e0$0cf06aa0$@gmail.com> I just did an update and had no problems... Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon > Sent: Thursday, September 09, 2010 7:56 AM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] CVS time out > > Dear all, > > I running into: > $ cvs update > cvs [update aborted]: connect to [cvs.open-bio.org]:2401 failed: > Connection timed out > > Am I the only one ? > > Thanks, > > Pierre > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From Sebastien.Carrere at toulouse.inra.fr Thu Sep 9 11:15:20 2010 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Thu, 09 Sep 2010 17:15:20 +0200 Subject: [MOBY-dev] CVS time out In-Reply-To: <001001cb5030$59a578e0$0cf06aa0$@gmail.com> References: <1284044176.3506.91.camel@lab.localdomain> <001001cb5030$59a578e0$0cf06aa0$@gmail.com> Message-ID: <4C88FA08.2030006@toulouse.inra.fr> Bonjour, same problem from Toulouse: cvs [update aborted]: connect to cvs.open-bio.org(66.92.69.19):2401 failed: Connection timed out Sebastien On 09/09/2010 17:04, Edward Kawas wrote: > I just did an update and had no problems... > > Eddie > > >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- >> bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon >> Sent: Thursday, September 09, 2010 7:56 AM >> To: moby-dev at lists.open-bio.org >> Subject: [MOBY-dev] CVS time out >> >> Dear all, >> >> I running into: >> $ cvs update >> cvs [update aborted]: connect to [cvs.open-bio.org]:2401 failed: >> Connection timed out >> >> Am I the only one ? >> >> Thanks, >> >> Pierre >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From markw at illuminae.com Thu Sep 9 11:30:59 2010 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 09 Sep 2010 08:30:59 -0700 Subject: [MOBY-dev] CVS time out In-Reply-To: <4C88FA08.2030006@toulouse.inra.fr> References: <1284044176.3506.91.camel@lab.localdomain> <001001cb5030$59a578e0$0cf06aa0$@gmail.com> <4C88FA08.2030006@toulouse.inra.fr> Message-ID: I have the same problem from here at the hospital. I'll check with the open-bio roots and see what's up. Thanks for letting us know! Mark On Thu, 09 Sep 2010 08:15:20 -0700, Sebastien Carrere wrote: > Bonjour, > > same problem from Toulouse: > > cvs [update aborted]: connect to cvs.open-bio.org(66.92.69.19):2401 > failed: Connection timed out > > Sebastien > > On 09/09/2010 17:04, Edward Kawas wrote: >> I just did an update and had no problems... >> >> Eddie >> >> >>> -----Original Message----- >>> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- >>> bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon >>> Sent: Thursday, September 09, 2010 7:56 AM >>> To: moby-dev at lists.open-bio.org >>> Subject: [MOBY-dev] CVS time out >>> >>> Dear all, >>> >>> I running into: >>> $ cvs update >>> cvs [update aborted]: connect to [cvs.open-bio.org]:2401 failed: >>> Connection timed out >>> >>> Am I the only one ? >>> >>> Thanks, >>> >>> Pierre >>> >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > -- -- Dr. Mark Wilkinson Assistant Professor, Medical Genetics PI Bioinformatics, Heart + Lung Institute St. Paul's Hospital/UBC Vancouver, BC, Canada From edward.kawas at gmail.com Thu Sep 9 12:17:14 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 9 Sep 2010 09:17:14 -0700 Subject: [MOBY-dev] CVS time out In-Reply-To: References: <1284044176.3506.91.camel@lab.localdomain> <001001cb5030$59a578e0$0cf06aa0$@gmail.com> <4C88FA08.2030006@toulouse.inra.fr> Message-ID: <004401cb503a$77a8fd80$66faf880$@gmail.com> This is strange, because I have been doing cvs updates, a single commit, creating tags and have yet to time out. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Mark Wilkinson > Sent: Thursday, September 09, 2010 8:31 AM > To: moby-dev at lists.open-bio.org; Sebastien Carrere > Subject: Re: [MOBY-dev] CVS time out > > I have the same problem from here at the hospital. I'll check with the open- > bio roots and see what's up. > > Thanks for letting us know! > > Mark > > > > > > On Thu, 09 Sep 2010 08:15:20 -0700, Sebastien Carrere > wrote: > > > Bonjour, > > > > same problem from Toulouse: > > > > cvs [update aborted]: connect to cvs.open-bio.org(66.92.69.19):2401 > > failed: Connection timed out > > > > Sebastien > > > > On 09/09/2010 17:04, Edward Kawas wrote: > >> I just did an update and had no problems... > >> > >> Eddie > >> > >> > >>> -----Original Message----- > >>> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > >>> bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon > >>> Sent: Thursday, September 09, 2010 7:56 AM > >>> To: moby-dev at lists.open-bio.org > >>> Subject: [MOBY-dev] CVS time out > >>> > >>> Dear all, > >>> > >>> I running into: > >>> $ cvs update > >>> cvs [update aborted]: connect to [cvs.open-bio.org]:2401 failed: > >>> Connection timed out > >>> > >>> Am I the only one ? > >>> > >>> Thanks, > >>> > >>> Pierre > >>> > >>> _______________________________________________ > >>> MOBY-dev mailing list > >>> MOBY-dev at lists.open-bio.org > >>> http://lists.open-bio.org/mailman/listinfo/moby-dev > >>> > >> _______________________________________________ > >> MOBY-dev mailing list > >> MOBY-dev at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/moby-dev > >> > > > > > -- > -- > Dr. Mark Wilkinson > Assistant Professor, Medical Genetics > PI Bioinformatics, Heart + Lung Institute St. Paul's Hospital/UBC Vancouver, > BC, Canada _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Thu Sep 9 12:19:07 2010 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 09 Sep 2010 09:19:07 -0700 Subject: [MOBY-dev] CVS time out In-Reply-To: <004401cb503a$77a8fd80$66faf880$@gmail.com> References: <1284044176.3506.91.camel@lab.localdomain> <001001cb5030$59a578e0$0cf06aa0$@gmail.com> <4C88FA08.2030006@toulouse.inra.fr> <004401cb503a$77a8fd80$66faf880$@gmail.com> Message-ID: You're not using the ANONYMOUS cvs, are you? (not if you're doing commits! LOL!) M On Thu, 09 Sep 2010 09:17:14 -0700, Edward Kawas wrote: > This is strange, because I have been doing cvs updates, a single commit, > creating tags and have yet to time out. > > Eddie > >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- >> bounces at lists.open-bio.org] On Behalf Of Mark Wilkinson >> Sent: Thursday, September 09, 2010 8:31 AM >> To: moby-dev at lists.open-bio.org; Sebastien Carrere >> Subject: Re: [MOBY-dev] CVS time out >> >> I have the same problem from here at the hospital. I'll check with the > open- >> bio roots and see what's up. >> >> Thanks for letting us know! >> >> Mark >> >> >> >> >> >> On Thu, 09 Sep 2010 08:15:20 -0700, Sebastien Carrere >> wrote: >> >> > Bonjour, >> > >> > same problem from Toulouse: >> > >> > cvs [update aborted]: connect to cvs.open-bio.org(66.92.69.19):2401 >> > failed: Connection timed out >> > >> > Sebastien >> > >> > On 09/09/2010 17:04, Edward Kawas wrote: >> >> I just did an update and had no problems... >> >> >> >> Eddie >> >> >> >> >> >>> -----Original Message----- >> >>> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- >> >>> bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon >> >>> Sent: Thursday, September 09, 2010 7:56 AM >> >>> To: moby-dev at lists.open-bio.org >> >>> Subject: [MOBY-dev] CVS time out >> >>> >> >>> Dear all, >> >>> >> >>> I running into: >> >>> $ cvs update >> >>> cvs [update aborted]: connect to [cvs.open-bio.org]:2401 failed: >> >>> Connection timed out >> >>> >> >>> Am I the only one ? >> >>> >> >>> Thanks, >> >>> >> >>> Pierre >> >>> >> >>> _______________________________________________ >> >>> MOBY-dev mailing list >> >>> MOBY-dev at lists.open-bio.org >> >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >>> >> >> _______________________________________________ >> >> MOBY-dev mailing list >> >> MOBY-dev at lists.open-bio.org >> >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> >> > >> >> >> -- >> -- >> Dr. Mark Wilkinson >> Assistant Professor, Medical Genetics >> PI Bioinformatics, Heart + Lung Institute St. Paul's Hospital/UBC > Vancouver, >> BC, Canada _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- -- Dr. Mark Wilkinson Assistant Professor, Medical Genetics PI Bioinformatics, Heart + Lung Institute St. Paul's Hospital/UBC Vancouver, BC, Canada From py at pingoured.fr Fri Sep 10 03:02:21 2010 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Fri, 10 Sep 2010 09:02:21 +0200 Subject: [MOBY-dev] CVS time out In-Reply-To: References: <1284044176.3506.91.camel@lab.localdomain> <001001cb5030$59a578e0$0cf06aa0$@gmail.com> <4C88FA08.2030006@toulouse.inra.fr> Message-ID: <1284102141.10973.0.camel@lab.localdomain> I just ran a cvs update (as anonymous) and it seems to be back. Thanks, Pierre On Thu, 2010-09-09 at 08:30 -0700, Mark Wilkinson wrote: > I have the same problem from here at the hospital. I'll check with the > open-bio roots and see what's up. > > Thanks for letting us know! > > Mark > > > > > > On Thu, 09 Sep 2010 08:15:20 -0700, Sebastien Carrere > wrote: > > > Bonjour, > > > > same problem from Toulouse: > > > > cvs [update aborted]: connect to cvs.open-bio.org(66.92.69.19):2401 > > failed: Connection timed out > > > > Sebastien > > > > On 09/09/2010 17:04, Edward Kawas wrote: > >> I just did an update and had no problems... > >> > >> Eddie > >> > >> > >>> -----Original Message----- > >>> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > >>> bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon > >>> Sent: Thursday, September 09, 2010 7:56 AM > >>> To: moby-dev at lists.open-bio.org > >>> Subject: [MOBY-dev] CVS time out > >>> > >>> Dear all, > >>> > >>> I running into: > >>> $ cvs update > >>> cvs [update aborted]: connect to [cvs.open-bio.org]:2401 failed: > >>> Connection timed out > >>> > >>> Am I the only one ? > >>> > >>> Thanks, > >>> > >>> Pierre > >>> > >>> _______________________________________________ > >>> MOBY-dev mailing list > >>> MOBY-dev at lists.open-bio.org > >>> http://lists.open-bio.org/mailman/listinfo/moby-dev > >>> > >> _______________________________________________ > >> MOBY-dev mailing list > >> MOBY-dev at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/moby-dev > >> > > > > From r.biczok at dkfz-heidelberg.de Tue Sep 28 06:01:27 2010 From: r.biczok at dkfz-heidelberg.de (Biczok Rudolf) Date: Tue, 28 Sep 2010 12:01:27 +0200 Subject: [MOBY-dev] CVS can't create temporary directory Message-ID: <4F91222C659D5B4E8C89CE4D710BB08E4AEC86BBCD@DKFZEX01.ad.dkfz-heidelberg.de> Good Morning, I have just a little problem with checking out from the BioMOBY CVS. Today I tried it on two clients, and both gave me the following error while looking through the repository: > $ cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby co -P moby-live > $ can't create temporary directory /tmp/cvs-serv16061 > $ Read-only file system So maybe it's a server-site error or I'm dumb. Best wishes, Rudolf Rudolf Biczok Molecular Genome Analysis Mobile Phone : +49 171 6289148 Phone: +49 (0) 6221 42 4711 Deutsches Krebsforschungszentrum Im Neuenheimer Feld 280 D-69120 Heidelberg [cid:image002.png at 01CB5F04.E1373270] -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.png Type: image/png Size: 12782 bytes Desc: image002.png URL: From martin.senger at gmail.com Tue Sep 28 07:15:08 2010 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 28 Sep 2010 14:15:08 +0300 Subject: [MOBY-dev] CVS can't create temporary directory In-Reply-To: <4F91222C659D5B4E8C89CE4D710BB08E4AEC86BBCD@DKFZEX01.ad.dkfz-heidelberg.de> References: <4F91222C659D5B4E8C89CE4D710BB08E4AEC86BBCD@DKFZEX01.ad.dkfz-heidelberg.de> Message-ID: Yes, according to my knowledge it is, indeed, a server-site problem. I am cc-ing your email to Chris who can fix it I believe. Thanks, Chris. Martin On Tue, Sep 28, 2010 at 1:01 PM, Biczok Rudolf wrote: > Good Morning, > > I have just a little problem with checking out from the BioMOBY CVS. > > Today I tried it on two clients, and both gave me the following error while > looking through > the repository: > > > $ cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby co -P > moby-live > > $ can't create temporary directory /tmp/cvs-serv16061 > > $ Read-only file system > > So maybe it's a server-site error or I'm dumb. > > Best wishes, > Rudolf > > > Rudolf Biczok > Molecular Genome Analysis > Mobile Phone : +49 171 6289148 > Phone: +49 (0) 6221 42 4711 > > Deutsches Krebsforschungszentrum > Im Neuenheimer Feld 280 > D-69120 Heidelberg > > [cid:image002.png at 01CB5F04.E1373270] > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > -- Martin Senger email: martin.senger at gmail.com,martin.senger at kaust.edu.sa skype: martinsenger From dag at sonsorol.org Tue Sep 28 10:49:35 2010 From: dag at sonsorol.org (Chris Dagdigian) Date: Tue, 28 Sep 2010 10:49:35 -0400 Subject: [MOBY-dev] CVS can't create temporary directory In-Reply-To: References: <4F91222C659D5B4E8C89CE4D710BB08E4AEC86BBCD@DKFZEX01.ad.dkfz-heidelberg.de> Message-ID: <4CA2007F.1070109@sonsorol.org> Fixed. Filesystem corruption within the VM. -Chris Martin Senger wrote: > Yes, according to my knowledge it is, indeed, a server-site problem. I > am cc-ing your email to Chris who can fix it I believe. Thanks, Chris. > > Martin > > On Tue, Sep 28, 2010 at 1:01 PM, Biczok Rudolf > > wrote: > > Good Morning, > > I have just a little problem with checking out from the BioMOBY CVS. > > Today I tried it on two clients, and both gave me the following > error while looking through > the repository: > > > $ cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby co > -P moby-live > > $ can't create temporary directory /tmp/cvs-serv16061 > > $ Read-only file system > > So maybe it's a server-site error or I'm dumb. > > Best wishes, > Rudolf > > > Rudolf Biczok > Molecular Genome Analysis > Mobile Phone : +49 171 6289148 > Phone: +49 (0) 6221 42 4711 > > Deutsches Krebsforschungszentrum > Im Neuenheimer Feld 280 > D-69120 Heidelberg > > [cid:image002.png at 01CB5F04.E1373270] > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > > > -- > Martin Senger > email: martin.senger at gmail.com > ,martin.senger at kaust.edu.sa > > skype: martinsenger From markw at illuminae.com Tue Sep 28 10:58:11 2010 From: markw at illuminae.com (Mark) Date: Tue, 28 Sep 2010 07:58:11 -0700 Subject: [MOBY-dev] CVS can't create temporary directory In-Reply-To: <4CA2007F.1070109@sonsorol.org> References: <4F91222C659D5B4E8C89CE4D710BB08E4AEC86BBCD@DKFZEX01.ad.dkfz-heidelberg.de> <4CA2007F.1070109@sonsorol.org> Message-ID: wow! Problem identified and solved before I even woke up :-) thanks Chris! M On Tue, 28 Sep 2010 07:49:35 -0700, Chris Dagdigian wrote: > > Fixed. Filesystem corruption within the VM. > > -Chris From r.biczok at Dkfz-Heidelberg.de Wed Sep 29 09:38:51 2010 From: r.biczok at Dkfz-Heidelberg.de (Biczok Rudolf) Date: Wed, 29 Sep 2010 15:38:51 +0200 Subject: [MOBY-dev] CVS can't create temporary directory In-Reply-To: References: <4F91222C659D5B4E8C89CE4D710BB08E4AEC86BBCD@DKFZEX01.ad.dkfz-heidelberg.de> <4CA2007F.1070109@sonsorol.org> Message-ID: <4F91222C659D5B4E8C89CE4D710BB08E4AEC86BBF5@DKFZEX01.ad.dkfz-heidelberg.de> Hello, year, that solved it thanks. I?m not sure but I can't find the maven artifact "jdic:jdic:1.0" in any known maven repository. Why that matters? Because the initmaven task in JMoby's build.xml prints the following when I run "ant install" command: ... [artifact:dependencies] Downloading: jdic/jdic/1.0/jdic-1.0.pom from kysoh [artifact:dependencies] Transferring 0K from kysoh [artifact:dependencies] [WARNING] *** CHECKSUM FAILED - Checksum failed on download: local = 'f9c9151b31e92b90e5adc3852ca1bde4716d8e50'; remote = ' 302 Found

Found

The document has moved here.

Well removing the dependency from the project.pom solved that for me. Best whishes Rudolf Biczok -----Urspr?ngliche Nachricht----- Von: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] Im Auftrag von Mark Gesendet: Dienstag, 28. September 2010 16:58 An: Martin Senger; Chris Dagdigian; Core developer announcements Betreff: Re: [MOBY-dev] CVS can't create temporary directory wow! Problem identified and solved before I even woke up :-) thanks Chris! M On Tue, 28 Sep 2010 07:49:35 -0700, Chris Dagdigian wrote: > > Fixed. Filesystem corruption within the VM. > > -Chris _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From martin.senger at gmail.com Wed Sep 1 08:29:05 2010 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 1 Sep 2010 11:29:05 +0300 Subject: [MOBY-dev] =?iso-8859-1?q?Fwd=3A_Security_Settings_Violations/Vio?= =?iso-8859-1?q?lation_des_r=E8gles_de_s=E9curit=E9s?= In-Reply-To: <4C7E0369.3060400@cirad.fr> References: <201008311451.o7VEpFkm031707@bessin.cirad.fr> <4C7E0369.3060400@cirad.fr> Message-ID: > Having a look at the Moby Dashboard, we couldn't find a registry that > contains both types GCP_SimpleIdentifierWithTypeOperatorAndCount and > GCP_GenomicFeatureVariant. Even stranger, GCP_GenomicFeatureVariant is > missing from IRRI registry whereas it contains a service named > GetTropgeneAlleleV2 (in tropgenedb.cirad.fr) that actually uses that > datatype as output... > A simple answer is that, probably, the IRRI registry is not in the best shape. From the beginning, and by its nature (I would say) the BioMoby project had two (at least) parts: one part are services and one part are the registries of services. And these two parts do not need necessarily be synchronized. One can run a service that is not registered, at all. But some software clients expect this synchronization to happen - and the software using the jar file you are looking for (a jar file with Java classes represented known BioMoby data types) is one of them. The best way out is to update IRRI (or whatever) registry by the missing data types, I would suggest. Martin -- Martin Senger email: martin.senger at gmail.com,martin.senger at kaust.edu.sa skype: martinsenger From py at pingoured.fr Thu Sep 9 14:56:16 2010 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Thu, 09 Sep 2010 16:56:16 +0200 Subject: [MOBY-dev] CVS time out Message-ID: <1284044176.3506.91.camel@lab.localdomain> Dear all, I running into: $ cvs update cvs [update aborted]: connect to [cvs.open-bio.org]:2401 failed: Connection timed out Am I the only one ? Thanks, Pierre From edward.kawas at gmail.com Thu Sep 9 15:04:48 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 9 Sep 2010 08:04:48 -0700 Subject: [MOBY-dev] CVS time out In-Reply-To: <1284044176.3506.91.camel@lab.localdomain> References: <1284044176.3506.91.camel@lab.localdomain> Message-ID: <001001cb5030$59a578e0$0cf06aa0$@gmail.com> I just did an update and had no problems... Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon > Sent: Thursday, September 09, 2010 7:56 AM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] CVS time out > > Dear all, > > I running into: > $ cvs update > cvs [update aborted]: connect to [cvs.open-bio.org]:2401 failed: > Connection timed out > > Am I the only one ? > > Thanks, > > Pierre > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From Sebastien.Carrere at toulouse.inra.fr Thu Sep 9 15:15:20 2010 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Thu, 09 Sep 2010 17:15:20 +0200 Subject: [MOBY-dev] CVS time out In-Reply-To: <001001cb5030$59a578e0$0cf06aa0$@gmail.com> References: <1284044176.3506.91.camel@lab.localdomain> <001001cb5030$59a578e0$0cf06aa0$@gmail.com> Message-ID: <4C88FA08.2030006@toulouse.inra.fr> Bonjour, same problem from Toulouse: cvs [update aborted]: connect to cvs.open-bio.org(66.92.69.19):2401 failed: Connection timed out Sebastien On 09/09/2010 17:04, Edward Kawas wrote: > I just did an update and had no problems... > > Eddie > > >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- >> bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon >> Sent: Thursday, September 09, 2010 7:56 AM >> To: moby-dev at lists.open-bio.org >> Subject: [MOBY-dev] CVS time out >> >> Dear all, >> >> I running into: >> $ cvs update >> cvs [update aborted]: connect to [cvs.open-bio.org]:2401 failed: >> Connection timed out >> >> Am I the only one ? >> >> Thanks, >> >> Pierre >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From markw at illuminae.com Thu Sep 9 15:30:59 2010 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 09 Sep 2010 08:30:59 -0700 Subject: [MOBY-dev] CVS time out In-Reply-To: <4C88FA08.2030006@toulouse.inra.fr> References: <1284044176.3506.91.camel@lab.localdomain> <001001cb5030$59a578e0$0cf06aa0$@gmail.com> <4C88FA08.2030006@toulouse.inra.fr> Message-ID: I have the same problem from here at the hospital. I'll check with the open-bio roots and see what's up. Thanks for letting us know! Mark On Thu, 09 Sep 2010 08:15:20 -0700, Sebastien Carrere wrote: > Bonjour, > > same problem from Toulouse: > > cvs [update aborted]: connect to cvs.open-bio.org(66.92.69.19):2401 > failed: Connection timed out > > Sebastien > > On 09/09/2010 17:04, Edward Kawas wrote: >> I just did an update and had no problems... >> >> Eddie >> >> >>> -----Original Message----- >>> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- >>> bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon >>> Sent: Thursday, September 09, 2010 7:56 AM >>> To: moby-dev at lists.open-bio.org >>> Subject: [MOBY-dev] CVS time out >>> >>> Dear all, >>> >>> I running into: >>> $ cvs update >>> cvs [update aborted]: connect to [cvs.open-bio.org]:2401 failed: >>> Connection timed out >>> >>> Am I the only one ? >>> >>> Thanks, >>> >>> Pierre >>> >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > -- -- Dr. Mark Wilkinson Assistant Professor, Medical Genetics PI Bioinformatics, Heart + Lung Institute St. Paul's Hospital/UBC Vancouver, BC, Canada From edward.kawas at gmail.com Thu Sep 9 16:17:14 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 9 Sep 2010 09:17:14 -0700 Subject: [MOBY-dev] CVS time out In-Reply-To: References: <1284044176.3506.91.camel@lab.localdomain> <001001cb5030$59a578e0$0cf06aa0$@gmail.com> <4C88FA08.2030006@toulouse.inra.fr> Message-ID: <004401cb503a$77a8fd80$66faf880$@gmail.com> This is strange, because I have been doing cvs updates, a single commit, creating tags and have yet to time out. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Mark Wilkinson > Sent: Thursday, September 09, 2010 8:31 AM > To: moby-dev at lists.open-bio.org; Sebastien Carrere > Subject: Re: [MOBY-dev] CVS time out > > I have the same problem from here at the hospital. I'll check with the open- > bio roots and see what's up. > > Thanks for letting us know! > > Mark > > > > > > On Thu, 09 Sep 2010 08:15:20 -0700, Sebastien Carrere > wrote: > > > Bonjour, > > > > same problem from Toulouse: > > > > cvs [update aborted]: connect to cvs.open-bio.org(66.92.69.19):2401 > > failed: Connection timed out > > > > Sebastien > > > > On 09/09/2010 17:04, Edward Kawas wrote: > >> I just did an update and had no problems... > >> > >> Eddie > >> > >> > >>> -----Original Message----- > >>> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > >>> bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon > >>> Sent: Thursday, September 09, 2010 7:56 AM > >>> To: moby-dev at lists.open-bio.org > >>> Subject: [MOBY-dev] CVS time out > >>> > >>> Dear all, > >>> > >>> I running into: > >>> $ cvs update > >>> cvs [update aborted]: connect to [cvs.open-bio.org]:2401 failed: > >>> Connection timed out > >>> > >>> Am I the only one ? > >>> > >>> Thanks, > >>> > >>> Pierre > >>> > >>> _______________________________________________ > >>> MOBY-dev mailing list > >>> MOBY-dev at lists.open-bio.org > >>> http://lists.open-bio.org/mailman/listinfo/moby-dev > >>> > >> _______________________________________________ > >> MOBY-dev mailing list > >> MOBY-dev at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/moby-dev > >> > > > > > -- > -- > Dr. Mark Wilkinson > Assistant Professor, Medical Genetics > PI Bioinformatics, Heart + Lung Institute St. Paul's Hospital/UBC Vancouver, > BC, Canada _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Thu Sep 9 16:19:07 2010 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 09 Sep 2010 09:19:07 -0700 Subject: [MOBY-dev] CVS time out In-Reply-To: <004401cb503a$77a8fd80$66faf880$@gmail.com> References: <1284044176.3506.91.camel@lab.localdomain> <001001cb5030$59a578e0$0cf06aa0$@gmail.com> <4C88FA08.2030006@toulouse.inra.fr> <004401cb503a$77a8fd80$66faf880$@gmail.com> Message-ID: You're not using the ANONYMOUS cvs, are you? (not if you're doing commits! LOL!) M On Thu, 09 Sep 2010 09:17:14 -0700, Edward Kawas wrote: > This is strange, because I have been doing cvs updates, a single commit, > creating tags and have yet to time out. > > Eddie > >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- >> bounces at lists.open-bio.org] On Behalf Of Mark Wilkinson >> Sent: Thursday, September 09, 2010 8:31 AM >> To: moby-dev at lists.open-bio.org; Sebastien Carrere >> Subject: Re: [MOBY-dev] CVS time out >> >> I have the same problem from here at the hospital. I'll check with the > open- >> bio roots and see what's up. >> >> Thanks for letting us know! >> >> Mark >> >> >> >> >> >> On Thu, 09 Sep 2010 08:15:20 -0700, Sebastien Carrere >> wrote: >> >> > Bonjour, >> > >> > same problem from Toulouse: >> > >> > cvs [update aborted]: connect to cvs.open-bio.org(66.92.69.19):2401 >> > failed: Connection timed out >> > >> > Sebastien >> > >> > On 09/09/2010 17:04, Edward Kawas wrote: >> >> I just did an update and had no problems... >> >> >> >> Eddie >> >> >> >> >> >>> -----Original Message----- >> >>> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- >> >>> bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon >> >>> Sent: Thursday, September 09, 2010 7:56 AM >> >>> To: moby-dev at lists.open-bio.org >> >>> Subject: [MOBY-dev] CVS time out >> >>> >> >>> Dear all, >> >>> >> >>> I running into: >> >>> $ cvs update >> >>> cvs [update aborted]: connect to [cvs.open-bio.org]:2401 failed: >> >>> Connection timed out >> >>> >> >>> Am I the only one ? >> >>> >> >>> Thanks, >> >>> >> >>> Pierre >> >>> >> >>> _______________________________________________ >> >>> MOBY-dev mailing list >> >>> MOBY-dev at lists.open-bio.org >> >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >>> >> >> _______________________________________________ >> >> MOBY-dev mailing list >> >> MOBY-dev at lists.open-bio.org >> >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> >> > >> >> >> -- >> -- >> Dr. Mark Wilkinson >> Assistant Professor, Medical Genetics >> PI Bioinformatics, Heart + Lung Institute St. Paul's Hospital/UBC > Vancouver, >> BC, Canada _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- -- Dr. Mark Wilkinson Assistant Professor, Medical Genetics PI Bioinformatics, Heart + Lung Institute St. Paul's Hospital/UBC Vancouver, BC, Canada From py at pingoured.fr Fri Sep 10 07:02:21 2010 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Fri, 10 Sep 2010 09:02:21 +0200 Subject: [MOBY-dev] CVS time out In-Reply-To: References: <1284044176.3506.91.camel@lab.localdomain> <001001cb5030$59a578e0$0cf06aa0$@gmail.com> <4C88FA08.2030006@toulouse.inra.fr> Message-ID: <1284102141.10973.0.camel@lab.localdomain> I just ran a cvs update (as anonymous) and it seems to be back. Thanks, Pierre On Thu, 2010-09-09 at 08:30 -0700, Mark Wilkinson wrote: > I have the same problem from here at the hospital. I'll check with the > open-bio roots and see what's up. > > Thanks for letting us know! > > Mark > > > > > > On Thu, 09 Sep 2010 08:15:20 -0700, Sebastien Carrere > wrote: > > > Bonjour, > > > > same problem from Toulouse: > > > > cvs [update aborted]: connect to cvs.open-bio.org(66.92.69.19):2401 > > failed: Connection timed out > > > > Sebastien > > > > On 09/09/2010 17:04, Edward Kawas wrote: > >> I just did an update and had no problems... > >> > >> Eddie > >> > >> > >>> -----Original Message----- > >>> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > >>> bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon > >>> Sent: Thursday, September 09, 2010 7:56 AM > >>> To: moby-dev at lists.open-bio.org > >>> Subject: [MOBY-dev] CVS time out > >>> > >>> Dear all, > >>> > >>> I running into: > >>> $ cvs update > >>> cvs [update aborted]: connect to [cvs.open-bio.org]:2401 failed: > >>> Connection timed out > >>> > >>> Am I the only one ? > >>> > >>> Thanks, > >>> > >>> Pierre > >>> > >>> _______________________________________________ > >>> MOBY-dev mailing list > >>> MOBY-dev at lists.open-bio.org > >>> http://lists.open-bio.org/mailman/listinfo/moby-dev > >>> > >> _______________________________________________ > >> MOBY-dev mailing list > >> MOBY-dev at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/moby-dev > >> > > > > From r.biczok at dkfz-heidelberg.de Tue Sep 28 10:01:27 2010 From: r.biczok at dkfz-heidelberg.de (Biczok Rudolf) Date: Tue, 28 Sep 2010 12:01:27 +0200 Subject: [MOBY-dev] CVS can't create temporary directory Message-ID: <4F91222C659D5B4E8C89CE4D710BB08E4AEC86BBCD@DKFZEX01.ad.dkfz-heidelberg.de> Good Morning, I have just a little problem with checking out from the BioMOBY CVS. Today I tried it on two clients, and both gave me the following error while looking through the repository: > $ cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby co -P moby-live > $ can't create temporary directory /tmp/cvs-serv16061 > $ Read-only file system So maybe it's a server-site error or I'm dumb. Best wishes, Rudolf Rudolf Biczok Molecular Genome Analysis Mobile Phone : +49 171 6289148 Phone: +49 (0) 6221 42 4711 Deutsches Krebsforschungszentrum Im Neuenheimer Feld 280 D-69120 Heidelberg [cid:image002.png at 01CB5F04.E1373270] -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.png Type: image/png Size: 12782 bytes Desc: image002.png URL: From martin.senger at gmail.com Tue Sep 28 11:15:08 2010 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 28 Sep 2010 14:15:08 +0300 Subject: [MOBY-dev] CVS can't create temporary directory In-Reply-To: <4F91222C659D5B4E8C89CE4D710BB08E4AEC86BBCD@DKFZEX01.ad.dkfz-heidelberg.de> References: <4F91222C659D5B4E8C89CE4D710BB08E4AEC86BBCD@DKFZEX01.ad.dkfz-heidelberg.de> Message-ID: Yes, according to my knowledge it is, indeed, a server-site problem. I am cc-ing your email to Chris who can fix it I believe. Thanks, Chris. Martin On Tue, Sep 28, 2010 at 1:01 PM, Biczok Rudolf wrote: > Good Morning, > > I have just a little problem with checking out from the BioMOBY CVS. > > Today I tried it on two clients, and both gave me the following error while > looking through > the repository: > > > $ cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby co -P > moby-live > > $ can't create temporary directory /tmp/cvs-serv16061 > > $ Read-only file system > > So maybe it's a server-site error or I'm dumb. > > Best wishes, > Rudolf > > > Rudolf Biczok > Molecular Genome Analysis > Mobile Phone : +49 171 6289148 > Phone: +49 (0) 6221 42 4711 > > Deutsches Krebsforschungszentrum > Im Neuenheimer Feld 280 > D-69120 Heidelberg > > [cid:image002.png at 01CB5F04.E1373270] > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > -- Martin Senger email: martin.senger at gmail.com,martin.senger at kaust.edu.sa skype: martinsenger From dag at sonsorol.org Tue Sep 28 14:49:35 2010 From: dag at sonsorol.org (Chris Dagdigian) Date: Tue, 28 Sep 2010 10:49:35 -0400 Subject: [MOBY-dev] CVS can't create temporary directory In-Reply-To: References: <4F91222C659D5B4E8C89CE4D710BB08E4AEC86BBCD@DKFZEX01.ad.dkfz-heidelberg.de> Message-ID: <4CA2007F.1070109@sonsorol.org> Fixed. Filesystem corruption within the VM. -Chris Martin Senger wrote: > Yes, according to my knowledge it is, indeed, a server-site problem. I > am cc-ing your email to Chris who can fix it I believe. Thanks, Chris. > > Martin > > On Tue, Sep 28, 2010 at 1:01 PM, Biczok Rudolf > > wrote: > > Good Morning, > > I have just a little problem with checking out from the BioMOBY CVS. > > Today I tried it on two clients, and both gave me the following > error while looking through > the repository: > > > $ cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby co > -P moby-live > > $ can't create temporary directory /tmp/cvs-serv16061 > > $ Read-only file system > > So maybe it's a server-site error or I'm dumb. > > Best wishes, > Rudolf > > > Rudolf Biczok > Molecular Genome Analysis > Mobile Phone : +49 171 6289148 > Phone: +49 (0) 6221 42 4711 > > Deutsches Krebsforschungszentrum > Im Neuenheimer Feld 280 > D-69120 Heidelberg > > [cid:image002.png at 01CB5F04.E1373270] > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > > > -- > Martin Senger > email: martin.senger at gmail.com > ,martin.senger at kaust.edu.sa > > skype: martinsenger From markw at illuminae.com Tue Sep 28 14:58:11 2010 From: markw at illuminae.com (Mark) Date: Tue, 28 Sep 2010 07:58:11 -0700 Subject: [MOBY-dev] CVS can't create temporary directory In-Reply-To: <4CA2007F.1070109@sonsorol.org> References: <4F91222C659D5B4E8C89CE4D710BB08E4AEC86BBCD@DKFZEX01.ad.dkfz-heidelberg.de> <4CA2007F.1070109@sonsorol.org> Message-ID: wow! Problem identified and solved before I even woke up :-) thanks Chris! M On Tue, 28 Sep 2010 07:49:35 -0700, Chris Dagdigian wrote: > > Fixed. Filesystem corruption within the VM. > > -Chris From r.biczok at Dkfz-Heidelberg.de Wed Sep 29 13:38:51 2010 From: r.biczok at Dkfz-Heidelberg.de (Biczok Rudolf) Date: Wed, 29 Sep 2010 15:38:51 +0200 Subject: [MOBY-dev] CVS can't create temporary directory In-Reply-To: References: <4F91222C659D5B4E8C89CE4D710BB08E4AEC86BBCD@DKFZEX01.ad.dkfz-heidelberg.de> <4CA2007F.1070109@sonsorol.org> Message-ID: <4F91222C659D5B4E8C89CE4D710BB08E4AEC86BBF5@DKFZEX01.ad.dkfz-heidelberg.de> Hello, year, that solved it thanks. I?m not sure but I can't find the maven artifact "jdic:jdic:1.0" in any known maven repository. Why that matters? Because the initmaven task in JMoby's build.xml prints the following when I run "ant install" command: ... [artifact:dependencies] Downloading: jdic/jdic/1.0/jdic-1.0.pom from kysoh [artifact:dependencies] Transferring 0K from kysoh [artifact:dependencies] [WARNING] *** CHECKSUM FAILED - Checksum failed on download: local = 'f9c9151b31e92b90e5adc3852ca1bde4716d8e50'; remote = ' 302 Found

Found

The document has moved here.

Well removing the dependency from the project.pom solved that for me. Best whishes Rudolf Biczok -----Urspr?ngliche Nachricht----- Von: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] Im Auftrag von Mark Gesendet: Dienstag, 28. September 2010 16:58 An: Martin Senger; Chris Dagdigian; Core developer announcements Betreff: Re: [MOBY-dev] CVS can't create temporary directory wow! Problem identified and solved before I even woke up :-) thanks Chris! M On Tue, 28 Sep 2010 07:49:35 -0700, Chris Dagdigian wrote: > > Fixed. Filesystem corruption within the VM. > > -Chris _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev