From klee at mpiz-koeln.mpg.de Tue Dec 1 09:07:53 2009 From: klee at mpiz-koeln.mpg.de (Kathrin Klee) Date: Tue, 01 Dec 2009 15:07:53 +0100 Subject: [MOBY-dev] Compiling datatypes In-Reply-To: <4b13e124.171bf30a.6a3b.33d3@mx.google.com> References: <4B0FDD4C.801@mpiz-koeln.mpg.de> <4d93f07c0911291352j1571fc4fy9ef07cefc265f2dd@mail.gmail.com> <4b13e124.171bf30a.6a3b.33d3@mx.google.com> Message-ID: <4B152339.7080604@mpiz-koeln.mpg.de> Thanks for your help so far. Now I've removed my hole cache (by hand as well as via ant-clean) and tried to run jar-datatypes. Copying the class files to my build folder worked fine but while compiling datatypes it still failed with the fallowing error messages. compile-datatypes: [javac] Compiling 1 source file to /home/pcb/klee/workspace/jMoby/build/others/datatypes [javac] /home/pcb/klee/workspace/jMoby/generated/datatypes/org/biomoby/shared/datatypes/GCP_Contact.java:95: getMoby_affiliation() in org.biomoby.shared.datatypes.GCP_Contact cannot override getMoby_affiliation() in org.biomoby.shared.datatypes.GCP_Person; attempting to use incompatible return type [javac] found : org.biomoby.shared.datatypes.GCP_Organization [javac] required: org.biomoby.shared.datatypes.GCP_LegalEntity[] [javac] public GCP_Organization getMoby_affiliation() { [javac] ^ [javac] 1 error BUILD FAILED I am working on the testing registry and I'm using Java 1.5 If you have some more suggestions I would be happy to hear them. Thanks a lot Kathrin Edward Kawas wrote: > Okay, I just removed my .m2/ folder (maven dependencies), ant clean, > followed by ant jar-datatypes and I had no problems. > > So perhaps, like Martin said, you may want to clear your cache (ant clean > should do it) and try again. If that doesn't help, and you are using java 6, > maybe check for an upgrade to the java 6 update that you have. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger > Sent: Sunday, November 29, 2009 1:52 PM > To: Core developer announcements > Subject: Re: [MOBY-dev] Compiling datatypes > > Hi, > > Which moby registry are you using? Probably the default one? Anyway, your > local cache may have some incompatible (meaning older) datatypes. The first > step would be to remove the whole cache and let it fill again (from the > Dashboard or by the command-line programs). > > Sorry for this vague answer, but I am now travelling and I cannot check it > on my computer. Perhaps Eddie can be more specific (he works now with moby > much much more than I do :-)). > > Cheers, > Martin > > -- -------------------------------------------------- Kathrin Klee Bioinformatician Max Planck Institute for Plant Breeding Research Plant Computational Biology Carl-von-Linne Weg 10 50829 Koeln Germany +49 (0)221 / 5062 - 449 -------------------------------------------------- From edward.kawas at gmail.com Tue Dec 1 10:21:56 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 1 Dec 2009 07:21:56 -0800 Subject: [MOBY-dev] Compiling datatypes In-Reply-To: <4B152339.7080604@mpiz-koeln.mpg.de> References: <4B0FDD4C.801@mpiz-koeln.mpg.de> <4d93f07c0911291352j1571fc4fy9ef07cefc265f2dd@mail.gmail.com> <4b13e124.171bf30a.6a3b.33d3@mx.google.com> <4B152339.7080604@mpiz-koeln.mpg.de> Message-ID: <4b153496.151bf30a.258e.06c4@mx.google.com> Hmm, I tried generating for both the old test registry (bioinfo.icapture.ubc.ca) and the new one (mobytest.biordf.net) and I got both times: compile-datatypes: [javac] Compiling 586 source files to /home/ubuntu/moby-live/Java/build/others/datatypes jar-datatypes: [jar] Building jar: /home/ubuntu/moby-live/Java/build/lib/biomoby-datatypes.jar BUILD SUCCESSFUL How are you generating the datatypes (from the command line or through dashboard)? If through dashboard, delete the cache directory that dashboard uses (usually /tmp/your_username/). If you are using the command line, try typing in 'ant clean' then look for a directory called myCache and remove it. If a directory called generated also exists, remove that too. Then try again. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Kathrin Klee Sent: Tuesday, December 01, 2009 6:08 AM To: Core developer announcements Subject: Re: [MOBY-dev] Compiling datatypes Thanks for your help so far. Now I've removed my hole cache (by hand as well as via ant-clean) and tried to run jar-datatypes. Copying the class files to my build folder worked fine but while compiling datatypes it still failed with the fallowing error messages. compile-datatypes: [javac] Compiling 1 source file to /home/pcb/klee/workspace/jMoby/build/others/datatypes [javac] /home/pcb/klee/workspace/jMoby/generated/datatypes/org/biomoby/shared/dataty pes/GCP_Contact.java:95: getMoby_affiliation() in org.biomoby.shared.datatypes.GCP_Contact cannot override getMoby_affiliation() in org.biomoby.shared.datatypes.GCP_Person; attempting to use incompatible return type [javac] found : org.biomoby.shared.datatypes.GCP_Organization [javac] required: org.biomoby.shared.datatypes.GCP_LegalEntity[] [javac] public GCP_Organization getMoby_affiliation() { [javac] ^ [javac] 1 error BUILD FAILED I am working on the testing registry and I'm using Java 1.5 If you have some more suggestions I would be happy to hear them. Thanks a lot Kathrin Edward Kawas wrote: > Okay, I just removed my .m2/ folder (maven dependencies), ant clean, > followed by ant jar-datatypes and I had no problems. > > So perhaps, like Martin said, you may want to clear your cache (ant clean > should do it) and try again. If that doesn't help, and you are using java 6, > maybe check for an upgrade to the java 6 update that you have. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger > Sent: Sunday, November 29, 2009 1:52 PM > To: Core developer announcements > Subject: Re: [MOBY-dev] Compiling datatypes > > Hi, > > Which moby registry are you using? Probably the default one? Anyway, your > local cache may have some incompatible (meaning older) datatypes. The first > step would be to remove the whole cache and let it fill again (from the > Dashboard or by the command-line programs). > > Sorry for this vague answer, but I am now travelling and I cannot check it > on my computer. Perhaps Eddie can be more specific (he works now with moby > much much more than I do :-)). > > Cheers, > Martin > > -- -------------------------------------------------- Kathrin Klee Bioinformatician Max Planck Institute for Plant Breeding Research Plant Computational Biology Carl-von-Linne Weg 10 50829 Koeln Germany +49 (0)221 / 5062 - 449 -------------------------------------------------- _______________________________________________ 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 Tue Dec 1 20:44:37 2009 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 2 Dec 2009 01:44:37 +0000 Subject: [MOBY-dev] Compiling datatypes In-Reply-To: <4B0FDD4C.801@mpiz-koeln.mpg.de> References: <4B0FDD4C.801@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0912011744s32ba9f7fl8dcebbff00dc5978@mail.gmail.com> Hi, [Sorry for a delayed reply. Thanks to Eddie for helping meantime.] The problem you have is because you still have an old (not anymore existing) datatype GCP_Contact. This is how to get rid of it: 1) Make sure that you have the latest contents of the registry you want to work with. From the dashboard: a) Select "Known registries" to "testing". b) Local Cache -> Update -> select "All" and press "Reload" When this is done you can check that GCP_Contact is not anymore in your cache: Right click on "Data types" subpanel, select "Search" and type "GCP_". Look that no GCP_Contact is selected (in red or whatever). 2) You need also remove the old datatypes from (previously) generated sources: ant clean-datatypes After this step, you can check that your directory "/home/pcb/klee/workspace/jMoby/generated/datatypes" is, indeed, empty. 3) Now, you can re-generate and compile all datatypes. Remember that if you are using command-line (as I did - see below) you need to specify in you build.properties which register you are accessing (otherwise it will use the default registry). For the "testing" registry, use the following prooerties: default.endpoint = http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl default.namespace = http://bioinfo.icapture.ubc.ca/MOBY/Central The command-line is: ant moses-datatypes You can see also the number of compiled datatypes. In my case, it was this: compile-datatypes: [javac] Compiling 586 source files to /home/senger/moby-live/Java/build/others/datatypes while in your case, it was: compile-datatypes: > [javac] Compiling 587 source files to > /home/pcb/klee/workspace/jMoby/build/others/datatypes > That indicates the culprit. I hope that this helps you. If not please do not hesitate and contact me again. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From klee at mpiz-koeln.mpg.de Wed Dec 2 05:56:13 2009 From: klee at mpiz-koeln.mpg.de (Kathrin Klee) Date: Wed, 02 Dec 2009 11:56:13 +0100 Subject: [MOBY-dev] Compiling datatypes In-Reply-To: <4d93f07c0912011744s32ba9f7fl8dcebbff00dc5978@mail.gmail.com> References: <4B0FDD4C.801@mpiz-koeln.mpg.de> <4d93f07c0912011744s32ba9f7fl8dcebbff00dc5978@mail.gmail.com> Message-ID: <4B1647CD.9020005@mpiz-koeln.mpg.de> Thanks a lot, that worked. Cheers Kathrin Martin Senger wrote: > Hi, > > [Sorry for a delayed reply. Thanks to Eddie for helping meantime.] > > The problem you have is because you still have an old (not anymore existing) > datatype GCP_Contact. This is how to get rid of it: > > 1) Make sure that you have the latest contents of the registry you want to > work with. From the dashboard: > > a) Select "Known registries" to "testing". > b) Local Cache -> Update -> select "All" and press "Reload" > > When this is done you can check that GCP_Contact is not anymore in your > cache: Right click on "Data types" subpanel, select "Search" and type > "GCP_". Look that no GCP_Contact is selected (in red or whatever). > > 2) You need also remove the old datatypes from (previously) generated > sources: > > ant clean-datatypes > > After this step, you can check that your directory > "/home/pcb/klee/workspace/jMoby/generated/datatypes" is, indeed, empty. > > 3) Now, you can re-generate and compile all datatypes. Remember that if you > are using command-line (as I did - see below) you need to specify in you > build.properties which register you are accessing (otherwise it will use the > default registry). For the "testing" registry, use the following prooerties: > > default.endpoint = > http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl > default.namespace = http://bioinfo.icapture.ubc.ca/MOBY/Central > > The command-line is: > > ant moses-datatypes > > You can see also the number of compiled datatypes. In my case, it was this: > > compile-datatypes: > [javac] Compiling 586 source files to > /home/senger/moby-live/Java/build/others/datatypes > > while in your case, it was: > > compile-datatypes: > >> [javac] Compiling 587 source files to >> /home/pcb/klee/workspace/jMoby/build/others/datatypes >> >> > > That indicates the culprit. > > I hope that this helps you. If not please do not hesitate and contact me > again. > > Cheers, > Martin > > -- -------------------------------------------------- Kathrin Klee Bioinformatician Max Planck Institute for Plant Breeding Research Plant Computational Biology Carl-von-Linne Weg 10 50829 Koeln Germany +49 (0)221 / 5062 - 449 -------------------------------------------------- From Sebastien.Carrere at toulouse.inra.fr Wed Dec 9 09:42:30 2009 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Wed, 09 Dec 2009 15:42:30 +0100 Subject: [MOBY-dev] moby.ucalgary.ca down ? Message-ID: <4B1FB756.60604@toulouse.inra.fr> Bonjour, ping moby.ucalgary.ca does not answer anything ... Is there any problem or is it just a french problem ? Merci, Sebastien -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From edward.kawas at gmail.com Wed Dec 9 10:03:49 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 9 Dec 2009 07:03:49 -0800 Subject: [MOBY-dev] moby.ucalgary.ca down ? In-Reply-To: <4B1FB756.60604@toulouse.inra.fr> References: <4B1FB756.60604@toulouse.inra.fr> Message-ID: <4b1fbc59.9513f30a.50d4.7765@mx.google.com> Possibly a French problem. I can hit the machine from Vancouver. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien Carrere Sent: Wednesday, December 09, 2009 6:43 AM To: Core developer announcements Subject: [MOBY-dev] moby.ucalgary.ca down ? Bonjour, ping moby.ucalgary.ca does not answer anything ... Is there any problem or is it just a french problem ? Merci, Sebastien From py at pingoured.fr Wed Dec 9 10:08:17 2009 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Wed, 09 Dec 2009 16:08:17 +0100 Subject: [MOBY-dev] moby.ucalgary.ca down ? In-Reply-To: <4B1FB756.60604@toulouse.inra.fr> References: <4B1FB756.60604@toulouse.inra.fr> Message-ID: <1260371297.30916.3.camel@localhost.localdomain> On Wed, 2009-12-09 at 15:42 +0100, Sebastien Carrere wrote: > Bonjour, > > ping moby.ucalgary.ca does not answer anything ... > > Is there any problem or is it just a french problem ? --- moby.ucalgary.ca ping statistics --- 16 packets transmitted, 0 received, 100% packet loss, time 15393ms Not only french then >From the Netherlands, Pierre From edward.kawas at gmail.com Wed Dec 9 10:21:58 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 9 Dec 2009 07:21:58 -0800 Subject: [MOBY-dev] moby.ucalgary.ca down ? In-Reply-To: <1260371297.30916.3.camel@localhost.localdomain> References: <4B1FB756.60604@toulouse.inra.fr> <1260371297.30916.3.camel@localhost.localdomain> Message-ID: <4b1fc099.9513f30a.50d4.78ea@mx.google.com> I cant ping the machine, but I can browse and call services using gbrowse @ http://moby.ucalgary.ca/gbrowse_moby. Strange indeed! 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: Wednesday, December 09, 2009 7:08 AM To: Core developer announcements Subject: Re: [MOBY-dev] moby.ucalgary.ca down ? On Wed, 2009-12-09 at 15:42 +0100, Sebastien Carrere wrote: > Bonjour, > > ping moby.ucalgary.ca does not answer anything ... > > Is there any problem or is it just a french problem ? --- moby.ucalgary.ca ping statistics --- 16 packets transmitted, 0 received, 100% packet loss, time 15393ms Not only french then >From the Netherlands, Pierre _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From alanrw at cs.man.ac.uk Wed Dec 9 10:02:44 2009 From: alanrw at cs.man.ac.uk (Alan Williams) Date: Wed, 09 Dec 2009 15:02:44 +0000 Subject: [MOBY-dev] moby.ucalgary.ca down ? In-Reply-To: <4b1fbc59.9513f30a.50d4.7765@mx.google.com> References: <4B1FB756.60604@toulouse.inra.fr> <4b1fbc59.9513f30a.50d4.7765@mx.google.com> Message-ID: <4B1FBC14.6090207@cs.man.ac.uk> Edward Kawas wrote: > Possibly a French problem. I can hit the machine from Vancouver. Must be fog in the Atlantic as it can't be seen from Manchester, UK. > Eddie Alan From haase_dirk at web.de Wed Dec 9 10:23:19 2009 From: haase_dirk at web.de (Dirk Haase) Date: Wed, 09 Dec 2009 16:23:19 +0100 Subject: [MOBY-dev] moby.ucalgary.ca down ? Message-ID: <1440623059@web.de> Hi, Same prob for Germany. No ping reply... Best, dirk > -----Urspr?ngliche Nachricht----- > Von: "Edward Kawas" > Gesendet: 09.12.09 16:11:01 > An: "'Core developer announcements'" > Betreff: Re: [MOBY-dev] moby.ucalgary.ca down ? > Possibly a French problem. I can hit the machine from Vancouver. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien Carrere > Sent: Wednesday, December 09, 2009 6:43 AM > To: Core developer announcements > Subject: [MOBY-dev] moby.ucalgary.ca down ? > > Bonjour, > > ping moby.ucalgary.ca does not answer anything ... > > Is there any problem or is it just a french problem ? > > Merci, > Sebastien > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From gordonp at ucalgary.ca Wed Dec 9 11:30:28 2009 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 09 Dec 2009 09:30:28 -0700 Subject: [MOBY-dev] moby.ucalgary.ca down ? In-Reply-To: <4b1fc099.9513f30a.50d4.78ea@mx.google.com> References: <4B1FB756.60604@toulouse.inra.fr> <1260371297.30916.3.camel@localhost.localdomain> <4b1fc099.9513f30a.50d4.78ea@mx.google.com> Message-ID: <4B1FD0A4.6070602@ucalgary.ca> I can ping from our subnet...doing a traceroute it looks like ICMP traffic is blocked between our ISP (Telus) and the university. So while you cannot ping, IP traffic is fine. Edward Kawas wrote: > I cant ping the machine, but I can browse and call services using gbrowse @ > http://moby.ucalgary.ca/gbrowse_moby. > > Strange indeed! > > 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: Wednesday, December 09, 2009 7:08 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] moby.ucalgary.ca down ? > > On Wed, 2009-12-09 at 15:42 +0100, Sebastien Carrere wrote: > >> Bonjour, >> >> ping moby.ucalgary.ca does not answer anything ... >> >> Is there any problem or is it just a french problem ? >> > --- moby.ucalgary.ca ping statistics --- > 16 packets transmitted, 0 received, 100% packet loss, time 15393ms > > Not only french then > > > >From the Netherlands, > 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 markw at illuminae.com Mon Dec 21 07:57:35 2009 From: markw at illuminae.com (Mark) Date: Mon, 21 Dec 2009 04:57:35 -0800 Subject: [MOBY-dev] Services down ? In-Reply-To: <4B2F419C.6050706@toulouse.inra.fr> References: <4B2F419C.6050706@toulouse.inra.fr> Message-ID: On Mon, 21 Dec 2009 01:36:28 -0800, Sebastien Carrere wrote: > Bonjour Mark, > > This endpoint seems not available (timeout): > > http://moby.ucalgary.ca/moby_services/Services.cgi > > Do you confirm ? > > renderGFF is for example unavailable, but its RDF file is > (http://moby.ucalgary.ca/signatures/localservices.rdf) > > > Merci et joyeuses fetes ! > > Sebastien > > From edward.kawas at gmail.com Mon Dec 21 10:10:57 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 21 Dec 2009 07:10:57 -0800 Subject: [MOBY-dev] Services down ? In-Reply-To: References: <4B2F419C.6050706@toulouse.inra.fr> Message-ID: <4b2f9002.9413f30a.5f4a.ffffff44@mx.google.com> Hi Sebastien, That endpoint is available (from here anyways). Maybe the problem was intermittent? 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 Sent: Monday, December 21, 2009 4:58 AM To: Core developer announcements Subject: Re: [MOBY-dev] Services down ? On Mon, 21 Dec 2009 01:36:28 -0800, Sebastien Carrere wrote: > Bonjour Mark, > > This endpoint seems not available (timeout): > > http://moby.ucalgary.ca/moby_services/Services.cgi > > Do you confirm ? > > renderGFF is for example unavailable, but its RDF file is > (http://moby.ucalgary.ca/signatures/localservices.rdf) > > > Merci et joyeuses fetes ! > > Sebastien > > _______________________________________________ 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 Mon Dec 21 10:20:14 2009 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Mon, 21 Dec 2009 16:20:14 +0100 Subject: [MOBY-dev] Services down ? In-Reply-To: <4b2f9002.9413f30a.5f4a.ffffff44@mx.google.com> References: <4B2F419C.6050706@toulouse.inra.fr> <4b2f9002.9413f30a.5f4a.ffffff44@mx.google.com> Message-ID: <4B2F922E.8050103@toulouse.inra.fr> Hi, Yes, now It seems to be okay. There's a lot of traffic problems the last past weeks between Europe and Canada... Merci, Sebastien Edward Kawas wrote: > Hi Sebastien, > > That endpoint is available (from here anyways). Maybe the problem was > intermittent? > > 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 > Sent: Monday, December 21, 2009 4:58 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Services down ? > > On Mon, 21 Dec 2009 01:36:28 -0800, Sebastien Carrere > wrote: > > >> Bonjour Mark, >> >> This endpoint seems not available (timeout): >> >> http://moby.ucalgary.ca/moby_services/Services.cgi >> >> Do you confirm ? >> >> renderGFF is for example unavailable, but its RDF file is >> (http://moby.ucalgary.ca/signatures/localservices.rdf) >> >> >> Merci et joyeuses fetes ! >> >> Sebastien >> >> >> > > _______________________________________________ > 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 edward.kawas at gmail.com Mon Dec 21 10:35:11 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 21 Dec 2009 07:35:11 -0800 Subject: [MOBY-dev] Services down ? In-Reply-To: <4B2F922E.8050103@toulouse.inra.fr> References: <4B2F419C.6050706@toulouse.inra.fr> <4b2f9002.9413f30a.5f4a.ffffff44@mx.google.com> <4B2F922E.8050103@toulouse.inra.fr> Message-ID: <4b2f95af.9613f30a.7197.fffffba9@mx.google.com> I blame global warming ;-) Have a happy holiday! Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien Carrere Sent: Monday, December 21, 2009 7:20 AM To: Core developer announcements Subject: Re: [MOBY-dev] Services down ? Hi, Yes, now It seems to be okay. There's a lot of traffic problems the last past weeks between Europe and Canada... Merci, Sebastien Edward Kawas wrote: > Hi Sebastien, > > That endpoint is available (from here anyways). Maybe the problem was > intermittent? > > 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 > Sent: Monday, December 21, 2009 4:58 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Services down ? > > On Mon, 21 Dec 2009 01:36:28 -0800, Sebastien Carrere > wrote: > > >> Bonjour Mark, >> >> This endpoint seems not available (timeout): >> >> http://moby.ucalgary.ca/moby_services/Services.cgi >> >> Do you confirm ? >> >> renderGFF is for example unavailable, but its RDF file is >> (http://moby.ucalgary.ca/signatures/localservices.rdf) >> >> >> Merci et joyeuses fetes ! >> >> Sebastien >> >> >> > > _______________________________________________ > 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 markw at illuminae.com Mon Dec 21 10:55:35 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 21 Dec 2009 07:55:35 -0800 Subject: [MOBY-dev] Services down ? In-Reply-To: <4b2f95af.9613f30a.7197.fffffba9@mx.google.com> References: <4B2F419C.6050706@toulouse.inra.fr> <4b2f9002.9413f30a.5f4a.ffffff44@mx.google.com> <4B2F922E.8050103@toulouse.inra.fr> <4b2f95af.9613f30a.7197.fffffba9@mx.google.com> Message-ID: Well, it's not "global warming" per se, it's the increased resistance caused by the buildup of carbon in the atmosphere. It makes it harder for the electrons to get through... M On Mon, 21 Dec 2009 07:35:11 -0800, Edward Kawas wrote: > I blame global warming ;-) > > Have a happy holiday! > > Eddie -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research Providence Heart + Lung Institute University of British Columbia - St. Paul's Hospital Vancouver, BC, Canada From klee at mpiz-koeln.mpg.de Tue Dec 1 14:07:53 2009 From: klee at mpiz-koeln.mpg.de (Kathrin Klee) Date: Tue, 01 Dec 2009 15:07:53 +0100 Subject: [MOBY-dev] Compiling datatypes In-Reply-To: <4b13e124.171bf30a.6a3b.33d3@mx.google.com> References: <4B0FDD4C.801@mpiz-koeln.mpg.de> <4d93f07c0911291352j1571fc4fy9ef07cefc265f2dd@mail.gmail.com> <4b13e124.171bf30a.6a3b.33d3@mx.google.com> Message-ID: <4B152339.7080604@mpiz-koeln.mpg.de> Thanks for your help so far. Now I've removed my hole cache (by hand as well as via ant-clean) and tried to run jar-datatypes. Copying the class files to my build folder worked fine but while compiling datatypes it still failed with the fallowing error messages. compile-datatypes: [javac] Compiling 1 source file to /home/pcb/klee/workspace/jMoby/build/others/datatypes [javac] /home/pcb/klee/workspace/jMoby/generated/datatypes/org/biomoby/shared/datatypes/GCP_Contact.java:95: getMoby_affiliation() in org.biomoby.shared.datatypes.GCP_Contact cannot override getMoby_affiliation() in org.biomoby.shared.datatypes.GCP_Person; attempting to use incompatible return type [javac] found : org.biomoby.shared.datatypes.GCP_Organization [javac] required: org.biomoby.shared.datatypes.GCP_LegalEntity[] [javac] public GCP_Organization getMoby_affiliation() { [javac] ^ [javac] 1 error BUILD FAILED I am working on the testing registry and I'm using Java 1.5 If you have some more suggestions I would be happy to hear them. Thanks a lot Kathrin Edward Kawas wrote: > Okay, I just removed my .m2/ folder (maven dependencies), ant clean, > followed by ant jar-datatypes and I had no problems. > > So perhaps, like Martin said, you may want to clear your cache (ant clean > should do it) and try again. If that doesn't help, and you are using java 6, > maybe check for an upgrade to the java 6 update that you have. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger > Sent: Sunday, November 29, 2009 1:52 PM > To: Core developer announcements > Subject: Re: [MOBY-dev] Compiling datatypes > > Hi, > > Which moby registry are you using? Probably the default one? Anyway, your > local cache may have some incompatible (meaning older) datatypes. The first > step would be to remove the whole cache and let it fill again (from the > Dashboard or by the command-line programs). > > Sorry for this vague answer, but I am now travelling and I cannot check it > on my computer. Perhaps Eddie can be more specific (he works now with moby > much much more than I do :-)). > > Cheers, > Martin > > -- -------------------------------------------------- Kathrin Klee Bioinformatician Max Planck Institute for Plant Breeding Research Plant Computational Biology Carl-von-Linne Weg 10 50829 Koeln Germany +49 (0)221 / 5062 - 449 -------------------------------------------------- From edward.kawas at gmail.com Tue Dec 1 15:21:56 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 1 Dec 2009 07:21:56 -0800 Subject: [MOBY-dev] Compiling datatypes In-Reply-To: <4B152339.7080604@mpiz-koeln.mpg.de> References: <4B0FDD4C.801@mpiz-koeln.mpg.de> <4d93f07c0911291352j1571fc4fy9ef07cefc265f2dd@mail.gmail.com> <4b13e124.171bf30a.6a3b.33d3@mx.google.com> <4B152339.7080604@mpiz-koeln.mpg.de> Message-ID: <4b153496.151bf30a.258e.06c4@mx.google.com> Hmm, I tried generating for both the old test registry (bioinfo.icapture.ubc.ca) and the new one (mobytest.biordf.net) and I got both times: compile-datatypes: [javac] Compiling 586 source files to /home/ubuntu/moby-live/Java/build/others/datatypes jar-datatypes: [jar] Building jar: /home/ubuntu/moby-live/Java/build/lib/biomoby-datatypes.jar BUILD SUCCESSFUL How are you generating the datatypes (from the command line or through dashboard)? If through dashboard, delete the cache directory that dashboard uses (usually /tmp/your_username/). If you are using the command line, try typing in 'ant clean' then look for a directory called myCache and remove it. If a directory called generated also exists, remove that too. Then try again. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Kathrin Klee Sent: Tuesday, December 01, 2009 6:08 AM To: Core developer announcements Subject: Re: [MOBY-dev] Compiling datatypes Thanks for your help so far. Now I've removed my hole cache (by hand as well as via ant-clean) and tried to run jar-datatypes. Copying the class files to my build folder worked fine but while compiling datatypes it still failed with the fallowing error messages. compile-datatypes: [javac] Compiling 1 source file to /home/pcb/klee/workspace/jMoby/build/others/datatypes [javac] /home/pcb/klee/workspace/jMoby/generated/datatypes/org/biomoby/shared/dataty pes/GCP_Contact.java:95: getMoby_affiliation() in org.biomoby.shared.datatypes.GCP_Contact cannot override getMoby_affiliation() in org.biomoby.shared.datatypes.GCP_Person; attempting to use incompatible return type [javac] found : org.biomoby.shared.datatypes.GCP_Organization [javac] required: org.biomoby.shared.datatypes.GCP_LegalEntity[] [javac] public GCP_Organization getMoby_affiliation() { [javac] ^ [javac] 1 error BUILD FAILED I am working on the testing registry and I'm using Java 1.5 If you have some more suggestions I would be happy to hear them. Thanks a lot Kathrin Edward Kawas wrote: > Okay, I just removed my .m2/ folder (maven dependencies), ant clean, > followed by ant jar-datatypes and I had no problems. > > So perhaps, like Martin said, you may want to clear your cache (ant clean > should do it) and try again. If that doesn't help, and you are using java 6, > maybe check for an upgrade to the java 6 update that you have. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger > Sent: Sunday, November 29, 2009 1:52 PM > To: Core developer announcements > Subject: Re: [MOBY-dev] Compiling datatypes > > Hi, > > Which moby registry are you using? Probably the default one? Anyway, your > local cache may have some incompatible (meaning older) datatypes. The first > step would be to remove the whole cache and let it fill again (from the > Dashboard or by the command-line programs). > > Sorry for this vague answer, but I am now travelling and I cannot check it > on my computer. Perhaps Eddie can be more specific (he works now with moby > much much more than I do :-)). > > Cheers, > Martin > > -- -------------------------------------------------- Kathrin Klee Bioinformatician Max Planck Institute for Plant Breeding Research Plant Computational Biology Carl-von-Linne Weg 10 50829 Koeln Germany +49 (0)221 / 5062 - 449 -------------------------------------------------- _______________________________________________ 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 Dec 2 01:44:37 2009 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 2 Dec 2009 01:44:37 +0000 Subject: [MOBY-dev] Compiling datatypes In-Reply-To: <4B0FDD4C.801@mpiz-koeln.mpg.de> References: <4B0FDD4C.801@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0912011744s32ba9f7fl8dcebbff00dc5978@mail.gmail.com> Hi, [Sorry for a delayed reply. Thanks to Eddie for helping meantime.] The problem you have is because you still have an old (not anymore existing) datatype GCP_Contact. This is how to get rid of it: 1) Make sure that you have the latest contents of the registry you want to work with. From the dashboard: a) Select "Known registries" to "testing". b) Local Cache -> Update -> select "All" and press "Reload" When this is done you can check that GCP_Contact is not anymore in your cache: Right click on "Data types" subpanel, select "Search" and type "GCP_". Look that no GCP_Contact is selected (in red or whatever). 2) You need also remove the old datatypes from (previously) generated sources: ant clean-datatypes After this step, you can check that your directory "/home/pcb/klee/workspace/jMoby/generated/datatypes" is, indeed, empty. 3) Now, you can re-generate and compile all datatypes. Remember that if you are using command-line (as I did - see below) you need to specify in you build.properties which register you are accessing (otherwise it will use the default registry). For the "testing" registry, use the following prooerties: default.endpoint = http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl default.namespace = http://bioinfo.icapture.ubc.ca/MOBY/Central The command-line is: ant moses-datatypes You can see also the number of compiled datatypes. In my case, it was this: compile-datatypes: [javac] Compiling 586 source files to /home/senger/moby-live/Java/build/others/datatypes while in your case, it was: compile-datatypes: > [javac] Compiling 587 source files to > /home/pcb/klee/workspace/jMoby/build/others/datatypes > That indicates the culprit. I hope that this helps you. If not please do not hesitate and contact me again. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From klee at mpiz-koeln.mpg.de Wed Dec 2 10:56:13 2009 From: klee at mpiz-koeln.mpg.de (Kathrin Klee) Date: Wed, 02 Dec 2009 11:56:13 +0100 Subject: [MOBY-dev] Compiling datatypes In-Reply-To: <4d93f07c0912011744s32ba9f7fl8dcebbff00dc5978@mail.gmail.com> References: <4B0FDD4C.801@mpiz-koeln.mpg.de> <4d93f07c0912011744s32ba9f7fl8dcebbff00dc5978@mail.gmail.com> Message-ID: <4B1647CD.9020005@mpiz-koeln.mpg.de> Thanks a lot, that worked. Cheers Kathrin Martin Senger wrote: > Hi, > > [Sorry for a delayed reply. Thanks to Eddie for helping meantime.] > > The problem you have is because you still have an old (not anymore existing) > datatype GCP_Contact. This is how to get rid of it: > > 1) Make sure that you have the latest contents of the registry you want to > work with. From the dashboard: > > a) Select "Known registries" to "testing". > b) Local Cache -> Update -> select "All" and press "Reload" > > When this is done you can check that GCP_Contact is not anymore in your > cache: Right click on "Data types" subpanel, select "Search" and type > "GCP_". Look that no GCP_Contact is selected (in red or whatever). > > 2) You need also remove the old datatypes from (previously) generated > sources: > > ant clean-datatypes > > After this step, you can check that your directory > "/home/pcb/klee/workspace/jMoby/generated/datatypes" is, indeed, empty. > > 3) Now, you can re-generate and compile all datatypes. Remember that if you > are using command-line (as I did - see below) you need to specify in you > build.properties which register you are accessing (otherwise it will use the > default registry). For the "testing" registry, use the following prooerties: > > default.endpoint = > http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl > default.namespace = http://bioinfo.icapture.ubc.ca/MOBY/Central > > The command-line is: > > ant moses-datatypes > > You can see also the number of compiled datatypes. In my case, it was this: > > compile-datatypes: > [javac] Compiling 586 source files to > /home/senger/moby-live/Java/build/others/datatypes > > while in your case, it was: > > compile-datatypes: > >> [javac] Compiling 587 source files to >> /home/pcb/klee/workspace/jMoby/build/others/datatypes >> >> > > That indicates the culprit. > > I hope that this helps you. If not please do not hesitate and contact me > again. > > Cheers, > Martin > > -- -------------------------------------------------- Kathrin Klee Bioinformatician Max Planck Institute for Plant Breeding Research Plant Computational Biology Carl-von-Linne Weg 10 50829 Koeln Germany +49 (0)221 / 5062 - 449 -------------------------------------------------- From Sebastien.Carrere at toulouse.inra.fr Wed Dec 9 14:42:30 2009 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Wed, 09 Dec 2009 15:42:30 +0100 Subject: [MOBY-dev] moby.ucalgary.ca down ? Message-ID: <4B1FB756.60604@toulouse.inra.fr> Bonjour, ping moby.ucalgary.ca does not answer anything ... Is there any problem or is it just a french problem ? Merci, Sebastien -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From edward.kawas at gmail.com Wed Dec 9 15:03:49 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 9 Dec 2009 07:03:49 -0800 Subject: [MOBY-dev] moby.ucalgary.ca down ? In-Reply-To: <4B1FB756.60604@toulouse.inra.fr> References: <4B1FB756.60604@toulouse.inra.fr> Message-ID: <4b1fbc59.9513f30a.50d4.7765@mx.google.com> Possibly a French problem. I can hit the machine from Vancouver. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien Carrere Sent: Wednesday, December 09, 2009 6:43 AM To: Core developer announcements Subject: [MOBY-dev] moby.ucalgary.ca down ? Bonjour, ping moby.ucalgary.ca does not answer anything ... Is there any problem or is it just a french problem ? Merci, Sebastien From py at pingoured.fr Wed Dec 9 15:08:17 2009 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Wed, 09 Dec 2009 16:08:17 +0100 Subject: [MOBY-dev] moby.ucalgary.ca down ? In-Reply-To: <4B1FB756.60604@toulouse.inra.fr> References: <4B1FB756.60604@toulouse.inra.fr> Message-ID: <1260371297.30916.3.camel@localhost.localdomain> On Wed, 2009-12-09 at 15:42 +0100, Sebastien Carrere wrote: > Bonjour, > > ping moby.ucalgary.ca does not answer anything ... > > Is there any problem or is it just a french problem ? --- moby.ucalgary.ca ping statistics --- 16 packets transmitted, 0 received, 100% packet loss, time 15393ms Not only french then >From the Netherlands, Pierre From edward.kawas at gmail.com Wed Dec 9 15:21:58 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 9 Dec 2009 07:21:58 -0800 Subject: [MOBY-dev] moby.ucalgary.ca down ? In-Reply-To: <1260371297.30916.3.camel@localhost.localdomain> References: <4B1FB756.60604@toulouse.inra.fr> <1260371297.30916.3.camel@localhost.localdomain> Message-ID: <4b1fc099.9513f30a.50d4.78ea@mx.google.com> I cant ping the machine, but I can browse and call services using gbrowse @ http://moby.ucalgary.ca/gbrowse_moby. Strange indeed! 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: Wednesday, December 09, 2009 7:08 AM To: Core developer announcements Subject: Re: [MOBY-dev] moby.ucalgary.ca down ? On Wed, 2009-12-09 at 15:42 +0100, Sebastien Carrere wrote: > Bonjour, > > ping moby.ucalgary.ca does not answer anything ... > > Is there any problem or is it just a french problem ? --- moby.ucalgary.ca ping statistics --- 16 packets transmitted, 0 received, 100% packet loss, time 15393ms Not only french then >From the Netherlands, Pierre _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From alanrw at cs.man.ac.uk Wed Dec 9 15:02:44 2009 From: alanrw at cs.man.ac.uk (Alan Williams) Date: Wed, 09 Dec 2009 15:02:44 +0000 Subject: [MOBY-dev] moby.ucalgary.ca down ? In-Reply-To: <4b1fbc59.9513f30a.50d4.7765@mx.google.com> References: <4B1FB756.60604@toulouse.inra.fr> <4b1fbc59.9513f30a.50d4.7765@mx.google.com> Message-ID: <4B1FBC14.6090207@cs.man.ac.uk> Edward Kawas wrote: > Possibly a French problem. I can hit the machine from Vancouver. Must be fog in the Atlantic as it can't be seen from Manchester, UK. > Eddie Alan From haase_dirk at web.de Wed Dec 9 15:23:19 2009 From: haase_dirk at web.de (Dirk Haase) Date: Wed, 09 Dec 2009 16:23:19 +0100 Subject: [MOBY-dev] moby.ucalgary.ca down ? Message-ID: <1440623059@web.de> Hi, Same prob for Germany. No ping reply... Best, dirk > -----Urspr?ngliche Nachricht----- > Von: "Edward Kawas" > Gesendet: 09.12.09 16:11:01 > An: "'Core developer announcements'" > Betreff: Re: [MOBY-dev] moby.ucalgary.ca down ? > Possibly a French problem. I can hit the machine from Vancouver. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien Carrere > Sent: Wednesday, December 09, 2009 6:43 AM > To: Core developer announcements > Subject: [MOBY-dev] moby.ucalgary.ca down ? > > Bonjour, > > ping moby.ucalgary.ca does not answer anything ... > > Is there any problem or is it just a french problem ? > > Merci, > Sebastien > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From gordonp at ucalgary.ca Wed Dec 9 16:30:28 2009 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 09 Dec 2009 09:30:28 -0700 Subject: [MOBY-dev] moby.ucalgary.ca down ? In-Reply-To: <4b1fc099.9513f30a.50d4.78ea@mx.google.com> References: <4B1FB756.60604@toulouse.inra.fr> <1260371297.30916.3.camel@localhost.localdomain> <4b1fc099.9513f30a.50d4.78ea@mx.google.com> Message-ID: <4B1FD0A4.6070602@ucalgary.ca> I can ping from our subnet...doing a traceroute it looks like ICMP traffic is blocked between our ISP (Telus) and the university. So while you cannot ping, IP traffic is fine. Edward Kawas wrote: > I cant ping the machine, but I can browse and call services using gbrowse @ > http://moby.ucalgary.ca/gbrowse_moby. > > Strange indeed! > > 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: Wednesday, December 09, 2009 7:08 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] moby.ucalgary.ca down ? > > On Wed, 2009-12-09 at 15:42 +0100, Sebastien Carrere wrote: > >> Bonjour, >> >> ping moby.ucalgary.ca does not answer anything ... >> >> Is there any problem or is it just a french problem ? >> > --- moby.ucalgary.ca ping statistics --- > 16 packets transmitted, 0 received, 100% packet loss, time 15393ms > > Not only french then > > > >From the Netherlands, > 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 markw at illuminae.com Mon Dec 21 12:57:35 2009 From: markw at illuminae.com (Mark) Date: Mon, 21 Dec 2009 04:57:35 -0800 Subject: [MOBY-dev] Services down ? In-Reply-To: <4B2F419C.6050706@toulouse.inra.fr> References: <4B2F419C.6050706@toulouse.inra.fr> Message-ID: On Mon, 21 Dec 2009 01:36:28 -0800, Sebastien Carrere wrote: > Bonjour Mark, > > This endpoint seems not available (timeout): > > http://moby.ucalgary.ca/moby_services/Services.cgi > > Do you confirm ? > > renderGFF is for example unavailable, but its RDF file is > (http://moby.ucalgary.ca/signatures/localservices.rdf) > > > Merci et joyeuses fetes ! > > Sebastien > > From edward.kawas at gmail.com Mon Dec 21 15:10:57 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 21 Dec 2009 07:10:57 -0800 Subject: [MOBY-dev] Services down ? In-Reply-To: References: <4B2F419C.6050706@toulouse.inra.fr> Message-ID: <4b2f9002.9413f30a.5f4a.ffffff44@mx.google.com> Hi Sebastien, That endpoint is available (from here anyways). Maybe the problem was intermittent? 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 Sent: Monday, December 21, 2009 4:58 AM To: Core developer announcements Subject: Re: [MOBY-dev] Services down ? On Mon, 21 Dec 2009 01:36:28 -0800, Sebastien Carrere wrote: > Bonjour Mark, > > This endpoint seems not available (timeout): > > http://moby.ucalgary.ca/moby_services/Services.cgi > > Do you confirm ? > > renderGFF is for example unavailable, but its RDF file is > (http://moby.ucalgary.ca/signatures/localservices.rdf) > > > Merci et joyeuses fetes ! > > Sebastien > > _______________________________________________ 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 Mon Dec 21 15:20:14 2009 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Mon, 21 Dec 2009 16:20:14 +0100 Subject: [MOBY-dev] Services down ? In-Reply-To: <4b2f9002.9413f30a.5f4a.ffffff44@mx.google.com> References: <4B2F419C.6050706@toulouse.inra.fr> <4b2f9002.9413f30a.5f4a.ffffff44@mx.google.com> Message-ID: <4B2F922E.8050103@toulouse.inra.fr> Hi, Yes, now It seems to be okay. There's a lot of traffic problems the last past weeks between Europe and Canada... Merci, Sebastien Edward Kawas wrote: > Hi Sebastien, > > That endpoint is available (from here anyways). Maybe the problem was > intermittent? > > 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 > Sent: Monday, December 21, 2009 4:58 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Services down ? > > On Mon, 21 Dec 2009 01:36:28 -0800, Sebastien Carrere > wrote: > > >> Bonjour Mark, >> >> This endpoint seems not available (timeout): >> >> http://moby.ucalgary.ca/moby_services/Services.cgi >> >> Do you confirm ? >> >> renderGFF is for example unavailable, but its RDF file is >> (http://moby.ucalgary.ca/signatures/localservices.rdf) >> >> >> Merci et joyeuses fetes ! >> >> Sebastien >> >> >> > > _______________________________________________ > 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 edward.kawas at gmail.com Mon Dec 21 15:35:11 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 21 Dec 2009 07:35:11 -0800 Subject: [MOBY-dev] Services down ? In-Reply-To: <4B2F922E.8050103@toulouse.inra.fr> References: <4B2F419C.6050706@toulouse.inra.fr> <4b2f9002.9413f30a.5f4a.ffffff44@mx.google.com> <4B2F922E.8050103@toulouse.inra.fr> Message-ID: <4b2f95af.9613f30a.7197.fffffba9@mx.google.com> I blame global warming ;-) Have a happy holiday! Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien Carrere Sent: Monday, December 21, 2009 7:20 AM To: Core developer announcements Subject: Re: [MOBY-dev] Services down ? Hi, Yes, now It seems to be okay. There's a lot of traffic problems the last past weeks between Europe and Canada... Merci, Sebastien Edward Kawas wrote: > Hi Sebastien, > > That endpoint is available (from here anyways). Maybe the problem was > intermittent? > > 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 > Sent: Monday, December 21, 2009 4:58 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Services down ? > > On Mon, 21 Dec 2009 01:36:28 -0800, Sebastien Carrere > wrote: > > >> Bonjour Mark, >> >> This endpoint seems not available (timeout): >> >> http://moby.ucalgary.ca/moby_services/Services.cgi >> >> Do you confirm ? >> >> renderGFF is for example unavailable, but its RDF file is >> (http://moby.ucalgary.ca/signatures/localservices.rdf) >> >> >> Merci et joyeuses fetes ! >> >> Sebastien >> >> >> > > _______________________________________________ > 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 markw at illuminae.com Mon Dec 21 15:55:35 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 21 Dec 2009 07:55:35 -0800 Subject: [MOBY-dev] Services down ? In-Reply-To: <4b2f95af.9613f30a.7197.fffffba9@mx.google.com> References: <4B2F419C.6050706@toulouse.inra.fr> <4b2f9002.9413f30a.5f4a.ffffff44@mx.google.com> <4B2F922E.8050103@toulouse.inra.fr> <4b2f95af.9613f30a.7197.fffffba9@mx.google.com> Message-ID: Well, it's not "global warming" per se, it's the increased resistance caused by the buildup of carbon in the atmosphere. It makes it harder for the electrons to get through... M On Mon, 21 Dec 2009 07:35:11 -0800, Edward Kawas wrote: > I blame global warming ;-) > > Have a happy holiday! > > Eddie -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research Providence Heart + Lung Institute University of British Columbia - St. Paul's Hospital Vancouver, BC, Canada