[Jalview-discuss] Jalview 2.8 throws exception (was Re: Fw: jalview problem)

James Procter j.procter at dundee.ac.uk
Mon Mar 9 13:44:08 GMT 2015


Hello Dharmender.

You are using a fairly old version of Jalview - in fact, we released a 
bug fix for that version which should fix the error you have reported.

You can download the installer for 2.8.0b1 here:
http://www.jalview.org/old/v2_8_0b1/Web_Installers/InstData/MacOSX/NoVM/install-jalview.zip

Ideally, of course, you should be using the very latest version of 
Jalview (2.8.2b1) - but for that you will need to obtain java 7 for your 
macbook pro.. which will mean you'll also need upgrade the operating 
system from 10.6.8 to at least Lion (10.7).

Let me know how you get on !
Jim.
#
On 09/03/2015 13:23, D. Kumar wrote:
>
> Hi
>
> I was trying to launch the Jalview in my Macbook pro (10.6.8) and it 
> consistently show the message of unable to launch (Pic is attached). I 
> re-installed and updated  java for 10.6.8 version of Macbook pro. Can 
> you please help me to sort out this problem ?
>
>
> Kind regards
>
> Kumar
>
>
>
>
> ------------------------------------------------------------------------
> *D. Kumar C/o Dr. S.MacIntyre*
> PhD student
> Knight Building (AMS)
> University of Reading,UK
> RG6 6AJ
>
>
> ------------------------------------------------------------------------
> *From:* Dharmender Kumar
> *Sent:* 22 January 2013 12:03 PM
> *To:* jprocter at dundee.ac.uk
> *Subject:* jalview problem
> Jalview Desktop 2.8
> Build Date: 20 January 2013
> Java version: 1.6.0_37
> x86_64 Mac OS X 10.6.8
> WARN - Exception when discovering One Way services:
> WARN - Exception when discovering One Way services:
> Jan 22, 2013 11:59:59 AM compbio.ws.client.Jws2Client connectToRegistry
> INFO: Connected to RegistryWS successfully!
> Connecting to JABAWS version 2 service
> Jan 22, 2013 12:00:00 PM compbio.ws.client.Jws2Client connect
> INFO: Connected successfully!
> Discovered service: http://www.compbio.dundee.ac.uk/jabaws 
> jalview.ws.jws2.jabaws2.Jws2Instance at 45033fb5
> Connecting to JABAWS version 2 service
> Jan 22, 2013 12:00:01 PM compbio.ws.client.Jws2Client connect
> INFO: Connected successfully!
> Discovered service: http://www.compbio.dundee.ac.uk/jabaws 
> jalview.ws.jws2.jabaws2.Jws2Instance at 5426807f
> Connecting to JABAWS version 2 service
> Jan 22, 2013 12:00:01 PM compbio.ws.client.Jws2Client connect
> INFO: Connected successfully!
> Discovered service: http://www.compbio.dundee.ac.uk/jabaws 
> jalview.ws.jws2.jabaws2.Jws2Instance at 62c8aeb3
> Connecting to JABAWS version 2 service
> Jan 22, 2013 12:00:02 PM compbio.ws.client.Jws2Client connect
> INFO: Connected successfully!
> Discovered service: http://www.compbio.dundee.ac.uk/jabaws 
> jalview.ws.jws2.jabaws2.Jws2Instance at 18247418
> Connecting to JABAWS version 2 service
> Jan 22, 2013 12:00:02 PM compbio.ws.client.Jws2Client connect
> INFO: Connected successfully!
> Discovered service: http://www.compbio.dundee.ac.uk/jabaws 
> jalview.ws.jws2.jabaws2.Jws2Instance at 500c4c05
> Jan 22, 2013 12:00:03 PM compbio.ws.client.Jws2Client connect
> INFO: Connected successfully!
> Discovered service: http://www.compbio.dundee.ac.uk/jabaws 
> jalview.ws.jws2.jabaws2.Jws2Instance at 705789f3
> Jan 22, 2013 12:00:04 PM compbio.ws.client.Jws2Client connect
> INFO: Connected successfully!
> Discovered service: http://www.compbio.dundee.ac.uk/jabaws 
> jalview.ws.jws2.jabaws2.Jws2Instance at 36422510
> Jan 22, 2013 12:00:04 PM compbio.ws.client.Jws2Client connect
> INFO: Connected successfully!
> Discovered service: http://www.compbio.dundee.ac.uk/jabaws 
> jalview.ws.jws2.jabaws2.Jws2Instance at 7a0d637d
> INFO - Initialising googletracker for usage stats.
> INFO - Constructing news reader.
> INFO - Completed construction of reader.
> Connecting to JABAWS version 2 service
> Jan 22, 2013 12:00:06 PM compbio.ws.client.Jws2Client connect
> INFO: Connected successfully!
> Discovered service: http://www.compbio.dundee.ac.uk/jabaws 
> jalview.ws.jws2.jabaws2.Jws2Instance at c6a26b
> Jan 22, 2013 12:00:06 PM compbio.ws.client.Jws2Client connect
> INFO: Connected successfully!
> Discovered service: http://www.compbio.dundee.ac.uk/jabaws 
> jalview.ws.jws2.jabaws2.Jws2Instance at b7cf28b
> Jan 22, 2013 12:00:07 PM compbio.ws.client.Jws2Client connect
> INFO: Connected successfully!
> Discovered service: http://www.compbio.dundee.ac.uk/jabaws 
> jalview.ws.jws2.jabaws2.Jws2Instance at 1ddd40f3
> INFO - Saved last read date as Jan 4, 2013 3:59:21 PM
> INFO - Saved last read date as Jan 4, 2013 3:59:21 PM
> INFO - Saved last read date as Jan 4, 2013 3:59:21 PM
> Building ws menu again Thread[Thread-28,6,main]
> header key X-DAS-Server=[regrest/1.5]
> header key Content-Type=[application/xml]
> header key Date=[Tue, 22 Jan 2013 12:00:17 GMT]
> header key Transfer-Encoding=[chunked]
> header key Access-Control-Allow-Origin=[*]
> header key X-DAS-Status=[200]
> Added another sequence DB source for 
> Anolis_carolinensis.AnoCar2.0.reference 
> (Anolis_carolinensis.AnoCar2.0.reference (AnoCar Contig 2.0) (DAS))
> Added another sequence DB source for 
> Anolis_carolinensis.AnoCar2.0.reference 
> (Anolis_carolinensis.AnoCar2.0.reference (AnoCar Scaffold 2.0) (DAS))
> Added another sequence DB source for Bos_taurus.UMD3.1.reference 
> (Bos_taurus.UMD3.1.reference (UMD Scaffold 3.1) (DAS))
> Added another sequence DB source for 
> Callithrix_jacchus.C_jacchus3.2.1.reference 
> (Callithrix_jacchus.C_jacchus3.2.1.reference (C_jacchus Chromosome 
> 3.2.1) (DAS))
> Added another sequence DB source for 
> Choloepus_hoffmanni.choHof1.reference 
> (Choloepus_hoffmanni.choHof1.reference (choHof Gene Scaffold 1) (DAS))
> Added another sequence DB source for Danio_rerio.Zv9.reference 
> (Danio_rerio.Zv9.reference (Zv Scaffold 9) (DAS))
> Added another sequence DB source for 
> Dasypus_novemcinctus.dasNov2.reference 
> (Dasypus_novemcinctus.dasNov2.reference (dasNov Scaffold 2) (DAS))
> Added another sequence DB source for Dipodomys_ordii.dipOrd1.reference 
> (Dipodomys_ordii.dipOrd1.reference (dipOrd Scaffold 1) (DAS))
> Added another sequence DB source for 
> Echinops_telfairi.TENREC.reference (Echinops_telfairi.TENREC.reference 
> (TENREC Scaffold) (DAS))
> Added another sequence DB source for 
> Erinaceus_europaeus.HEDGEHOG.reference 
> (Erinaceus_europaeus.HEDGEHOG.reference (HEDGEHOG Scaffold) (DAS))
> Added another sequence DB source for Felis_catus.CAT.reference 
> (Felis_catus.CAT.reference (CAT Gene Scaffold) (DAS))
> Added another sequence DB source for Gadus_morhua.gadMor1.reference 
> (Gadus_morhua.gadMor1.reference (gadMor Gene Scaffold 1) (DAS))
> Added another sequence DB source for Gadus_morhua.gadMor1.reference 
> (Gadus_morhua.gadMor1.reference (gadMor Scaffold 1) (DAS))
> Added another sequence DB source for 
> Gasterosteus_aculeatus.BROADS1.reference 
> (Gasterosteus_aculeatus.BROADS1.reference (BROADS Scaffold 1) (DAS))
> Added another sequence DB source for Homo_sapiens.GRCh37.reference 
> (Homo_sapiens.GRCh37.reference (GRCh Chromosome 37) (DAS))
> Added another sequence DB source for Macaca_mulatta.MMUL_1.reference 
> (Macaca_mulatta.MMUL_1.reference (MMUL Chromosome 1) (DAS))
> Added another sequence DB source for 
> Macropus_eugenii.Meug_1.0.reference 
> (Macropus_eugenii.Meug_1.0.reference (Meug Scaffold 1.0) (DAS))
> Added another sequence DB source for 
> Meleagris_gallopavo.UMD2.reference (Meleagris_gallopavo.UMD2.reference 
> (UMD Scaffold 2) (DAS))
> Added another sequence DB source for 
> Meleagris_gallopavo.UMD2.reference (Meleagris_gallopavo.UMD2.reference 
> (UMD Contig 2) (DAS))
> Added another sequence DB source for 
> Microcebus_murinus.micMur1.reference 
> (Microcebus_murinus.micMur1.reference (micMur Scaffold 1) (DAS))
> Added another sequence DB source for Mus_musculus.NCBIM37.reference 
> (Mus_musculus.NCBIM37.reference (NCBIM Supercontig 37) (DAS))
> Added another sequence DB source for 
> Nomascus_leucogenys.Nleu1.0.reference 
> (Nomascus_leucogenys.Nleu1.0.reference (Nleu Contig 1.0) (DAS))
> Added another sequence DB source for Ochotona_princeps.pika.reference 
> (Ochotona_princeps.pika.reference (pika Gene Scaffold) (DAS))
> Added another sequence DB source for 
> Ornithorhynchus_anatinus.OANA5.reference 
> (Ornithorhynchus_anatinus.OANA5.reference (OANA Ultracontig 5) (DAS))
> Added another sequence DB source for 
> Ornithorhynchus_anatinus.OANA5.reference 
> (Ornithorhynchus_anatinus.OANA5.reference (OANA Supercontig 5) (DAS))
> Added another sequence DB source for 
> Oryctolagus_cuniculus.oryCun2.reference 
> (Oryctolagus_cuniculus.oryCun2.reference (oryCun Chromosome 2) (DAS))
> Added another sequence DB source for Oryzias_latipes.MEDAKA1.reference 
> (Oryzias_latipes.MEDAKA1.reference (MEDAKA Scaffold 1) (DAS))
> Added another sequence DB source for Oryzias_latipes.MEDAKA1.reference 
> (Oryzias_latipes.MEDAKA1.reference (MEDAKA Chromosome 1) (DAS))
> Added another sequence DB source for 
> Pan_troglodytes.CHIMP2.1.4.reference 
> (Pan_troglodytes.CHIMP2.1.4.reference (CHIMP Chromosome 2.1.4) (DAS))
> Added another sequence DB source for 
> Procavia_capensis.proCap1.reference 
> (Procavia_capensis.proCap1.reference (proCap Gene Scaffold 1) (DAS))
> Added another sequence DB source for 
> Pteropus_vampyrus.pteVam1.reference 
> (Pteropus_vampyrus.pteVam1.reference (pteVam Gene Scaffold 1) (DAS))
> Added another sequence DB source for 
> Sorex_araneus.COMMON_SHREW1.reference 
> (Sorex_araneus.COMMON_SHREW1.reference (COMMON_SHREW Gene Scaffold 1) 
> (DAS))
> Added another sequence DB source for 
> Spermophilus_tridecemlineatus.SQUIRREL.reference 
> (Spermophilus_tridecemlineatus.SQUIRREL.reference (SQUIRREL Gene 
> Scaffold) (DAS))
> Added another sequence DB source for 
> Tarsius_syrichta.tarSyr1.reference (Tarsius_syrichta.tarSyr1.reference 
> (tarSyr Scaffold 1) (DAS))
> Added another sequence DB source for 
> Tupaia_belangeri.TREESHREW.reference 
> (Tupaia_belangeri.TREESHREW.reference (TREESHREW Scaffold) (DAS))
> Added another sequence DB source for 
> Tursiops_truncatus.turTru1.reference 
> (Tursiops_truncatus.turTru1.reference (turTru Gene Scaffold 1) (DAS))
> Added another sequence DB source for Vicugna_pacos.vicPac1.reference 
> (Vicugna_pacos.vicPac1.reference (vicPac Gene Scaffold 1) (DAS))
> Added another sequence DB source for Ciona_intestinalis.JGI2.reference 
> (Ciona_intestinalis.JGI2.reference (JGI Chromosome 2) (DAS))
> Added another sequence DB source for Bos_taurus.Btau_4.0.reference 
> (Bos_taurus.Btau_4.0.reference (Btau Contig 4.0) (DAS))
> Added another sequence DB source for 
> Otolemur_garnettii.BUSHBABY1.reference 
> (Otolemur_garnettii.BUSHBABY1.reference (BUSHBABY Scaffold 1) (DAS))
> Added another sequence DB source for 
> Myotis_lucifugus.MICROBAT1.reference 
> (Myotis_lucifugus.MICROBAT1.reference (MICROBAT Scaffold 1) (DAS))
> Added another sequence DB source for Danio_rerio.Zv8.reference 
> (Danio_rerio.Zv8.reference (Zv Scaffold 8) (DAS))
> Added another sequence DB source for Gorilla_gorilla.gorGor1.reference 
> (Gorilla_gorilla.gorGor1.reference (gorGor Gene Scaffold 1) (DAS))
> Added another sequence DB source for 
> Loxodonta_africana.loxAfr2.reference 
> (Loxodonta_africana.loxAfr2.reference (loxAfr Scaffold 2) (DAS))
> Added another sequence DB source for 
> Oryctolagus_cuniculus.RABBIT.reference 
> (Oryctolagus_cuniculus.RABBIT.reference (RABBIT Scaffold) (DAS))
> Added another sequence DB source for Homo_sapiens.NCBI36.reference 
> (Homo_sapiens.NCBI36.reference (NCBI Supercontig 36) (DAS))
> Added another sequence DB source for Danio_rerio.ZFISH7.reference 
> (Danio_rerio.ZFISH7.reference (ZFISH Scaffold 7) (DAS))
> Exception in thread "Thread-30" java.lang.NullPointerException
>     at java.util.ArrayList.addAll(ArrayList.java:472)
>     at jalview.ws.DBRefFetcher.<init>(DBRefFetcher.java:139)
>     at jalview.ws.DBRefFetcher.<init>(DBRefFetcher.java:94)
>     at 
> jalview.ws.DasSequenceFeatureFetcher$FetchDBRefs.run(DasSequenceFeatureFetcher.java:248)
>     at java.lang.Thread.run(Thread.java:680)
>
>
>
> ------------------------------------------------------------------------
> *D. Kumar C/o Dr. S. MacIntyre
> *PhD student
> Lab no. 160
> Knight Building (AMS)
> School of Biological Sciences
> The University of Reading
> Whiteknights
> Reading RG6 6AJ
> UK
>

-- 
-------------------------------------------------------------------
Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, College of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk
The University of Dundee is registered Scottish charity: No.SC015096

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