From volker.roessler at googlemail.com Mon Nov 15 06:31:55 2010 From: volker.roessler at googlemail.com (=?ISO-8859-1?Q?Volker_R=F6ssler?=) Date: Mon, 15 Nov 2010 12:31:55 +0100 Subject: [MOBY-dev] Strange problems with nested moby objects Message-ID: Hi everyone, I'm experiencing a rather strange problem when trying to build the response object. What I'd like to achieve is building an 'AnnotatedSNPAndTranscriptLocation' object which contains an array of 'SNPTranscript' objects. My code for building the response object looks like this, but this causes some strange problems: @SNP_list = mymethod($some_user_input); foreach my $SNP (@SNP_list) { my @listOfBiomobyTranscriptObjects; my $transcriptList = $SNP->get_transcript_list(); foreach my $trans (@$transcriptList) { my $snp_type = $trans->get_field('snp_type'); my $database_references = new MOSES::MOBY::Data::Object ( id => $trans->get_field('name'), namespace => 'Ensembl' ); my $strand = $trans->get_field('strand'); my $description = $trans->get_field('description'); my $name = $trans->get_field('name'); my $start = $trans->get_field('start'); my $stop = $trans->get_field('stop'); my $newTranscript => new MOSES::MOBY::Data::SNPTranscript ( snp_type => $snp_type, #database_references => $database_references, strand => $strand, description => $description, name => $name, start => $start, stop => $stop ); push (@listOfBiomobyTranscriptObjects, $newTranscript); } my $output_snp_transcripts = new MOSES::MOBY::Data::AnnotatedSNPAndTranscriptLocation ( snp_transcripts => \@listOfBiomobyTranscriptObjects, coverage_all => $SNP->get_snp_coverage_all(), coverage_new_allele => $SNP->get_snp_coverage_new_allele(), genetype_allele => $SNP->get_snp_genotype_allele(), reference_allele => $SNP->get_snp_reference_allele(), confidence => $SNP->get_snp_score(), Position => new MOSES::MOBY::Data::Position ( end => $SNP->get_snp_position(), start => $SNP->get_snp_position(), chromosome => $SNP->get_snp_chromosome() ), Strain => $strain ); $response->add_output_snp_transcripts($output_snp_transcripts); } When I'm trying to run this, I get the following error message: 2010/11/15 12:26:02 (71764) FATAL> [13065] (eval 1068):155 - ------------- EXCEPTION: MOSES::MOBY::Data::SNPTranscript ------------- MSG: No such method: MOSES::MOBY::Data::SNPTranscript::value I suspect, that this error happens, because I am trying to use an array of MOSES::MOBY::Data::Object (stored in @listOfBiomobyTranscriptObjects), but I'm not quite sure. Any help or suggestions are greaty appreciated! Yours, Volker From edward.kawas at gmail.com Mon Nov 15 13:35:16 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 15 Nov 2010 10:35:16 -0800 Subject: [MOBY-dev] Strange problems with nested moby objects In-Reply-To: References: Message-ID: <01d201cb84f3$dc27b420$94771c60$@gmail.com> Hi, The problem is with your line my $newTranscript => new MOSES::MOBY::Data::SNPTranscript that should actually read my $newTranscript = new MOSES::MOBY::Data::SNPTranscript an equal sign not a => Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Volker R?ssler Sent: Monday, November 15, 2010 3:32 AM To: moby-dev at lists.open-bio.org Subject: [MOBY-dev] Strange problems with nested moby objects Hi everyone, I'm experiencing a rather strange problem when trying to build the response object. What I'd like to achieve is building an 'AnnotatedSNPAndTranscriptLocation' object which contains an array of 'SNPTranscript' objects. My code for building the response object looks like this, but this causes some strange problems: @SNP_list = mymethod($some_user_input); foreach my $SNP (@SNP_list) { my @listOfBiomobyTranscriptObjects; my $transcriptList = $SNP->get_transcript_list(); foreach my $trans (@$transcriptList) { my $snp_type = $trans->get_field('snp_type'); my $database_references = new MOSES::MOBY::Data::Object ( id => $trans->get_field('name'), namespace => 'Ensembl' ); my $strand = $trans->get_field('strand'); my $description = $trans->get_field('description'); my $name = $trans->get_field('name'); my $start = $trans->get_field('start'); my $stop = $trans->get_field('stop'); my $newTranscript => new MOSES::MOBY::Data::SNPTranscript ( snp_type => $snp_type, #database_references => $database_references, strand => $strand, description => $description, name => $name, start => $start, stop => $stop ); push (@listOfBiomobyTranscriptObjects, $newTranscript); } my $output_snp_transcripts = new MOSES::MOBY::Data::AnnotatedSNPAndTranscriptLocation ( snp_transcripts => \@listOfBiomobyTranscriptObjects, coverage_all => $SNP->get_snp_coverage_all(), coverage_new_allele => $SNP->get_snp_coverage_new_allele(), genetype_allele => $SNP->get_snp_genotype_allele(), reference_allele => $SNP->get_snp_reference_allele(), confidence => $SNP->get_snp_score(), Position => new MOSES::MOBY::Data::Position ( end => $SNP->get_snp_position(), start => $SNP->get_snp_position(), chromosome => $SNP->get_snp_chromosome() ), Strain => $strain ); $response->add_output_snp_transcripts($output_snp_transcripts); } When I'm trying to run this, I get the following error message: 2010/11/15 12:26:02 (71764) FATAL> [13065] (eval 1068):155 - ------------- EXCEPTION: MOSES::MOBY::Data::SNPTranscript ------------- MSG: No such method: MOSES::MOBY::Data::SNPTranscript::value I suspect, that this error happens, because I am trying to use an array of MOSES::MOBY::Data::Object (stored in @listOfBiomobyTranscriptObjects), but I'm not quite sure. Any help or suggestions are greaty appreciated! Yours, Volker _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From amorimlb at gmail.com Mon Nov 15 15:04:49 2010 From: amorimlb at gmail.com (Lucas Amorim) Date: Mon, 15 Nov 2010 17:04:49 -0300 Subject: [MOBY-dev] IRC channel Message-ID: Hello, Does Moby have a IRC channel for discussing topics related to installation/configuration/usage of the project? Thank you. Lucas Amorim Instituto de Computa??o Universidade Federal de Alagoas Curriculum Lattes: http://lattes.cnpq.br/2470781099632240 Linux User #425305 From edward.kawas at gmail.com Mon Nov 15 15:14:15 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 15 Nov 2010 12:14:15 -0800 Subject: [MOBY-dev] IRC channel In-Reply-To: References: Message-ID: <01f601cb8501$ad978140$08c683c0$@gmail.com> No IRC channel, just this mailing list. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Lucas Amorim Sent: Monday, November 15, 2010 12:05 PM To: moby-dev at lists.open-bio.org Subject: [MOBY-dev] IRC channel Hello, Does Moby have a IRC channel for discussing topics related to installation/configuration/usage of the project? Thank you. Lucas Amorim Instituto de Computa??o Universidade Federal de Alagoas Curriculum Lattes: http://lattes.cnpq.br/2470781099632240 Linux User #425305 _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From amorimlb at gmail.com Mon Nov 15 15:32:45 2010 From: amorimlb at gmail.com (Lucas Amorim) Date: Mon, 15 Nov 2010 17:32:45 -0300 Subject: [MOBY-dev] IRC channel In-Reply-To: <01f601cb8501$ad978140$08c683c0$@gmail.com> References: <01f601cb8501$ad978140$08c683c0$@gmail.com> Message-ID: Ok, Thank you Eddie. I am really having trouble trying to run the "FeatureClient.jar" as I said in a previews discussion, the problem us that I was not able to setup all the dependencies needed. Can someone please provide me with a link to download a working copy of a FeatureClient with all the dependencies already setup? Just upload yours to somewhere I can download. The reason why I am asking this is because I need it to implement program that will make biomoby service composition using an evolutionary algorithm which I have already implemented and I just need to access information about the services in order to feed my algorithm and then invoke the services. This is my Course Conclusion Work (Bachelor in Computer Science) and I am already late... If you can't point me to a working copy then please tell me how I could make the official one work. Thanks in advance! Lucas Amorim Instituto de Computa??o Universidade Federal de Alagoas Curriculum Lattes: http://lattes.cnpq.br/2470781099632240 Linux User #425305 On 15 November 2010 17:14, Edward Kawas wrote: > No IRC channel, just this mailing list. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Lucas Amorim > Sent: Monday, November 15, 2010 12:05 PM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] IRC channel > > Hello, > > Does Moby have a IRC channel for discussing topics related to > installation/configuration/usage of the project? > > Thank you. > > Lucas Amorim > > Instituto de Computa??o > Universidade Federal de Alagoas > Curriculum Lattes: http://lattes.cnpq.br/2470781099632240 > > Linux User #425305 > > _______________________________________________ > 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 edward.kawas at gmail.com Mon Nov 15 16:15:35 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 15 Nov 2010 13:15:35 -0800 Subject: [MOBY-dev] IRC channel In-Reply-To: References: <01f601cb8501$ad978140$08c683c0$@gmail.com> Message-ID: <021901cb850a$3f40f560$bdc2e020$@gmail.com> Hi Lucas, I generated a build and placed it at http://dev.biordf.net/~kawas/featureClient-2010-11-15.tar.gz Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Lucas Amorim Sent: Monday, November 15, 2010 12:33 PM To: Core developer announcements Subject: Re: [MOBY-dev] IRC channel Ok, Thank you Eddie. I am really having trouble trying to run the "FeatureClient.jar" as I said in a previews discussion, the problem us that I was not able to setup all the dependencies needed. Can someone please provide me with a link to download a working copy of a FeatureClient with all the dependencies already setup? Just upload yours to somewhere I can download. The reason why I am asking this is because I need it to implement program that will make biomoby service composition using an evolutionary algorithm which I have already implemented and I just need to access information about the services in order to feed my algorithm and then invoke the services. This is my Course Conclusion Work (Bachelor in Computer Science) and I am already late... If you can't point me to a working copy then please tell me how I could make the official one work. Thanks in advance! Lucas Amorim Instituto de Computa??o Universidade Federal de Alagoas Curriculum Lattes: http://lattes.cnpq.br/2470781099632240 Linux User #425305 On 15 November 2010 17:14, Edward Kawas wrote: > No IRC channel, just this mailing list. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Lucas Amorim > Sent: Monday, November 15, 2010 12:05 PM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] IRC channel > > Hello, > > Does Moby have a IRC channel for discussing topics related to > installation/configuration/usage of the project? > > Thank you. > > Lucas Amorim > > Instituto de Computa??o > Universidade Federal de Alagoas > Curriculum Lattes: http://lattes.cnpq.br/2470781099632240 > > Linux User #425305 > > _______________________________________________ > 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 > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From amorimlb at gmail.com Mon Nov 15 16:23:56 2010 From: amorimlb at gmail.com (Lucas Amorim) Date: Mon, 15 Nov 2010 18:23:56 -0300 Subject: [MOBY-dev] IRC channel In-Reply-To: <021901cb850a$3f40f560$bdc2e020$@gmail.com> References: <01f601cb8501$ad978140$08c683c0$@gmail.com> <021901cb850a$3f40f560$bdc2e020$@gmail.com> Message-ID: Thank you very much Eddie, I am downloading now to test later! :) Lucas Amorim Instituto de Computa??o Universidade Federal de Alagoas Curriculum Lattes: http://lattes.cnpq.br/2470781099632240 Linux User #425305 On 15 November 2010 18:15, Edward Kawas wrote: > Hi Lucas, > > I generated a build and placed it at > http://dev.biordf.net/~kawas/featureClient-2010-11-15.tar.gz > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Lucas Amorim > Sent: Monday, November 15, 2010 12:33 PM > To: Core developer announcements > Subject: Re: [MOBY-dev] IRC channel > > Ok, Thank you Eddie. > > I am really having trouble trying to run the "FeatureClient.jar" as I said > in a previews discussion, the problem us that I was not able to setup all > the dependencies needed. Can someone please provide me with a link to > download a working copy of a FeatureClient with all the dependencies > already > setup? Just upload yours to somewhere I can download. > The reason why I am asking this is because I need it to implement program > that will make biomoby service composition using an evolutionary algorithm > which I have already implemented and I just need to access information > about > the services in order to feed my algorithm and then invoke the services. > > This is my Course Conclusion Work (Bachelor in Computer Science) and I am > already late... > > If you can't point me to a working copy then please tell me how I could > make > the official one work. > > Thanks in advance! > Lucas Amorim > > Instituto de Computa??o > Universidade Federal de Alagoas > Curriculum Lattes: http://lattes.cnpq.br/2470781099632240 > > Linux User #425305 > > > On 15 November 2010 17:14, Edward Kawas wrote: > > > No IRC channel, just this mailing list. > > > > Eddie > > > > -----Original Message----- > > From: moby-dev-bounces at lists.open-bio.org > > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Lucas Amorim > > Sent: Monday, November 15, 2010 12:05 PM > > To: moby-dev at lists.open-bio.org > > Subject: [MOBY-dev] IRC channel > > > > Hello, > > > > Does Moby have a IRC channel for discussing topics related to > > installation/configuration/usage of the project? > > > > Thank you. > > > > Lucas Amorim > > > > Instituto de Computa??o > > Universidade Federal de Alagoas > > Curriculum Lattes: http://lattes.cnpq.br/2470781099632240 > > > > Linux User #425305 > > > > _______________________________________________ > > 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 > > > > _______________________________________________ > 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 volker.roessler at googlemail.com Tue Nov 16 03:12:00 2010 From: volker.roessler at googlemail.com (=?ISO-8859-1?Q?Volker_R=F6ssler?=) Date: Tue, 16 Nov 2010 09:12:00 +0100 Subject: [MOBY-dev] Strange problems with nested moby objects In-Reply-To: <01d201cb84f3$dc27b420$94771c60$@gmail.com> References: <01d201cb84f3$dc27b420$94771c60$@gmail.com> Message-ID: Hi Eddie, thank you so much for your fast and helpful response! Now the code finally works for me. I was already pretty frustrated, because I had taken every single bit of the code apart, searching for the error, but the error messages from the moses-service-testing script were not really helpful. But somehow I couldn't not see the forest for the trees... ;-) Volker On Mon, Nov 15, 2010 at 7:35 PM, Edward Kawas wrote: > Hi, > > The problem is with your line > > my $newTranscript => new MOSES::MOBY::Data::SNPTranscript > > that should actually read > > my $newTranscript = new MOSES::MOBY::Data::SNPTranscript > > an equal sign not a => > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Volker R?ssler > Sent: Monday, November 15, 2010 3:32 AM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] Strange problems with nested moby objects > > Hi everyone, > > I'm experiencing a rather strange problem when trying to build the response > object. What I'd like to achieve is building an > 'AnnotatedSNPAndTranscriptLocation' object which contains an array of > 'SNPTranscript' objects. > > My code for building the response object looks like this, but this causes > some strange problems: > > > @SNP_list = mymethod($some_user_input); > > foreach my $SNP (@SNP_list) { > > ? ? ? ?my @listOfBiomobyTranscriptObjects; > > ? ? ? ?my $transcriptList = $SNP->get_transcript_list(); > > ? ? ? ?foreach my $trans (@$transcriptList) { > > ? ? ? ? ? ?my $snp_type = $trans->get_field('snp_type'); > ? ? ? ? ? ?my $database_references = new MOSES::MOBY::Data::Object > ? ? ? ? ? ? ? ?( > ? ? ? ? ? ? ? ? ? ?id => $trans->get_field('name'), > ? ? ? ? ? ? ? ? ? ?namespace => 'Ensembl' > ? ? ? ? ? ? ? ?); > ? ? ? ? ? ?my $strand = $trans->get_field('strand'); > ? ? ? ? ? ?my $description = $trans->get_field('description'); > ? ? ? ? ? ?my $name = $trans->get_field('name'); > ? ? ? ? ? ?my $start = $trans->get_field('start'); > ? ? ? ? ? ?my $stop = $trans->get_field('stop'); > > > ? ? ? ? ? ?my $newTranscript => new MOSES::MOBY::Data::SNPTranscript > ? ? ? ? ? ? ? ?( > ? ? ? ? ? ? ? ? ? ?snp_type => $snp_type, > ? ? ? ? ? ? ? ? ? ?#database_references => $database_references, > ? ? ? ? ? ? ? ? ? ?strand => $strand, > ? ? ? ? ? ? ? ? ? ?description => $description, > ? ? ? ? ? ? ? ? ? ?name => $name, > ? ? ? ? ? ? ? ? ? ?start => $start, > ? ? ? ? ? ? ? ? ? ?stop => $stop > ? ? ? ? ? ? ? ?); > ? ? ? ? ? ?push (@listOfBiomobyTranscriptObjects, $newTranscript); > ? ? ? ?} > > ? ? ? ?my $output_snp_transcripts = new > MOSES::MOBY::Data::AnnotatedSNPAndTranscriptLocation > ? ? ? ? ? ?( > > ? ? ? ? ? ? ? ?snp_transcripts => \@listOfBiomobyTranscriptObjects, > ? ? ? ? ? ? ? ?coverage_all => $SNP->get_snp_coverage_all(), > ? ? ? ? ? ? ? ?coverage_new_allele => $SNP->get_snp_coverage_new_allele(), > ? ? ? ? ? ? ? ?genetype_allele => $SNP->get_snp_genotype_allele(), > ? ? ? ? ? ? ? ?reference_allele => $SNP->get_snp_reference_allele(), > ? ? ? ? ? ? ? ?confidence => $SNP->get_snp_score(), > ? ? ? ? ? ? ? ?Position => new MOSES::MOBY::Data::Position > ? ? ? ? ? ? ? ? ? ?( > ? ? ? ? ? ? ? ? ? ? ? ?end => $SNP->get_snp_position(), > ? ? ? ? ? ? ? ? ? ? ? ?start => $SNP->get_snp_position(), > ? ? ? ? ? ? ? ? ? ? ? ?chromosome => $SNP->get_snp_chromosome() > ? ? ? ? ? ? ? ? ? ?), > ? ? ? ? ? ? ? ?Strain => $strain > ? ? ? ? ? ?); > ? ? ? ?$response->add_output_snp_transcripts($output_snp_transcripts); > ? ?} > > > > When I'm trying to run this, I get the following error message: > 2010/11/15 12:26:02 (71764) FATAL> [13065] (eval 1068):155 - > ------------- EXCEPTION: MOSES::MOBY::Data::SNPTranscript ------------- > MSG: No such method: MOSES::MOBY::Data::SNPTranscript::value > > I suspect, that this error happens, because I am trying to use an array of > MOSES::MOBY::Data::Object (stored in @listOfBiomobyTranscriptObjects), but > I'm not quite sure. > > Any help or suggestions are greaty appreciated! > > Yours, > Volker > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From maxgarcia at uma.es Tue Nov 23 11:32:45 2010 From: maxgarcia at uma.es (=?ISO-8859-1?Q?Max_Garc=EDa?=) Date: Tue, 23 Nov 2010 17:32:45 +0100 Subject: [MOBY-dev] CVS can't create temporary directory In-Reply-To: <4F91222C659D5B4E8C89CE4D710BB08E4AEC86BBF5@DKFZEX01.ad.dkfz-heidelberg.de> References: <4F91222C659D5B4E8C89CE4D710BB08E4AEC86BBCD@DKFZEX01.ad.dkfz-heidelberg.de> <4CA2007F.1070109@sonsorol.org> <4F91222C659D5B4E8C89CE4D710BB08E4AEC86BBF5@DKFZEX01.ad.dkfz-heidelberg.de> Message-ID: <4CEBECAD.4060700@uma.es> Hi all, the same problem? BR Max *maxgarcia at chirimoyo:~/testMOBY$ cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby co -P moby-live* *can't create temporary directory /tmp/cvs-serv32572* *Read-only file system* El 29/09/2010 15:38, Biczok Rudolf escribi?: > 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 = ' [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 = ' [artifact:dependencies] [WARNING] POM for 'jdic:jdic:pom:1.0:compile' is invalid. It will be ignored for artifact resolution. Reason: Not a v4.0.0 POM. for project jdic:jdic at /home/biczok/.m2/repository/jdic/jdic/1.0/jdic-1.0.pom > [artifact:dependencies] Downloading: jdic/jdic/1.0/jdic-1.0.jar from central > [artifact:dependencies] Downloading: jdic/jdic/1.0/jdic-1.0.jar from maven2-repository.dev.java.net > [artifact:dependencies] Downloading: jdic/jdic/1.0/jdic-1.0.jar from bio.maven.repository > [artifact:dependencies] Downloading: jdic/jdic/1.0/jdic-1.0.jar from java.net-m2 > [artifact:dependencies] Downloading: jdic/jdic/1.0/jdic-1.0.jar from jboss.repository > [artifact:dependencies] Downloading: jdic/jdic/1.0/jdic-1.0.jar from kysoh > [artifact:dependencies] Transferring 0K from kysoh > [artifact:dependencies] [WARNING] *** CHECKSUM FAILED - Checksum failed on download: local = 'f16a32acf581b54dcf99a6aef9203da1425fc783'; remote = ' [artifact:dependencies] Downloading: jdic/jdic/1.0/jdic-1.0.jar from kysoh > [artifact:dependencies] Transferring 0K from kysoh > [artifact:dependencies] [WARNING] *** CHECKSUM FAILED - Checksum failed on download: local = 'f16a32acf581b54dcf99a6aef9203da1425fc783'; remote = ' [artifact:dependencies] [WARNING] POM for 'jdic:jdic:pom:1.0:compile' is invalid. It will be ignored for artifact resolution. Reason: Not a v4.0.0 POM. for project jdic:jdic at /home/biczok/.m2/repository/jdic/jdic/1.0/jdic-1.0.pom > > init: > [taskdef] java.util.zip.ZipException: error in opening zip file > ... > > It seems that the Maven dependency jdci:jdci:1.0 does not exists anymore and the repository on kysoh > returns rubbish. See here (the jdic-1.0.pom): > > > 302 Found > >

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> > > 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 > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Maximiliano Garc?a Oliver Computer Architecture Dept. University of Malaga, Spain ETSI Informatica Telf. +34 952 13 7651 Edificio de Bioinnovaci?n C/ Severo Ochoa - 34 Parque Tecnol?gico de Andaluc?a, 29590, Malaga mailto:maxgarcia at ac.uma.es 'But I don't want to go among mad people,' Alice remarked. 'Oh, you can't help that,' said the Cat: 'we're all mad here. I'm mad. You're mad.' 'How do you know I'm mad?' said Alice. 'You must be,' said the Cat, 'or you wouldn't have come here.' Alice's Adventures in Wonderland Lewis Carroll (1832-1898) -- From volker.roessler at googlemail.com Mon Nov 15 11:31:55 2010 From: volker.roessler at googlemail.com (=?ISO-8859-1?Q?Volker_R=F6ssler?=) Date: Mon, 15 Nov 2010 12:31:55 +0100 Subject: [MOBY-dev] Strange problems with nested moby objects Message-ID: Hi everyone, I'm experiencing a rather strange problem when trying to build the response object. What I'd like to achieve is building an 'AnnotatedSNPAndTranscriptLocation' object which contains an array of 'SNPTranscript' objects. My code for building the response object looks like this, but this causes some strange problems: @SNP_list = mymethod($some_user_input); foreach my $SNP (@SNP_list) { my @listOfBiomobyTranscriptObjects; my $transcriptList = $SNP->get_transcript_list(); foreach my $trans (@$transcriptList) { my $snp_type = $trans->get_field('snp_type'); my $database_references = new MOSES::MOBY::Data::Object ( id => $trans->get_field('name'), namespace => 'Ensembl' ); my $strand = $trans->get_field('strand'); my $description = $trans->get_field('description'); my $name = $trans->get_field('name'); my $start = $trans->get_field('start'); my $stop = $trans->get_field('stop'); my $newTranscript => new MOSES::MOBY::Data::SNPTranscript ( snp_type => $snp_type, #database_references => $database_references, strand => $strand, description => $description, name => $name, start => $start, stop => $stop ); push (@listOfBiomobyTranscriptObjects, $newTranscript); } my $output_snp_transcripts = new MOSES::MOBY::Data::AnnotatedSNPAndTranscriptLocation ( snp_transcripts => \@listOfBiomobyTranscriptObjects, coverage_all => $SNP->get_snp_coverage_all(), coverage_new_allele => $SNP->get_snp_coverage_new_allele(), genetype_allele => $SNP->get_snp_genotype_allele(), reference_allele => $SNP->get_snp_reference_allele(), confidence => $SNP->get_snp_score(), Position => new MOSES::MOBY::Data::Position ( end => $SNP->get_snp_position(), start => $SNP->get_snp_position(), chromosome => $SNP->get_snp_chromosome() ), Strain => $strain ); $response->add_output_snp_transcripts($output_snp_transcripts); } When I'm trying to run this, I get the following error message: 2010/11/15 12:26:02 (71764) FATAL> [13065] (eval 1068):155 - ------------- EXCEPTION: MOSES::MOBY::Data::SNPTranscript ------------- MSG: No such method: MOSES::MOBY::Data::SNPTranscript::value I suspect, that this error happens, because I am trying to use an array of MOSES::MOBY::Data::Object (stored in @listOfBiomobyTranscriptObjects), but I'm not quite sure. Any help or suggestions are greaty appreciated! Yours, Volker From edward.kawas at gmail.com Mon Nov 15 18:35:16 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 15 Nov 2010 10:35:16 -0800 Subject: [MOBY-dev] Strange problems with nested moby objects In-Reply-To: References: Message-ID: <01d201cb84f3$dc27b420$94771c60$@gmail.com> Hi, The problem is with your line my $newTranscript => new MOSES::MOBY::Data::SNPTranscript that should actually read my $newTranscript = new MOSES::MOBY::Data::SNPTranscript an equal sign not a => Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Volker R?ssler Sent: Monday, November 15, 2010 3:32 AM To: moby-dev at lists.open-bio.org Subject: [MOBY-dev] Strange problems with nested moby objects Hi everyone, I'm experiencing a rather strange problem when trying to build the response object. What I'd like to achieve is building an 'AnnotatedSNPAndTranscriptLocation' object which contains an array of 'SNPTranscript' objects. My code for building the response object looks like this, but this causes some strange problems: @SNP_list = mymethod($some_user_input); foreach my $SNP (@SNP_list) { my @listOfBiomobyTranscriptObjects; my $transcriptList = $SNP->get_transcript_list(); foreach my $trans (@$transcriptList) { my $snp_type = $trans->get_field('snp_type'); my $database_references = new MOSES::MOBY::Data::Object ( id => $trans->get_field('name'), namespace => 'Ensembl' ); my $strand = $trans->get_field('strand'); my $description = $trans->get_field('description'); my $name = $trans->get_field('name'); my $start = $trans->get_field('start'); my $stop = $trans->get_field('stop'); my $newTranscript => new MOSES::MOBY::Data::SNPTranscript ( snp_type => $snp_type, #database_references => $database_references, strand => $strand, description => $description, name => $name, start => $start, stop => $stop ); push (@listOfBiomobyTranscriptObjects, $newTranscript); } my $output_snp_transcripts = new MOSES::MOBY::Data::AnnotatedSNPAndTranscriptLocation ( snp_transcripts => \@listOfBiomobyTranscriptObjects, coverage_all => $SNP->get_snp_coverage_all(), coverage_new_allele => $SNP->get_snp_coverage_new_allele(), genetype_allele => $SNP->get_snp_genotype_allele(), reference_allele => $SNP->get_snp_reference_allele(), confidence => $SNP->get_snp_score(), Position => new MOSES::MOBY::Data::Position ( end => $SNP->get_snp_position(), start => $SNP->get_snp_position(), chromosome => $SNP->get_snp_chromosome() ), Strain => $strain ); $response->add_output_snp_transcripts($output_snp_transcripts); } When I'm trying to run this, I get the following error message: 2010/11/15 12:26:02 (71764) FATAL> [13065] (eval 1068):155 - ------------- EXCEPTION: MOSES::MOBY::Data::SNPTranscript ------------- MSG: No such method: MOSES::MOBY::Data::SNPTranscript::value I suspect, that this error happens, because I am trying to use an array of MOSES::MOBY::Data::Object (stored in @listOfBiomobyTranscriptObjects), but I'm not quite sure. Any help or suggestions are greaty appreciated! Yours, Volker _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From amorimlb at gmail.com Mon Nov 15 20:04:49 2010 From: amorimlb at gmail.com (Lucas Amorim) Date: Mon, 15 Nov 2010 17:04:49 -0300 Subject: [MOBY-dev] IRC channel Message-ID: Hello, Does Moby have a IRC channel for discussing topics related to installation/configuration/usage of the project? Thank you. Lucas Amorim Instituto de Computa??o Universidade Federal de Alagoas Curriculum Lattes: http://lattes.cnpq.br/2470781099632240 Linux User #425305 From edward.kawas at gmail.com Mon Nov 15 20:14:15 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 15 Nov 2010 12:14:15 -0800 Subject: [MOBY-dev] IRC channel In-Reply-To: References: Message-ID: <01f601cb8501$ad978140$08c683c0$@gmail.com> No IRC channel, just this mailing list. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Lucas Amorim Sent: Monday, November 15, 2010 12:05 PM To: moby-dev at lists.open-bio.org Subject: [MOBY-dev] IRC channel Hello, Does Moby have a IRC channel for discussing topics related to installation/configuration/usage of the project? Thank you. Lucas Amorim Instituto de Computa??o Universidade Federal de Alagoas Curriculum Lattes: http://lattes.cnpq.br/2470781099632240 Linux User #425305 _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From amorimlb at gmail.com Mon Nov 15 20:32:45 2010 From: amorimlb at gmail.com (Lucas Amorim) Date: Mon, 15 Nov 2010 17:32:45 -0300 Subject: [MOBY-dev] IRC channel In-Reply-To: <01f601cb8501$ad978140$08c683c0$@gmail.com> References: <01f601cb8501$ad978140$08c683c0$@gmail.com> Message-ID: Ok, Thank you Eddie. I am really having trouble trying to run the "FeatureClient.jar" as I said in a previews discussion, the problem us that I was not able to setup all the dependencies needed. Can someone please provide me with a link to download a working copy of a FeatureClient with all the dependencies already setup? Just upload yours to somewhere I can download. The reason why I am asking this is because I need it to implement program that will make biomoby service composition using an evolutionary algorithm which I have already implemented and I just need to access information about the services in order to feed my algorithm and then invoke the services. This is my Course Conclusion Work (Bachelor in Computer Science) and I am already late... If you can't point me to a working copy then please tell me how I could make the official one work. Thanks in advance! Lucas Amorim Instituto de Computa??o Universidade Federal de Alagoas Curriculum Lattes: http://lattes.cnpq.br/2470781099632240 Linux User #425305 On 15 November 2010 17:14, Edward Kawas wrote: > No IRC channel, just this mailing list. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Lucas Amorim > Sent: Monday, November 15, 2010 12:05 PM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] IRC channel > > Hello, > > Does Moby have a IRC channel for discussing topics related to > installation/configuration/usage of the project? > > Thank you. > > Lucas Amorim > > Instituto de Computa??o > Universidade Federal de Alagoas > Curriculum Lattes: http://lattes.cnpq.br/2470781099632240 > > Linux User #425305 > > _______________________________________________ > 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 edward.kawas at gmail.com Mon Nov 15 21:15:35 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 15 Nov 2010 13:15:35 -0800 Subject: [MOBY-dev] IRC channel In-Reply-To: References: <01f601cb8501$ad978140$08c683c0$@gmail.com> Message-ID: <021901cb850a$3f40f560$bdc2e020$@gmail.com> Hi Lucas, I generated a build and placed it at http://dev.biordf.net/~kawas/featureClient-2010-11-15.tar.gz Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Lucas Amorim Sent: Monday, November 15, 2010 12:33 PM To: Core developer announcements Subject: Re: [MOBY-dev] IRC channel Ok, Thank you Eddie. I am really having trouble trying to run the "FeatureClient.jar" as I said in a previews discussion, the problem us that I was not able to setup all the dependencies needed. Can someone please provide me with a link to download a working copy of a FeatureClient with all the dependencies already setup? Just upload yours to somewhere I can download. The reason why I am asking this is because I need it to implement program that will make biomoby service composition using an evolutionary algorithm which I have already implemented and I just need to access information about the services in order to feed my algorithm and then invoke the services. This is my Course Conclusion Work (Bachelor in Computer Science) and I am already late... If you can't point me to a working copy then please tell me how I could make the official one work. Thanks in advance! Lucas Amorim Instituto de Computa??o Universidade Federal de Alagoas Curriculum Lattes: http://lattes.cnpq.br/2470781099632240 Linux User #425305 On 15 November 2010 17:14, Edward Kawas wrote: > No IRC channel, just this mailing list. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Lucas Amorim > Sent: Monday, November 15, 2010 12:05 PM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] IRC channel > > Hello, > > Does Moby have a IRC channel for discussing topics related to > installation/configuration/usage of the project? > > Thank you. > > Lucas Amorim > > Instituto de Computa??o > Universidade Federal de Alagoas > Curriculum Lattes: http://lattes.cnpq.br/2470781099632240 > > Linux User #425305 > > _______________________________________________ > 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 > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From amorimlb at gmail.com Mon Nov 15 21:23:56 2010 From: amorimlb at gmail.com (Lucas Amorim) Date: Mon, 15 Nov 2010 18:23:56 -0300 Subject: [MOBY-dev] IRC channel In-Reply-To: <021901cb850a$3f40f560$bdc2e020$@gmail.com> References: <01f601cb8501$ad978140$08c683c0$@gmail.com> <021901cb850a$3f40f560$bdc2e020$@gmail.com> Message-ID: Thank you very much Eddie, I am downloading now to test later! :) Lucas Amorim Instituto de Computa??o Universidade Federal de Alagoas Curriculum Lattes: http://lattes.cnpq.br/2470781099632240 Linux User #425305 On 15 November 2010 18:15, Edward Kawas wrote: > Hi Lucas, > > I generated a build and placed it at > http://dev.biordf.net/~kawas/featureClient-2010-11-15.tar.gz > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Lucas Amorim > Sent: Monday, November 15, 2010 12:33 PM > To: Core developer announcements > Subject: Re: [MOBY-dev] IRC channel > > Ok, Thank you Eddie. > > I am really having trouble trying to run the "FeatureClient.jar" as I said > in a previews discussion, the problem us that I was not able to setup all > the dependencies needed. Can someone please provide me with a link to > download a working copy of a FeatureClient with all the dependencies > already > setup? Just upload yours to somewhere I can download. > The reason why I am asking this is because I need it to implement program > that will make biomoby service composition using an evolutionary algorithm > which I have already implemented and I just need to access information > about > the services in order to feed my algorithm and then invoke the services. > > This is my Course Conclusion Work (Bachelor in Computer Science) and I am > already late... > > If you can't point me to a working copy then please tell me how I could > make > the official one work. > > Thanks in advance! > Lucas Amorim > > Instituto de Computa??o > Universidade Federal de Alagoas > Curriculum Lattes: http://lattes.cnpq.br/2470781099632240 > > Linux User #425305 > > > On 15 November 2010 17:14, Edward Kawas wrote: > > > No IRC channel, just this mailing list. > > > > Eddie > > > > -----Original Message----- > > From: moby-dev-bounces at lists.open-bio.org > > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Lucas Amorim > > Sent: Monday, November 15, 2010 12:05 PM > > To: moby-dev at lists.open-bio.org > > Subject: [MOBY-dev] IRC channel > > > > Hello, > > > > Does Moby have a IRC channel for discussing topics related to > > installation/configuration/usage of the project? > > > > Thank you. > > > > Lucas Amorim > > > > Instituto de Computa??o > > Universidade Federal de Alagoas > > Curriculum Lattes: http://lattes.cnpq.br/2470781099632240 > > > > Linux User #425305 > > > > _______________________________________________ > > 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 > > > > _______________________________________________ > 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 volker.roessler at googlemail.com Tue Nov 16 08:12:00 2010 From: volker.roessler at googlemail.com (=?ISO-8859-1?Q?Volker_R=F6ssler?=) Date: Tue, 16 Nov 2010 09:12:00 +0100 Subject: [MOBY-dev] Strange problems with nested moby objects In-Reply-To: <01d201cb84f3$dc27b420$94771c60$@gmail.com> References: <01d201cb84f3$dc27b420$94771c60$@gmail.com> Message-ID: Hi Eddie, thank you so much for your fast and helpful response! Now the code finally works for me. I was already pretty frustrated, because I had taken every single bit of the code apart, searching for the error, but the error messages from the moses-service-testing script were not really helpful. But somehow I couldn't not see the forest for the trees... ;-) Volker On Mon, Nov 15, 2010 at 7:35 PM, Edward Kawas wrote: > Hi, > > The problem is with your line > > my $newTranscript => new MOSES::MOBY::Data::SNPTranscript > > that should actually read > > my $newTranscript = new MOSES::MOBY::Data::SNPTranscript > > an equal sign not a => > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Volker R?ssler > Sent: Monday, November 15, 2010 3:32 AM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] Strange problems with nested moby objects > > Hi everyone, > > I'm experiencing a rather strange problem when trying to build the response > object. What I'd like to achieve is building an > 'AnnotatedSNPAndTranscriptLocation' object which contains an array of > 'SNPTranscript' objects. > > My code for building the response object looks like this, but this causes > some strange problems: > > > @SNP_list = mymethod($some_user_input); > > foreach my $SNP (@SNP_list) { > > ? ? ? ?my @listOfBiomobyTranscriptObjects; > > ? ? ? ?my $transcriptList = $SNP->get_transcript_list(); > > ? ? ? ?foreach my $trans (@$transcriptList) { > > ? ? ? ? ? ?my $snp_type = $trans->get_field('snp_type'); > ? ? ? ? ? ?my $database_references = new MOSES::MOBY::Data::Object > ? ? ? ? ? ? ? ?( > ? ? ? ? ? ? ? ? ? ?id => $trans->get_field('name'), > ? ? ? ? ? ? ? ? ? ?namespace => 'Ensembl' > ? ? ? ? ? ? ? ?); > ? ? ? ? ? ?my $strand = $trans->get_field('strand'); > ? ? ? ? ? ?my $description = $trans->get_field('description'); > ? ? ? ? ? ?my $name = $trans->get_field('name'); > ? ? ? ? ? ?my $start = $trans->get_field('start'); > ? ? ? ? ? ?my $stop = $trans->get_field('stop'); > > > ? ? ? ? ? ?my $newTranscript => new MOSES::MOBY::Data::SNPTranscript > ? ? ? ? ? ? ? ?( > ? ? ? ? ? ? ? ? ? ?snp_type => $snp_type, > ? ? ? ? ? ? ? ? ? ?#database_references => $database_references, > ? ? ? ? ? ? ? ? ? ?strand => $strand, > ? ? ? ? ? ? ? ? ? ?description => $description, > ? ? ? ? ? ? ? ? ? ?name => $name, > ? ? ? ? ? ? ? ? ? ?start => $start, > ? ? ? ? ? ? ? ? ? ?stop => $stop > ? ? ? ? ? ? ? ?); > ? ? ? ? ? ?push (@listOfBiomobyTranscriptObjects, $newTranscript); > ? ? ? ?} > > ? ? ? ?my $output_snp_transcripts = new > MOSES::MOBY::Data::AnnotatedSNPAndTranscriptLocation > ? ? ? ? ? ?( > > ? ? ? ? ? ? ? ?snp_transcripts => \@listOfBiomobyTranscriptObjects, > ? ? ? ? ? ? ? ?coverage_all => $SNP->get_snp_coverage_all(), > ? ? ? ? ? ? ? ?coverage_new_allele => $SNP->get_snp_coverage_new_allele(), > ? ? ? ? ? ? ? ?genetype_allele => $SNP->get_snp_genotype_allele(), > ? ? ? ? ? ? ? ?reference_allele => $SNP->get_snp_reference_allele(), > ? ? ? ? ? ? ? ?confidence => $SNP->get_snp_score(), > ? ? ? ? ? ? ? ?Position => new MOSES::MOBY::Data::Position > ? ? ? ? ? ? ? ? ? ?( > ? ? ? ? ? ? ? ? ? ? ? ?end => $SNP->get_snp_position(), > ? ? ? ? ? ? ? ? ? ? ? ?start => $SNP->get_snp_position(), > ? ? ? ? ? ? ? ? ? ? ? ?chromosome => $SNP->get_snp_chromosome() > ? ? ? ? ? ? ? ? ? ?), > ? ? ? ? ? ? ? ?Strain => $strain > ? ? ? ? ? ?); > ? ? ? ?$response->add_output_snp_transcripts($output_snp_transcripts); > ? ?} > > > > When I'm trying to run this, I get the following error message: > 2010/11/15 12:26:02 (71764) FATAL> [13065] (eval 1068):155 - > ------------- EXCEPTION: MOSES::MOBY::Data::SNPTranscript ------------- > MSG: No such method: MOSES::MOBY::Data::SNPTranscript::value > > I suspect, that this error happens, because I am trying to use an array of > MOSES::MOBY::Data::Object (stored in @listOfBiomobyTranscriptObjects), but > I'm not quite sure. > > Any help or suggestions are greaty appreciated! > > Yours, > Volker > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From maxgarcia at uma.es Tue Nov 23 16:32:45 2010 From: maxgarcia at uma.es (=?ISO-8859-1?Q?Max_Garc=EDa?=) Date: Tue, 23 Nov 2010 17:32:45 +0100 Subject: [MOBY-dev] CVS can't create temporary directory In-Reply-To: <4F91222C659D5B4E8C89CE4D710BB08E4AEC86BBF5@DKFZEX01.ad.dkfz-heidelberg.de> References: <4F91222C659D5B4E8C89CE4D710BB08E4AEC86BBCD@DKFZEX01.ad.dkfz-heidelberg.de> <4CA2007F.1070109@sonsorol.org> <4F91222C659D5B4E8C89CE4D710BB08E4AEC86BBF5@DKFZEX01.ad.dkfz-heidelberg.de> Message-ID: <4CEBECAD.4060700@uma.es> Hi all, the same problem? BR Max *maxgarcia at chirimoyo:~/testMOBY$ cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby co -P moby-live* *can't create temporary directory /tmp/cvs-serv32572* *Read-only file system* El 29/09/2010 15:38, Biczok Rudolf escribi?: > 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 = ' [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 = ' [artifact:dependencies] [WARNING] POM for 'jdic:jdic:pom:1.0:compile' is invalid. It will be ignored for artifact resolution. Reason: Not a v4.0.0 POM. for project jdic:jdic at /home/biczok/.m2/repository/jdic/jdic/1.0/jdic-1.0.pom > [artifact:dependencies] Downloading: jdic/jdic/1.0/jdic-1.0.jar from central > [artifact:dependencies] Downloading: jdic/jdic/1.0/jdic-1.0.jar from maven2-repository.dev.java.net > [artifact:dependencies] Downloading: jdic/jdic/1.0/jdic-1.0.jar from bio.maven.repository > [artifact:dependencies] Downloading: jdic/jdic/1.0/jdic-1.0.jar from java.net-m2 > [artifact:dependencies] Downloading: jdic/jdic/1.0/jdic-1.0.jar from jboss.repository > [artifact:dependencies] Downloading: jdic/jdic/1.0/jdic-1.0.jar from kysoh > [artifact:dependencies] Transferring 0K from kysoh > [artifact:dependencies] [WARNING] *** CHECKSUM FAILED - Checksum failed on download: local = 'f16a32acf581b54dcf99a6aef9203da1425fc783'; remote = ' [artifact:dependencies] Downloading: jdic/jdic/1.0/jdic-1.0.jar from kysoh > [artifact:dependencies] Transferring 0K from kysoh > [artifact:dependencies] [WARNING] *** CHECKSUM FAILED - Checksum failed on download: local = 'f16a32acf581b54dcf99a6aef9203da1425fc783'; remote = ' [artifact:dependencies] [WARNING] POM for 'jdic:jdic:pom:1.0:compile' is invalid. It will be ignored for artifact resolution. Reason: Not a v4.0.0 POM. for project jdic:jdic at /home/biczok/.m2/repository/jdic/jdic/1.0/jdic-1.0.pom > > init: > [taskdef] java.util.zip.ZipException: error in opening zip file > ... > > It seems that the Maven dependency jdci:jdci:1.0 does not exists anymore and the repository on kysoh > returns rubbish. See here (the jdic-1.0.pom): > > > 302 Found > >

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> > > 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 > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Maximiliano Garc?a Oliver Computer Architecture Dept. University of Malaga, Spain ETSI Informatica Telf. +34 952 13 7651 Edificio de Bioinnovaci?n C/ Severo Ochoa - 34 Parque Tecnol?gico de Andaluc?a, 29590, Malaga mailto:maxgarcia at ac.uma.es 'But I don't want to go among mad people,' Alice remarked. 'Oh, you can't help that,' said the Cat: 'we're all mad here. I'm mad. You're mad.' 'How do you know I'm mad?' said Alice. 'You must be,' said the Cat, 'or you wouldn't have come here.' Alice's Adventures in Wonderland Lewis Carroll (1832-1898) --