Dear Steffen Durinck, I downloaded today the biomaRt package from Bioconductor website and my R version is also the latest. When I use biomaRt without setting my proxy it gives me this error: > library(biomaRt) Loading required package: XML Loading required package: RCurl > ensembl <- useMart("ensembl") Error in validObject(.Object) : invalid class "Mart" object: invalid object for slot "vschema" in class "Mart": got class "NULL", should be or extend class "character" Best regards Jo?o Fadista Ph.d. student Danish Institute of Agricultural Sciences Research Centre Foulum Dept. of Genetics and Biotechnology Blichers All? 20, P.O. BOX 50 DK-8830 Tjele Phone: +45 8999 1900 Direct: +45 8999 8999 E-mail: Joao.Fadista at agrsci.dk Web: http://www.agrsci.org This email may contain information that is confidential. Any use or publication of this email without written permission from DIAS is not allowed. If you are not the intended recipient, please notify DIAS immediately and delete this email. -----Original Message----- From: Durinck, Steffen (NIH/NCI) [F] [mailto:durincks@mail.nih.gov] Sent: Thursday, November 30, 2006 3:23 PM To: Jo?o Fadista; bioconductor at stat.math.ethz.ch Subject: RE: [BioC] biomaRt Hi Joao, Are you sure you need to set your proxy? Try first to use biomaRt without setting it. library(biomaRt) ensembl <- useMart("ensembl") Also make sure you use the latest available version of biomaRt (biomaRt 1.8.1 in the release version or biomaRt 1.9.8 in the devel repository. The BioMart suite upgraded to version 0.5 this week and you'll need the latest biomaRt release to work with it. Best regards, Steffen -----Original Message----- From: Jo?o Fadista [mailto:Joao.Fadista@agrsci.dk] Sent: Thu 11/30/2006 9:01 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] biomaRt Dear all, I am having some trouble using the biomaRt useMart function. I do not know what seems to be the problem. Here is what I got: > Sys.putenv("http\_proxy" = "http://my.proxy.org:9999") ensembl <- > useMart("ensembl") Error in curlPerform(curl = curl, .opts = opts) : Could not resolve proxy: my.proxy.org; Host not found Best regards Jo?o Fadista Ph.d. student Danish Institute of Agricultural Sciences Research Centre Foulum Dept. of Genetics and Biotechnology Blichers All? 20, P.O. BOX 50 DK-8830 Tjele Phone: +45 8999 1900 Direct: +45 8999 8999 E-mail: Joao.Fadista at agrsci.dk <mailto:joao.fadista at="" agrsci.dk=""> Web: www.agrsci.org <http: www.agrsci.org=""/> ________________________________ News and news media <http: www.agrsci.org="" navigation="" nyheder_og_presse=""> . This email may contain information that is confidential. Any use or publication of this email without written permission from DIAS is not allowed. If you are not the intended recipient, please notify DIAS immediately and delete this email. [[alternative HTML version deleted]]

Dear Steffen Durinck, I am working on a Windows platform and I cannot install the biomaRt version via SVN. Perhaps tomorrow I will able to download the latest version from Bioconductor website. Best regards Jo?o Fadista Ph.d. student Danish Institute of Agricultural Sciences Research Centre Foulum Dept. of Genetics and Biotechnology Blichers All? 20, P.O. BOX 50 DK-8830 Tjele Phone: +45 8999 1900 Direct: +45 8999 8999 E-mail: Joao.Fadista at agrsci.dk Web: http://www.agrsci.org This email may contain information that is confidential. Any use or publication of this email without written permission from DIAS is not allowed. If you are not the intended recipient, please notify DIAS immediately and delete this email. -----Original Message----- From: Durinck, Steffen (NIH/NCI) [F] [mailto:durincks@mail.nih.gov] Sent: Thursday, November 30, 2006 3:44 PM To: Jo?o Fadista Cc: bioconductor at stat.math.ethz.ch Subject: RE: [BioC] biomaRt Hi Joao, >From the error it seems like you don't have the latest version. The packages were updated only yesterday and it looks like the builds are not yet available via the Bioconductor website. They are available via SVN and I hope they will be downloadable via the BioC website by tommorow. Here is how you can get the latest biomaRt version via SVN. http://wiki.fhcrc.org/bioc/SvnHowTo Alternatively if you work on a linux platform I could send you the latest version by mail, let me know. Best regards, Steffen -----Original Message----- From: Jo?o Fadista [mailto:Joao.Fadista@agrsci.dk] Sent: Thu 11/30/2006 9:27 AM To: Durinck, Steffen (NIH/NCI) [F] Cc: bioconductor at stat.math.ethz.ch Subject: RE: [BioC] biomaRt Dear Steffen Durinck, I downloaded today the biomaRt package from Bioconductor website and my R version is also the latest. When I use biomaRt without setting my proxy it gives me this error: > library(biomaRt) Loading required package: XML Loading required package: RCurl > ensembl <- useMart("ensembl") Error in validObject(.Object) : invalid class "Mart" object: invalid object for slot "vschema" in class "Mart": got class "NULL", should be or extend class "character" Best regards Jo?o Fadista Ph.d. student Danish Institute of Agricultural Sciences Research Centre Foulum Dept. of Genetics and Biotechnology Blichers All? 20, P.O. BOX 50 DK-8830 Tjele Phone: +45 8999 1900 Direct: +45 8999 8999 E-mail: Joao.Fadista at agrsci.dk Web: http://www.agrsci.org This email may contain information that is confidential. Any use or publication of this email without written permission from DIAS is not allowed. If you are not the intended recipient, please notify DIAS immediately and delete this email. -----Original Message----- From: Durinck, Steffen (NIH/NCI) [F] [mailto:durincks@mail.nih.gov] Sent: Thursday, November 30, 2006 3:23 PM To: Jo?o Fadista; bioconductor at stat.math.ethz.ch Subject: RE: [BioC] biomaRt Hi Joao, Are you sure you need to set your proxy? Try first to use biomaRt without setting it. library(biomaRt) ensembl <- useMart("ensembl") Also make sure you use the latest available version of biomaRt (biomaRt 1.8.1 in the release version or biomaRt 1.9.8 in the devel repository. The BioMart suite upgraded to version 0.5 this week and you'll need the latest biomaRt release to work with it. Best regards, Steffen -----Original Message----- From: Jo?o Fadista [mailto:Joao.Fadista@agrsci.dk] Sent: Thu 11/30/2006 9:01 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] biomaRt Dear all, I am having some trouble using the biomaRt useMart function. I do not know what seems to be the problem. Here is what I got: > Sys.putenv("http\_proxy" = "http://my.proxy.org:9999") ensembl <- > useMart("ensembl") Error in curlPerform(curl = curl, .opts = opts) : Could not resolve proxy: my.proxy.org; Host not found Best regards Jo?o Fadista Ph.d. student Danish Institute of Agricultural Sciences Research Centre Foulum Dept. of Genetics and Biotechnology Blichers All? 20, P.O. BOX 50 DK-8830 Tjele Phone: +45 8999 1900 Direct: +45 8999 8999 E-mail: Joao.Fadista at agrsci.dk <mailto:joao.fadista at="" agrsci.dk=""> Web: www.agrsci.org <http: www.agrsci.org=""/> ________________________________ News and news media <http: www.agrsci.org="" navigation="" nyheder_og_presse=""> . This email may contain information that is confidential. Any use or publication of this email without written permission from DIAS is not allowed. If you are not the intended recipient, please notify DIAS immediately and delete this email. [[alternative HTML version deleted]]