Dear list: I just installed biomaRt1.4.0, RMySQL, and DBI. I am using R2.2.0 with BioC 1.7. I got error message when trying to connect mart: > mart <- martConnect() Error in mysqlNewConnection(drv, ...) : RS-DBI driver: (could not connect anonymous at ensembldb.ensembl.org on dbname "(null)") Or > marts <- listMarts() Error in mysqlNewConnection(drv, ...) : RS-DBI driver: (could not connect anonymous at ensembldb.ensembl.org on dbname "(null)") IS there any special settings that I missed? Any help will be highly appreciated. Xiwei Wu, MD, PhD Assistant Research Scientist Department of Biomedical Informatics Beckman Research Institute City of Hope National Medical Center Duarte, CA 91010 "EMF <coh.org>" made the following annotations. ---------------------------------------------------------------------- -------- SECURITY/CONFIDENTIALITY WARNING: This message and any atta...{{dropped}}

Steffen, Thank you very much for your reply. I think it might be due to firewall issue, but a little confused on how MySQL qyeries works here. I thought firewall usually does not block out-going traffic. How to enable mysql queries in the firewall? Are there any specific ports need to be opened? Xiwei -----Original Message----- From: Steffen Durinck [mailto:sdurinck@ebi.ac.uk] Sent: Wednesday, November 16, 2005 1:55 AM To: Wu, Xiwei Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] BiomaRt connection error Hi Xiwei, Are you behind a firewall? Keep in mind that the current biomaRt will try to do MySQL queries to the databases, if you are behind a firewall then these queries won't go through and you get the error you show. You can either ask your systems to enable mysql queries or install a local version of the BioMart database you want to query with biomaRt. best, Steffen On which platform are you working? Do you have the XML package installed? Wu, Xiwei wrote: >Dear list: > >I just installed biomaRt1.4.0, RMySQL, and DBI. I am using R2.2.0 with >BioC 1.7. I got error message when trying to connect mart: > > > >>mart <- martConnect() >> >> >Error in mysqlNewConnection(drv, ...) : RS-DBI driver: (could not >connect anonymous at ensembldb.ensembl.org on dbname "(null)") > >Or > > > >>marts <- listMarts() >> >> >Error in mysqlNewConnection(drv, ...) : RS-DBI driver: (could not >connect anonymous at ensembldb.ensembl.org on dbname "(null)") > >IS there any special settings that I missed? Any help will be highly >appreciated. > >Xiwei Wu, MD, PhD >Assistant Research Scientist >Department of Biomedical Informatics >Beckman Research Institute >City of Hope National Medical Center >Duarte, CA 91010 > >"EMF <coh.org>" made the following annotations. >--------------------------------------------------------------------- -- >------- SECURITY/CONFIDENTIALITY WARNING: This message and any >atta...{{dropped}} > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > > >

Hi Xiwei, Are you behind a firewall? Keep in mind that the current biomaRt will try to do MySQL queries to the databases, if you are behind a firewall then these queries won't go through and you get the error you show. You can either ask your systems to enable mysql queries or install a local version of the BioMart database you want to query with biomaRt. best, Steffen On which platform are you working? Do you have the XML package installed? Wu, Xiwei wrote: >Dear list: > >I just installed biomaRt1.4.0, RMySQL, and DBI. I am using R2.2.0 with >BioC 1.7. I got error message when trying to connect mart: > > > >>mart <- martConnect() >> >> >Error in mysqlNewConnection(drv, ...) : RS-DBI driver: (could not >connect anonymous at ensembldb.ensembl.org on dbname "(null)") > >Or > > > >>marts <- listMarts() >> >> >Error in mysqlNewConnection(drv, ...) : RS-DBI driver: (could not >connect anonymous at ensembldb.ensembl.org on dbname "(null)") > >IS there any special settings that I missed? Any help will be highly >appreciated. > >Xiwei Wu, MD, PhD >Assistant Research Scientist >Department of Biomedical Informatics >Beckman Research Institute >City of Hope National Medical Center >Duarte, CA 91010 > >"EMF <coh.org>" made the following annotations. >--------------------------------------------------------------------- --------- >SECURITY/CONFIDENTIALITY WARNING: This message and any atta...{{dropped}} > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > > >

Hi... I just experienzed the same "problem". It seems that my connection takes a little minute to ... ehh.. establish itself. I guess this is initialization of the Rmysql.. but just guessing.. after trying patiently a few more times I got connected to ensembl & vega.. And I must say: what a wonderfull package biomaRt is !! :) best morten with biomaRt XML RMySQL DBI "1.4.0" "0.97-8" "0.5-6" "0.1-9" >Dear list: > >I just installed biomaRt1.4.0, RMySQL, and DBI. I am using R2.2.0 with >BioC 1.7. I got error message when trying to connect mart: > > > >>mart <- martConnect() >> >> >Error in mysqlNewConnection(drv, ...) : RS-DBI driver: (could not >connect anonymous at ensembldb.ensembl.org on dbname "(null)") > >Or > > > >>marts <- listMarts() >> >> >Error in mysqlNewConnection(drv, ...) : RS-DBI driver: (could not >connect anonymous at ensembldb.ensembl.org on dbname "(null)") > >IS there any special settings that I missed? Any help will be highly >appreciated. > >Xiwei Wu, MD, PhD >Assistant Research Scientist >Department of Biomedical Informatics >Beckman Research Institute >City of Hope National Medical Center >Duarte, CA 91010 > >"EMF <coh.org>" made the following annotations. >--------------------------------------------------------------------- --------- >SECURITY/CONFIDENTIALITY WARNING: This message and any atta...{{dropped}} > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > >

Francois, Thank you for your help. I asked our network admin to open up outgoing connection on port 3306, but I still got the same error. I am going to try it tonight from my home computer to see if there is anything wrong on my side first. Any other suggestions? Xiwei -----Original Message----- From: Francois Pepin [mailto:fpepin@cs.mcgill.ca] Sent: Wednesday, November 16, 2005 9:20 AM To: Wu, Xiwei Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] BiomaRt connection error Hi Xiwei, yes, MySQL queries are outgoing connections. On the other hand, it requires connection to a specific port (3306 if my memory serves). It's not too uncommon to only allow connections to predefined ports (say http, ftp and ssh). The easiest for you would be to ask your network administrator if the firewall would indeed be blocking an outgoing connection to an a server on port 3306. Francois On Wed, 2005-11-16 at 08:44 -0800, Wu, Xiwei wrote: > Steffen, > > Thank you very much for your reply. I think it might be due to > firewall issue, but a little confused on how MySQL qyeries works here. > I thought firewall usually does not block out-going traffic. > > How to enable mysql queries in the firewall? Are there any specific > ports need to be opened? > > Xiwei > > -----Original Message----- > From: Steffen Durinck [mailto:sdurinck at ebi.ac.uk] > Sent: Wednesday, November 16, 2005 1:55 AM > To: Wu, Xiwei > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] BiomaRt connection error > > Hi Xiwei, > > Are you behind a firewall? > Keep in mind that the current biomaRt will try to do MySQL queries to > the databases, if you are behind a firewall then these queries won't > go through and you get the error you show. > You can either ask your systems to enable mysql queries or install a > local version of the BioMart database you want to query with biomaRt. > > best, > Steffen > > On which platform are you working? Do you have the XML package > installed? > > Wu, Xiwei wrote: > > >Dear list: > > > >I just installed biomaRt1.4.0, RMySQL, and DBI. I am using R2.2.0 > >with BioC 1.7. I got error message when trying to connect mart: > > > > > > > >>mart <- martConnect() > >> > >> > >Error in mysqlNewConnection(drv, ...) : RS-DBI driver: (could not > >connect anonymous at ensembldb.ensembl.org on dbname "(null)") > > > >Or > > > > > > > >>marts <- listMarts() > >> > >> > >Error in mysqlNewConnection(drv, ...) : RS-DBI driver: (could not > >connect anonymous at ensembldb.ensembl.org on dbname "(null)") > > > >IS there any special settings that I missed? Any help will be highly > >appreciated. > > > >Xiwei Wu, MD, PhD > >Assistant Research Scientist > >Department of Biomedical Informatics > >Beckman Research Institute > >City of Hope National Medical Center > >Duarte, CA 91010 > > > >"EMF <coh.org>" made the following annotations. > >--------------------------------------------------------------------- > >-- > >------- SECURITY/CONFIDENTIALITY WARNING: This message and any > >atta...{{dropped}} > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor at stat.math.ethz.ch > >https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >