Michel, Yes, the problem was solved by opening outgoing port 3306. It is a firewall issue. As soon as the port was opened, the database connection had no problem. Please see response from other people to my question too. Good luck! Let me know if you need any other details. Xiwei >Date: Fri, 2 Dec 2005 09:11:43 +0100 >From: Michel JUGE <michel.juge at="" st.com=""> >Subject: [BioC] DB connection error >To: <bioconductor at="" stat.math.ethz.ch=""> >Message-ID: <000201c5f718$0d516100$2872400a at rou.st.com> >Content-Type: text/plain; charset="utf-8" > > >Xiwei Wu, > >I get same issue, did you solve your problem ? >It seems to me that the DBI driver is not appropriate to R2.2... > > regards > >--------------------------------------------------------------------- >>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)") "EMF <coh.org>" made the following annotations. ---------------------------------------------------------------------- -------- SECURITY/CONFIDENTIALITY WARNING: This message and any atta...{{dropped}}

thanks very much for your inputs ... It's working now -----Original Message----- From: Wu, Xiwei [mailto:XWu@coh.org] Sent: 06 December, 2005 18:12 To: bioconductor at stat.math.ethz.ch Cc: michel.juge at st.com Subject: RE: Bioconductor Digest, Vol 34, Issue 5 Michel, Yes, the problem was solved by opening outgoing port 3306. It is a firewall issue. As soon as the port was opened, the database connection had no problem. Please see response from other people to my question too. Good luck! Let me know if you need any other details. Xiwei >Date: Fri, 2 Dec 2005 09:11:43 +0100 >From: Michel JUGE <michel.juge at="" st.com=""> >Subject: [BioC] DB connection error >To: <bioconductor at="" stat.math.ethz.ch=""> >Message-ID: <000201c5f718$0d516100$2872400a at rou.st.com> >Content-Type: text/plain; charset="utf-8" > > >Xiwei Wu, > >I get same issue, did you solve your problem ? >It seems to me that the DBI driver is not appropriate to R2.2... > > regards > >--------------------------------------------------------------------- >>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)") "EMF <coh.org>" made the following annotations. ---------------------------------------------------------------------- ------ -- SECURITY/CONFIDENTIALITY WARNING: This message and any atta...{{dropped}}