Hi, everyone, I met an error message when I using biomaRt package. > listMarts() Error in if is.na(pattern)) { : argument is of length zero In addition: Warning message: is.na() applied to non-(list or vector) in: is.na(pattern) Does anyone know what's wrong? I'm running windows 2k, R 2.0.1, bioconductor 1.6, and biomaRt 1.1.2. Thanks a lot! Bin

Hi Bin, On 29 Jun 2005, binye at med.wayne.edu wrote: > I met an error message when I using biomaRt package. >> listMarts() > Error in if is.na(pattern)) { : argument is of length zero > In addition: Warning message: > is.na() applied to non-(list or vector) in: is.na(pattern) > > Does anyone know what's wrong? I'm running windows 2k, R 2.0.1, > bioconductor 1.6, and biomaRt 1.1.2. That may be part of what is wrong. BioC 1.6 packages are only known to work with R 2.1.x. Try upgrading R (and reinstalling the BioC packages) and see if that doesn't help. + seth

Is RMySQL installed? If so, what happens when you do: driv <- dbDriver('MySQL', force.reload=FALSE) conn <- dbConnect(driv,user='anonymous',password='',host='ensembldb.ensembl.or g' ) res <- dbGetQuery(conn,"show databases like '%mart%'") dbDisconnect(conn) res Do you get something that lists the databases like: ensembl_mart_27_1 ensembl_mart_28_1 .... Sean On Jun 29, 2005, at 3:33 PM, Ye, Bin wrote: > Hi, everyone, > > I met an error message when I using biomaRt package. >> listMarts() > Error in if is.na(pattern)) { : argument is of length zero > In addition: Warning message: > is.na() applied to non-(list or vector) in: is.na(pattern) > > Does anyone know what's wrong? I'm running windows 2k, R 2.0.1, > bioconductor 1.6, and biomaRt 1.1.2. > > Thanks a lot! > > > Bin > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor

Thank you Steffen, and thank you Sean! I really appreciate all your help! Bin -----Original Message----- From: Steffen Durinck [mailto:sdurinck@ebi.ac.uk] Sent: Thu 6/30/2005 3:47 AM To: Ye, Bin Cc: Sean Davis; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] biomaRt package listMarts() error Hi Bin, Thanks for reporting this, it is a bug the listMarts function and I will fix it. The BioMarts that are currently accessible with the biomaRt package are ensembl, vega, snp and sequence. If you want to connect to all or some of these you can do the following: > mart<-martConnect(biomarts=c("ensembl","snp","vega","sequence")) connected to: ensembl_mart_31 connected to: snp_mart_31 connected to: vega_mart_31 connected to: sequence_mart_31 Cheers, Steffen Sean Davis wrote: >Is RMySQL installed? > >If so, what happens when you do: > >driv <- dbDriver('MySQL', force.reload=FALSE) >conn <- >dbConnect(driv,user='anonymous',password='',host='ensembldb.ensembl.o rg' >) >res <- dbGetQuery(conn,"show databases like '%mart%'") >dbDisconnect(conn) >res > >Do you get something that lists the databases like: >ensembl_mart_27_1 >ensembl_mart_28_1 >.... > >Sean > > >On Jun 29, 2005, at 3:33 PM, Ye, Bin wrote: > > > >>Hi, everyone, >> >>I met an error message when I using biomaRt package. >> >> >>>listMarts() >>> >>> >>Error in if is.na(pattern)) { : argument is of length zero >>In addition: Warning message: >>is.na() applied to non-(list or vector) in: is.na(pattern) >> >>Does anyone know what's wrong? I'm running windows 2k, R 2.0.1, >>bioconductor 1.6, and biomaRt 1.1.2. >> >>Thanks a lot! >> >> >>Bin >> >>_______________________________________________ >>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 > > >