Hi Nicola,

is that really the script you are using? Running it from the shell? If 
so, there is a mistake in the header:
> #!/bin/bash
will run it as a bash script and not as R. The first line of the file 
should be:

> #! /usr/bin/Rscript --vanilla

As for the actual error, which probably came from the R console, I can't 
help you much there.

Best,
António


On 16/08/13 12:00, bioconductor-request@r-project.org wrote:
> On Aug 15, 2013, at 11:00 AM, Nicola Cole<ncole@utexas.edu>  wrote:
>
>> >Hi,
>> >
>> >I am trying to use RIPSeeker with bam files generated from Arabidopsis.  I have emailed the author numerous times, and she has finally referred me to you all.
>> >
>> >The error I am getting is:
>> >
>> >Error in useMart(dataset = biomaRt_dataset, ...) :
>> >  Incorrect BioMart name, use the listMarts function to see which BioMart databases are available
>> >Calls: ripSeek ... suppressMessages -> withCallingHandlers -> annotateRIP -> useMart
>> >Execution halted
>> >
>> >The script I am using is:
>> >
>> >#!/bin/bash
>> >
>> >source("http://bioconductor.org/biocLite.R")
>> >biocLite("RIPSeeker")
>> >library(RIPSeeker)
>> >biocLite("biomaRt")
>> >library(biomaRt)
>> >biocLite("ChIPpeakAnno")
>> >biocLite("GenomicFeatures")
>> >library(GenomicFeatures)
>> >library(GenomicRanges)
>> >library(rtracklayer)
>> >
>> >bamFiles<-list.files("/work/02044/ncole/Anna_Analysis/Bam_Files_for_RIPSeek/Temp_Bam_Files/","\\.bam$",
>> >recursive=TRUE, full.names=TRUE)
>> >cName <- "Control_ "
>> >outDir<-file.path(getwd(),"Nicola_4G_out")
>> >binSize<-NULL
>> >minBinSize <- 10000
>> >maxBinSize <- 10100
>> >multicore <- TRUE
>> >strandType <-NULL
>> >biomart <- "ENSEMBL_MART_PLANT"
>> >biomaRt_dataset <- "athaliana_eg_gene"
>> >goAnno <- "org.At.tair.db"
>> >
>> >seekOut.All_the_bams<- ripSeek(bamPath = bamFiles, cName = cName,
>> >reverseComplement = TRUE,strandType = strandType,
>> >uniqueHit = TRUE, assignMultihits = TRUE,
>> >rerunWithDisambiguatedMultihits = TRUE,
>> >binSize=binSize, minBinSize = minBinSize,
>> >maxBinSize = maxBinSize,
>> >biomart=biomart,
>> >biomaRt_dataset = biomaRt_dataset, goAnno = goAnno,
>> >multicore=multicore, outDir=outDir)
>> >
>> >q()
>> >
>> >While "ENSEMBL_MART_PLANT" comes up in the listMarts function when I try to use that in the useMart function, I get the error:
>> >
>> >Error in useMart(ENSEMBL_MART_PLANT, dataset, host = "www.biomart.org",  :
>> >  object 'ENSEMBL_MART_PLANT' not found
>> >
>> >
>> >Can you tell me what needs changing in my script?
>> >
>> >Thank  you,
>> >
>> >Nicola Cole
>> >Browning Lab
>> >PhD candidate
>> >UT Ausitn
>> >

-- 
António Miguel de Jesus Domingues, PhD
Neugebauer group
Max Planck Institute of Molecular Cell Biology and Genetics, Dresden
Pfotenhauerstrasse 108
01307 Dresden
Germany

e-mail: domingue@mpi-cbg.de
tel. +49 351 210 2481
The Unbearable Lightness of Molecular Biology


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