Hi, 

I've been working with a some Bos Taurus samples, and tried to use biomaRt to retrieve HGNC symbols, and descriptions based on Ensembl Gene Identifiers, using the getBM function. 

ensembl    <- useMart("ensembl")
ensembl    <- useDataset("btaurus_gene_ensembl",
                         mart = ensembl)
annotation <- getBM(attributes = c('ensembl_gene_id',  'hgnc_symbol', 'description'),
                    filters    = 'ensembl_gene_id',
                    values     = c("ENSBTAG00000045918", "ENSBTAG00000045919", 
                                   "ENSBTAG00000045920", "ENSBTAG00000045921", 
                                   "ENSBTAG00000045922", "ENSBTAG00000045923"),
                    mart       = ensembl)

Strangely, it seems that only a combination of the above query results in the error: 

Warning message:
In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
  EOF within quoted string

I can't isolate it to a single Gene ID, but rather this vector of IDs. Any advice is appreciated!

Cheers!

I coerced warnings to errors, ran your code, then used traceback() to see where things were going wrong.

options(warn=2)
annotation <- ...
+                     mart       = ensembl)
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  (converted from warning) EOF within quoted string
> traceback()
7: doWithOneRestart(return(expr), restart)
6: withOneRestart(expr, restarts[[1L]])
5: withRestarts({
       .Internal(.signalCondition(simpleWarning(msg, call), msg, 
           call))
       .Internal(.dfltWarn(msg, call))
   }, muffleWarning = function() NULL)
4: .signalSimpleWarning("EOF within quoted string", quote(scan(file = file, 
       what = what, sep = sep, quote = quote, dec = dec, nmax = nrows, 
       skip = 0, na.strings = na.strings, quiet = TRUE, fill = fill, 
       strip.white = strip.white, blank.lines.skip = blank.lines.skip, 
       multi.line = FALSE, comment.char = comment.char, allowEscapes = allowEscapes, 
       flush = flush, encoding = encoding, skipNul = skipNul)))
3: scan(file = file, what = what, sep = sep, quote = quote, dec = dec, 
       nmax = nrows, skip = 0, na.strings = na.strings, quiet = TRUE, 
       fill = fill, strip.white = strip.white, blank.lines.skip = blank.lines.skip, 
       multi.line = FALSE, comment.char = comment.char, allowEscapes = allowEscapes, 
       flush = flush, encoding = encoding, skipNul = skipNul)
2: read.table(con, sep = "\t", header = bmHeader, quote = "\"", 
       comment.char = "", check.names = FALSE, stringsAsFactors = FALSE)
1: getBM(attributes = c("ensembl_gene_id", "hgnc_symbol", "description"), 
       filters = "ensembl_gene_id", values = c("ENSBTAG00000045918", 
           "ENSBTAG00000045919", "ENSBTAG00000045920", "ENSBTAG00000045921", 
           "ENSBTAG00000045922", "ENSBTAG00000045923"), mart = ensembl)

Looks like it's in scan, so I debugged that and tried again

debug(scan)
annotation <- ...
...
debugging in: scan(file, what = "", sep = sep, quote = quote, nlines = 1, quiet = TRUE, 
    skip = 0, strip.white = TRUE, blank.lines.skip = blank.lines.skip, 
    comment.char = comment.char, allowEscapes = allowEscapes, 
    encoding = encoding, skipNul = skipNul)
...

I took a look at file, guessing it is what was returned by biomaRt

Browse[2]> readLines(file)
 [1] "ENSBTAG00000045918\t\t"                                                                                                                    
 [2] "ENSBTAG00000045919\t\tUncharacterized protein  [Source:UniProtKB/TrEMBL;Acc:G3N011]"                                                       
 [3] "ENSBTAG00000045920\t\t5S ribosomal RNA [Source:RFAM;Acc:RF00001]"                                                                          
 [4] "ENSBTAG00000045921\t\tUncharacterized protein  [Source:UniProtKB/TrEMBL;Acc:G3N082]"                                                       
 [5] "ENSBTAG00000045922\t\tOlfactory receptor  [Source:UniProtKB/TrEMBL;Acc:G3MX62]"                                                            
 [6] "ENSBTAG00000045918\t\t"                                                                                                                    
 [7] "ENSBTAG00000045919\t\tUncharacterized protein  [Source:UniProtKB/TrEMBL;Acc:G3N011]"                                                       
 [8] "ENSBTAG00000045920\t\t5S ribosomal RNA [Source:RFAM;Acc:RF00001]"                                                                          
 [9] "ENSBTAG00000045921\t\tUncharacterized protein  [Source:UniProtKB/TrEMBL;Acc:G3N082]"                                                       
[10] "ENSBTAG00000045922\t\tOlfactory receptor  [Source:UniProtKB/TrEMBL;Acc:G3MX62]"                                                            
[11] "ENSBTAG00000045923\t\tMHC class II antigen; Putative MHC class II antigen\"; Uncharacterized protein  [Source:UniProtKB/TrEMBL;Acc:Q70IB5]"
[12] ""                                                                                                                              

Line 11 looks suspicious - there's an escaped quote \", and I see that from the line numbered '2' in the traceback() that the code explicitly allows this to indicate the opening of a string. When I look online I see the same quotation mark. I think (a) it's a data entry error with biomart; (b) it's not easy to work around, in particular because it seems like the biomaRt author has explicitly indicated that the quotation mark should open a string; and (c) that this can be quite bad, for instance the reason that you can't isolate this to a single ID is because with a single ID scan() guesses the wrong number of fields to parse, and somehow biomaRt quietly ignores the record. I think the best bet is to get this fixed upstream.