Trouble using biomaRt to retrieve hgnc symbols from Ensembl transcript ids
You need to specify the number without the version. Instead of "ENSMUST00000178862.1" just "ENSMUST00000178862":

You can do this with one more line:

g &lt;- gsub("\\..*", "", rownames(txi.kallisto$counts))
(hgnc_symbols &lt;- getBM(attributes = c("hgnc_symbol", "chromosome_name", "ensembl_transcript_id"), filters = "ensembl_transcript_id", values = g, mart = mart))
##  hgnc_symbol chromosome_name ensembl_transcript_id
##1          NA              14    ENSMUST00000177564
##2          NA               6    ENSMUST00000178537
##3          NA               6    ENSMUST00000178862
##4          NA              12    ENSMUST00000179520
##5          NA              14    ENSMUST00000179664
##6          NA              14    ENSMUST00000196221


With these transcripts it doesn't seem that there is an equivalent hgnc_symbol. But is recognized, otherwise they are not recognized:

(hgnc_symbols &lt;- getBM(attributes = c("hgnc_symbol", "chromosome_name", "ensembl_transcript_id"), filters = "ensembl_transcript_id", values = rownames(txi.kallisto$counts), mart = mart))
## [1] hgnc_symbol           chromosome_name       ensembl_transcript_id
##&lt;0 rows&gt; (or 0-length row.names)


However you might be interested in doing something like this:

human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl")
getLDS(attributes = "ensembl_transcript_id",
       filters = "ensembl_transcript_id", values = g,mart = mouse,
      attributesL = "hgnc_symbol", martL = human)
## The query to the BioMart webservice returned an invalid result: the number of 
## columns in the result table does not equal the number of 
## attributes in the query. Please report this to the mailing list.