[BioC] building a refseq-based transcriptDb: warnings of interest?

[Vincent Carey]

> hg18r.txdb = makeTranscriptDbFromUCSC(tablename="refGene")
Download the refGene table ... OK
Download the refLink table ... OK
Extract the 'transcripts' data frame ... OK
Extract the 'splicings' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TranscriptDb object ... OK
There were 50 or more warnings (use warnings() to see the first 50)
> warnings()
Warning messages:
1: In .extractUCSCCdsStartEnd(cdsStart[i], cdsEnd[i],
exon_locs$start[[i]],  ... :
  UCSC data anomaly in transcript NM_017940: the cds cumulative length
is not a multiple of 3
2: In .extractUCSCCdsStartEnd(cdsStart[i], cdsEnd[i],
exon_locs$start[[i]],  ... :
  UCSC data anomaly in transcript NM_001037675: the cds cumulative
length is not a multiple of 3
3: In .extractUCSCCdsStartEnd(cdsStart[i], cdsEnd[i],
exon_locs$start[[i]],  ... :
  UCSC data anomaly in transcript NM_001039703: the cds cumulative
length is not a multiple of 3
4: In .extractUCSCCdsStartEnd(cdsStart[i], cdsEnd[i],
exon_locs$start[[i]],  ... :

and so on.  Does this need to be reported to UCSC?

>  sessionInfo()
R version 2.12.0 Under development (unstable) (2010-06-30 r52417)
Platform: x86_64-apple-darwin10.3.0/x86_64 (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices datasets  tools     utils     methods
[8] base

other attached packages:
[1] GenomicFeatures_1.1.6 GenomicRanges_1.1.15  IRanges_1.7.13
[4] weaver_1.15.0         codetools_0.2-2       digest_0.4.2

loaded via a namespace (and not attached):
[1] BSgenome_1.17.5    Biobase_2.9.0      Biostrings_2.17.26 DBI_0.2-5
[5] RCurl_1.4-2        RSQLite_0.9-1      XML_3.1-0          biomaRt_2.5.1
[9] rtracklayer_1.9.3