[Bioc-devel] cryptic error in VariantAnnotation::locateVariants()

[Valerie Obenchain]

Hi,

Thanks for the report. Now fixed in 1.13.31.

This problem, like the last one you reported, was related to CDSID 
becoming an IntegerList. When region=AllVariants, results are combined 
and ordered by QUERYID, TXID, CDSID and GENEID. In your example ties 
were not broken by QUERYID or TXID and so CDSID was tested. order() does 
work on 'List' objects but they must be the only argument. The error was 
complaining that when order() has multiple arguments they can't be 
'List's. This is a bit of a special case and is why you haven't seen 
this error for all runs of locateVariants().

Now that CDSID is an IntegerList (holds multiple values) it doesn't make 
sense to include it in the ordering so I have removed it.

Valerie


On 02/16/2015 07:44 AM, Robert Castelo wrote:
> hi Valerie,
>
> i'm afraid i have hit another cryptic error in locateVariants() related
> to some recent update of the devel version of the package, could you
> take a look at it? (code below..)
>
> thanks!!
>
> robert.
>
> ==========================================
>
> library(VariantAnnotation)
> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
>
> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
>
> gr <- GRanges("chrX", IRanges(start=128913961, width=1))
>
> loc <- locateVariants(gr, txdb,
>                        AllVariants(intergenic=IntergenicVariants(0, 0)))
> Error in ans[order(meta$QUERYID, meta$TXID, meta$CDSID, meta$GENEID),  :
>    error in evaluating the argument 'i' in selecting a method for
> function '[': Error in order(c(1L, 1L), c("76534", "76534"),
> list(integer(0), integer(0)),  :
>    unimplemented type 'list' in 'listgreater'
> 4: ans[order(meta$QUERYID, meta$TXID, meta$CDSID, meta$GENEID),
>         ]
> 3: .local(query, subject, region, ...)
> 2: locateVariants(gr, txdb, AllVariants(intergenic = IntergenicVariants(0,
>         0)))
> 1: locateVariants(gr, txdb, AllVariants(intergenic = IntergenicVariants(0,
>         0)))
> sessionInfo()
> R Under development (unstable) (2014-10-14 r66765)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF8       LC_NUMERIC=C LC_TIME=en_US.UTF8
> LC_COLLATE=en_US.UTF8
>   [5] LC_MONETARY=en_US.UTF8    LC_MESSAGES=en_US.UTF8
> LC_PAPER=en_US.UTF8       LC_NAME=C
>   [9] LC_ADDRESS=C              LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF8
> LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats4    parallel  stats     graphics  grDevices utils     datasets
>   methods   base
>
> other attached packages:
>   [1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.0.0 GenomicFeatures_1.19.18
>                AnnotationDbi_1.29.17
>   [4] Biobase_2.27.1                          VariantAnnotation_1.13.29
>                Rsamtools_1.19.27
>   [7] Biostrings_2.35.8                       XVector_0.7.4
>                GenomicRanges_1.19.37
> [10] GenomeInfoDb_1.3.13                     IRanges_2.1.38
> S4Vectors_0.5.19
> [13] BiocGenerics_0.13.4                     vimcom_1.0-0
> setwidth_1.0-3
> [16] colorout_1.0-3
>
> loaded via a namespace (and not attached):
>   [1] base64enc_0.1-2          BatchJobs_1.5            BBmisc_1.9
>           BiocParallel_1.1.13
>   [5] biomaRt_2.23.5           bitops_1.0-6             brew_1.0-6
>           BSgenome_1.35.17
>   [9] checkmate_1.5.1          codetools_0.2-10         DBI_0.3.1
>           digest_0.6.8
> [13] fail_1.2                 foreach_1.4.2 GenomicAlignments_1.3.27
> iterators_1.0.7
> [17] RCurl_1.95-4.5           RSQLite_1.0.0 rtracklayer_1.27.7
> sendmailR_1.2-1
> [21] stringr_0.6.2            tools_3.2.0              XML_3.98-1.1
>          zlibbioc_1.13.1


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