[BioC] annotate htmlpage error

[Martin Morgan]

On 03/14/2012 01:13 PM, Georg Otto wrote:
> Hi,
>
> after updating the annotate package from 1.32.1 to 1.32.2 I get an error
> using the htmlpage function. Here with the old version:

Sorry, probably my fault; I've tried to update this in v. 1.32.3. If you 
provide a fully reproducible example (deg$id, othernames, table.head as 
necessary to reproduce just the bug) I could be more sure of the fix. Martin

>
>> htmlpage(list(deg$id), file = "test-1.html", othernames = list(othernames), table.head = table.head, repository = list("ens"), species ="Rattus_norvegicus")
>
>> sessionInfo()
> R version 2.14.2 (2012-02-29)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>   [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] annotate_1.32.1       AnnotationDbi_1.16.19 Biobase_2.14.0
>
> loaded via a namespace (and not attached):
> [1] DBI_0.2-5      IRanges_1.12.6 RSQLite_0.11.1 xtable_1.7-0
>
>
> now with the new version:
>
>
>> htmlpage(list(deg$id), file = "test-1.html", othernames = list(othernames), table.head = table.head, repository = list("ens"), species ="Rattus_norvegicus")
> Error: To make links for Ensembl, you need to pass a 'species' argument.
>
>
>> sessionInfo()
> R version 2.14.2 (2012-02-29)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>   [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] annotate_1.32.2       AnnotationDbi_1.16.19 Biobase_2.14.0
>
> loaded via a namespace (and not attached):
> [1] DBI_0.2-5      IRanges_1.12.6 RSQLite_0.11.1 xtable_1.7-0
>
>
> It seems that the "species" argument is not passed correctly.
>
> Can this be fixed?
>
> Best,
>
> Georg
>
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