[BioC] annotate htmlpage error

[Georg Otto]

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:

> 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