[BioC] annotate htmlpage error

[James W. MacDonald]

Hi Martin,

On 3/14/2012 4:36 PM, Martin Morgan wrote:
> 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

library(annotate)
library(org.Hs.eg.db)
gnlst2 <- list(egs = head(Rkeys(org.Hs.egENSEMBL),3))
example(htmlpage)
htmlpage(gnlst2, "test.html","Some gene expression data", otherdata, 
c("Ens", table.head[-c(1:3)]), repository=list("ens"), species = 
"Homo_sapiens")

Best,

Jim



>
>>
>>> 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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>
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099