[BioC] annotate htmlpage error
Georg Otto
gwo at well.ox.ac.uk
Wed Mar 14 21:13:39 CET 2012
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
More information about the Bioconductor
mailing list