Error in R CMD check

[guido scarabelli]

Hi all, I was checking bio3d version 2.0-1 and I found this error when testing the example. It is related to the uniprot function, I guess.

R CMD check bio3d_2.0-1.tar.gz

...
* checking examples ... ERROR
Running examples in ‘bio3d-Ex.R’ failed
The error most likely occurred in:

> ### Name: uniprot
> ### Title: Fetch UniProt Entry Data.
> ### Aliases: uniprot
> ### Keywords: utilities
> 
> ### ** Examples
> 
> prot <- uniprot('PH4H_HUMAN')
trying URL 'http://www.uniprot.org/uniprot/PH4H_HUMAN.xml'
Content type 'application/xml' length unknown
opened URL
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
......
downloaded 106 Kb

Error in uniprot("PH4H_HUMAN") : could not find function "xmlRoot"
Execution halted

Thanks!!

[Barry Grant]

why do we need this function. There is a get.seq() already that should be able to work with uniprot/swiss-prot. What am I missing - why do we need this? There is also an old get.uniprot in the model.R file in the new_funs/ dir but I haven't looked at it for a long time as get.seq() should be place for this.

[Barry Grant]

Does get.seq() not work with uniprot in the way you need? If it works ok I suggest removing this function. Otherwise we should incorporate what ever it's new functionality is into get.seq().

[Lars Skjærven]

hmm.. you're probably right. I was doing some sequence analysis, and I wanted to quickly annotate the sequences I was working (e.g. with protein name, organism, taxonomic linage etc).

I would then like to do something like:

prot <- uniprot('PH4H_HUMAN')
prot$fullName
prot$organism

and then in a larger scale from my blast results from swissprot, obtaining e.g. organism, and label a plot etc.

For now, I agree that it stands a bit without much real application. Perhaps I should remove this, and include it again if/when it's more complete.

[Barry Grant]

If it has new features (such as extra annotation) then lets keep it. I just wanted to make sure it was not a duplicate of get.seq() Thanks for clarifying!

[Lars Skjærven]

ok. keeping- to be improved though

[Lars Skjærven]

added bugfix in recent commit