[BioC] Missing function locuslinkQuery and locuslinkBYID in annotate 1.18.0

[James W. MacDonald]

Hi Monnie,

McGee, Monnie wrote:
> Dear Mark,
> 
> Thank you.
> 
> I don't have access to the source tree.  Does this mean that I need
> to download the annotate library again, or can I grab the functions
> separately?   If the latter, how is that done?

You don't want to grab the functions separately. Just re-install using 
biocLite(), assuming the changes Marc made have propagated to the 
download server by now.

Best,

Jim


> 
> Best, Monnie
> 
> Monnie McGee, Ph.D. Associate Professor Department of Statistical
> Science Southern Methodist University Ph: 214-768-2462 Fax:
> 214-768-4035
> 
> 
> 
> -----Original Message----- From: Marc Carlson
> [mailto:mcarlson at fhcrc.org] Sent: Wed 10/8/2008 11:03 AM To: McGee,
> Monnie Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Missing
> function locuslinkQuery and locuslinkBYID in	annotate 1.18.0
> 
> Hi Monnie,
> 
> These functions seem to have disappeared as we moved from the older 
> annotations to the new kind.  I have just checked in some replacement
>  functions for you into the development branch (entrezGeneByID() and 
> entrezGeneQuery()).  If you have access to the source tree then these
>  are already available, but they should be on the website within 24
> hours.
> 
> Marc
> 
> 
> 
> McGee, Monnie wrote:
>> Dear List,
>> 
>> I was going through the examples in the query documentation
>> (written in June of 2008) for the annotate package when I came to
>> an error.   The function "locuslinkQuery" no longer seems to exist,
>> and neither does "locuslinkByID".    Here are my code and session
>> info:
>> 
>> 
>>> sessionInfo()
>>> 
>> R version 2.7.2 (2008-08-25) powerpc-apple-darwin8.11.1
>> 
>> locale: C
>> 
>> attached base packages: [1] splines   tools     stats     graphics
>> grDevices [6] utils     datasets  methods   base
>> 
>> other attached packages: [1] XML_1.96-0          cMAP_1.15.1
>>  [3] GOstats_2.6.0       Category_2.6.0 [5] genefilter_1.20.0
>> survival_2.34-1 [7] RBGL_1.16.0         annotate_1.18.0 [9]
>> xtable_1.5-3        GO.db_2.2.0 [11] hgu133a_2.2.0
>> RbcBook1_1.8.0 [13] graph_1.18.1        KEGG_2.2.0 [15]
>> hgu95av2.db_2.2.0   AnnotationDbi_1.2.1 [17] RSQLite_0.6-8
>> DBI_0.2-4 [19] Biobase_2.0.1       hgu95av2_2.2.0
>> 
>> loaded via a namespace (and not attached): [1] cluster_1.11.11
>> 
>> 
>>> locuslinkQuery("leukemia","Hs")
>>> 
>> Error: could not find function "locuslinkQuery"
>> 
>> The annotate package is attached, as are BioBase and XML, which are
>> the packages that the documentation states are needed.  I noticed
>> that the session info for the documenation had XML version 1.95.2
>> instead of 1.96-0 as in mine.   I also listed all of the functions
>> available in the annotate package, using ls(package:annotate) and
>> locuslinkQuery is not there.  I looked around for various
>> substitutes, but I could not find any.   Has this function been
>> removed?  If so, what is its replacement?  If not, what did I do
>> wrong?
>> 
>> I also searched the help archives, but did not find any reference
>> to this problem.
>> 
>> By the way, right now I have to set my locale to "C"  every time I
>> start R.  Is there a way to make this automatic?
>> 
>> Thanks, Monnie
>> 
>> Monnie McGee, Ph.D. Associate Professor Department of Statistical
>> Science Southern Methodist University Ph: 214-768-2462 Fax:
>> 214-768-4035
>> 
>> ------------------------------------------------------------------------
>> 
>> 
>> _______________________________________________ Bioconductor
>> mailing list Bioconductor at stat.math.ethz.ch 
>> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the
>> archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> _______________________________________________ Bioconductor mailing
> list Bioconductor at stat.math.ethz.ch 
> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the
> archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-5646
734-936-8662