[BioC] Missing function locuslinkQuery and locuslinkBYID in annotate 1.18.0

McGee, Monnie mmcgee at mail.smu.edu
Tue Oct 7 18:07:11 CEST 2008

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) 


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?


Monnie McGee, Ph.D.
Associate Professor
Department of Statistical Science
Southern Methodist University
Ph: 214-768-2462
Fax: 214-768-4035

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