[Seqinr-forum] Concerning the biological databases access and queries in the last version of seqinr

[Simon Penel]

Dear seqinr users/developers,

since the last version of R, it not possible to change an object 
belonging the global environment from a package.
This means that an object defined in seqinr (i.e. in the seqinr 
environment .seqinrEnv)  is not anymore defined  in the global environment.
This leads to errors in the examples. Typically :

choosebank("genbank")
query("bb", "sp=Borrelia burgdorferi")
# To get the names of the 4 first sequences:
sapply(bb$req[1:4], getName)
Error in lapply(X = X, FUN = FUN, ...) : object 'bb' not found


Instead using directly the bb object, you should now use 
get("bb",env=.seqinrEnv)

For example:


apply((get("bb",env=.seqinrEnv)$req[1:4]),getName)


more generally if you want to store to the results of the request you 
may type :

mybb <- (get("bb",env=.seqinrEnv)


We need to modify the examples and/or the R functions involved in the 
database queries in the next version of seqinr, we will do that as soon 
as possible.

We are thinking of a global solution  by creating a function "seqobj" ( 
aliased to  "so" ) :


seqobj <- function (obj) { get (obj,env=.seqinrEnv)}


And and to use so("x")  instead x in the examples.

Any suggestions are of course welcome.

Sorry for the troubles,
all the best

Simon

-- 
Simon Penel
Laboratoire de Biometrie et Biologie Evolutive
Bat 711 - CNRS UMR 5558 - Universite Lyon 1
43 bd du 11 novembre 1918 69622 Villeurbanne Cedex
Tel:   04 72 43 29 04      Fax:  04 72 43 13 88
http://lbbe.univ-lyon1.fr/-Penel-Simon-.html?lang=fr