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<div class="moz-cite-prefix">Dear seqinr users/developers,
<br>
<br>
the last version of seqinr (
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3.1-3) is now available on CRAN and R-forge.<br>
<br>
Examples dealing with databases access and queries have been
modified thanks to a suggestion from Tang Chin Cheung.<br>
<br>
all the best<br>
<br>
Simon<br>
<br>
<br>
<br>
<br>
Le 17/11/14 11:58, Simon Penel a écrit :<br>
</div>
<blockquote cite="mid:5469D4ED.9040407@univ-lyon1.fr" type="cite">Dear
seqinr users/developers,
<br>
<br>
since the last version of R, it not possible to change an object
belonging the global environment from a package.
<br>
This means that an object defined in seqinr (i.e. in the seqinr
environment .seqinrEnv) is not anymore defined in the global
environment.
<br>
This leads to errors in the examples. Typically :
<br>
<br>
choosebank("genbank")
<br>
query("bb", "sp=Borrelia burgdorferi")
<br>
# To get the names of the 4 first sequences:
<br>
sapply(bb$req[1:4], getName)
<br>
Error in lapply(X = X, FUN = FUN, ...) : object 'bb' not found
<br>
<br>
<br>
Instead using directly the bb object, you should now use
get("bb",env=.seqinrEnv)
<br>
<br>
For example:
<br>
<br>
<br>
apply((get("bb",env=.seqinrEnv)$req[1:4]),getName)
<br>
<br>
<br>
more generally if you want to store to the results of the request
you may type :
<br>
<br>
mybb <- (get("bb",env=.seqinrEnv)
<br>
<br>
<br>
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.
<br>
<br>
We are thinking of a global solution by creating a function
"seqobj" ( aliased to "so" ) :
<br>
<br>
<br>
seqobj <- function (obj) { get (obj,env=.seqinrEnv)}
<br>
<br>
<br>
And and to use so("x") instead x in the examples.
<br>
<br>
Any suggestions are of course welcome.
<br>
<br>
Sorry for the troubles,
<br>
all the best
<br>
<br>
Simon
<br>
<br>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
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
<a class="moz-txt-link-freetext" href="http://lbbe.univ-lyon1.fr/-Penel-Simon-.html?lang=fr">http://lbbe.univ-lyon1.fr/-Penel-Simon-.html?lang=fr</a></pre>
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