On 2013-03-12 16:44, Luca Beltrame wrote:
Hello,
I've been using "importr" successfully with the 2.2.x series, but since
upgrading today to the 2.3.x series I noticed a change in behavior.
I noticed this with the "graphite" package from Bioconductor:
graphite = importr("graphite")
This package provides a series of classes, in this case I wanted to access the
"kegg" class.
With 2.2.x, this
graphite.kegg
worked while in 2.3.x causes AttributeError.
Where I can start digging to find the problem?
I tried it myself and now I understand what is happening.
Two things:
- There were changes in R regarding datasets in packages and exported
symbols, that forced me to make changes to the way the datasets are
accessed (see below).
- There is something odd happening with the names of those datasets
(probably an error in rpy2)
The way to get the data is currently:
kegg_env = graphite.__rdata__.fetch("kegg (pathways)")
kegg = kegg_env['kegg']
Not as easy as it was, I agree...
L.
------------------------------------------------------------------------------
Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the
endpoint security space. For insight on selecting the right partner to
tackle endpoint security challenges, access the full report.
http://p.sf.net/sfu/symantec-dev2dev
_______________________________________________
rpy-list mailing list
rpy-list@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rpy-list
------------------------------------------------------------------------------
Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the
endpoint security space. For insight on selecting the right partner to
tackle endpoint security challenges, access the full report.
http://p.sf.net/sfu/symantec-dev2dev
_______________________________________________
rpy-list mailing list
rpy-list@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rpy-list
