Question

Error message when try to use affycoretools

0

Entering edit mode

sunearth • 0

@sunearth-7205

Last seen 10.9 years ago

United States

Below is what I got when try to use affycoretools, I have tried to re-install both R and R studio.

Still, same situation. I also tried to use ubuntu to run R and Rstudio. Same problem.

Did I make any mistake when installing ?

>source("http://www.bioconductor.org/biocLite.R")
>biocLite("affy")
>biocLite("affycoretools")

>library(affy)
>library(affycoretools)

Warning message:

In namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc, :
No generic function found corresponding to requested imported methods for "colnames<-" from package "annaffy" (malformed exports?)

software error • 1.2k views

ADD COMMENT • link updated 10.9 years ago by James W. MacDonald 68k • written 10.9 years ago by sunearth • 0

0

Entering edit mode

Please provide the output of the sessionInfo() command after loading affycoretools.

Note that what you are seeing is a warning, and it may be that affycoretools did load; again, sessionInfo() will tell us.

ADD REPLY • link 10.9 years ago Dan Tenenbaum ★ 8.2k

score 0 · Answer 1 · 2014-12-29

That's not an error message, it's a warning.

Anyway, this is the last release that affycoretools will rely on annaffy, so I haven't bothered to try to track that warning down. In future, affycoretools will be reliant on ReportingTools, which is nicer than annaffy, and is still being actively maintained (Colin Smith's last commit to annaffy was in 2007).

I would recommend using ReportingTools anyway, so even if there is a problem with annaffy it wouldn't affect you.