Dear All,
I am trying to build a package for a set of functions. I am
able to build the package and its working fine. When I check it with
R CMD check
I get a following warning : no visible global function
definition for ‘biocLite’
I have used biocLite to load a user defined library from
within a function if that library is not pre-installed
if(is.element(annotpkg, installed.packages()[,1]) ==
"FALSE"){
source("http://www.bioconductor.org/biocLite.R")
biocLite(annotpkg)
library(annotpkg,character.only=TRUE)
}
Should I ignore this error or there is a workaround for the
warning. My package is working fine though still I guess the warning has to
have significance. Please help in clarifying this
warning.
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On 6/05/2011 6:06 a.m., swaraj basu wrote:> Dear All, > I am trying to build a package for a set of functions. I am > able to build the package and its working fine. When I check it with > R CMD check > > I get a following warning : no visible global function > definition for ?biocLite? > > I have used biocLite to load a user defined library from > within a function if that library is not pre-installed > > if(is.element(annotpkg, installed.packages()[,1]) == "FALSE"){ > source("http://www.bioconductor.org/biocLite.R") > biocLite(annotpkg) > library(annotpkg,character.only=TRUE) > } > > Should I ignore this error or there is a workaround for the > warning. My package is working fine though still I guess the warning has to > have significance. Please help in clarifying this > warning. >Your source() call generates the function biocLite() in such a way that R CMD check cannot know, so a workaround is to precede the source() statement with something like: biocLite <- function(x) 0 [I don't know if there is a 'best' way to do this.] In general Warnings are just that - they point you to a possible fault, but there is not enough information for the code to make a final determination. HTH Ray Brownrigg
On 05/05/2011 11:06 AM, swaraj basu wrote:> Dear All, > I am trying to build a package for a set of functions. I am > able to build the package and its working fine. When I check it with > R CMD check > > I get a following warning : no visible global function > definition for ?biocLite? > > I have used biocLite to load a user defined library from > within a function if that library is not pre-installed > > if(is.element(annotpkg, installed.packages()[,1]) == "FALSE"){ > source("http://www.bioconductor.org/biocLite.R") > biocLite(annotpkg) > library(annotpkg,character.only=TRUE) > } > > Should I ignore this error or there is a workaround for the > warning. My package is working fine though still I guess the warning has to > have significance. Please help in clarifying this > warning.Better to ask on the Bioconductor list http://bioconductor.org/help/mailing-list/ where you'll hit an audience familiar with annotation packages. As a possible model, see affy::cdfFromBioC or annotate::getAnnMap Martin> > [[alternative HTML version deleted]] > > > > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.-- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793