Building R package: no visible global function definition for 'subject'

Question

I'm building an R package for the first time and am having some trouble. I am doing an R CMD Check and am getting the following error:

get.AlignedPositions: no visible global function definition for 'subject'

I am not sure what is causing this. I don't even have a "subject" variable in my code. The code is rather lengthy so I rather not paste all of it unless someone asks in a comment. Is there something specific I should look for? The only thing I can think of is that I have a line like this:

alignment <-pairwiseAlignment(pattern = canonical.protein, subject=protein.extracted, patternQuality=patternQuality,
                            subjectQuality=subjectQuality,type = type, substitutionMatrix= substitutionMatrix,
                            fuzzyMatrix=fuzzyMatrix,gapOpening=gapOpening,gapExtension=gapExtension,
                            scoreOnly=scoreOnly)

but subject is defined by the pairwiseAlignment function in the Biostrings package. Thank you for your help!

Look in your function get.AlignedPosition, you might be able to spot subject being used as a function, along the lines of subject(foo). The Bioconductor developer mailing list is designed to serve (nascent, too) Bioconductor developers. — Martin Morgan
In the function where you have this bit of code, right at the top, put in a subject <- NA then rm(subject) in the next line. Then do a build again and see what happens. — Maiasaura

Paul Hiemstra Paul Hiemstra · Accepted Answer · 2012-06-07T09:10:47

R spotted a function, subject, being used without a function called subject being available. One possible reason for this is explained in this discussion on R-devel. In that case code is used conditionally, e.g. if a certain package is installed we use its functionality. When checking the package on a system which does not have this package installed, we run in to these kinds of warnings. So please check if this might be the case. Alternatively, you might have made a mistake by calling subject while no function existed, e.g. subject was not a function but just an object.

Building R package: no visible global function definition for 'subject'

1 Answers