Dear Rob the package "maanova" passed "R CMD check" with R 2.8, and this is all that Bioconductor can and will test on community-contributed packages. (And believe me that for 294 packages, that is already lot to ask!) Obviously, not all the functionality of a package is exhaustively tested in the tests that are invoked by "R CMD check" (man page examples, vignette, explicit tests). You might raise this with the package authors. But I would remark that it is unrealistic to expect that "R CMD check" will find all, possibly subtle, errors. Best wishes Wolfgang ---------------------------------------------------- Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber Rob Tempelman ha scritto: > Dear Wolfgang, > > Indeed, there needs to be a fix. What I don't understand is how come this > sort of thing doesn't get diagnosed when maanova is included as part of > > "2008-10-22 BioC 2.3 consisting of 294 packages and designed to work with R > 2.8.z, was released today" > > as indicated from the main page of bioconductor.org? > > I suppose I would need to go through all of functions myself and make my own > fix. > > > Rob > > -----Original Message----- > From: Wolfgang Huber [mailto:huber at ebi.ac.uk] > Sent: Wednesday, November 12, 2008 4:53 AM > To: Rob Tempelman > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] error with get(getOption("device")) in maanova with R > 2.8.0 > > Rob Tempelman ha scritto: >> I downloaded the latest version of maanova (version 1.12.0) from > bioconductor that is presumably designed to work with R 2.8.0. However, > upon using some of the functions (say gridcheck on the dataset kidney > provided with the package), I get the following error message: >>> data(kidney) >>> gridcheck(kidney.raw) >> Error in get(getOption("device")) : invalid first argument >> >> >> It is my understanding that all of the get(getOption("device")) commands > now need to be replaced by dev.new() in R 2.8.0. If so, could this be done > with this particular package? >> Thanks, >> >> Rob Tempelman > > > > Hi Rob, > > just a guess, but you or the authors of maanova might find it > instructive to check the R 2.8 release notes "CHANGES IN R VERSION > 2.8.0": http://cran.at.r-project.org/src/base/NEW > > > The 'factory-fresh' defaults for options("device") have been > changed to refer to the devices as functions in the grDevices > namespace and not as names. This makes it more likely that > the incorrect (since R 2.5.0) assumption in packages that > get(getOption("device"))() will work will catch users of those > packages. > > > > Best wishes > Wolfgang > > ---------------------------------------------------- > Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber --