[BioC] Error loading reposTools

[Jeff Gentry]

On Tue, 13 May 2003, Warnes, Gregory R wrote:
> Sorry, if a "liblisting.Rda" fike created by an older (broken?) reposTools
> exists in the package directory syncLocalLibList() will fail with the

Gotcha.

> Error in if (e1[i] != e2[i]) return(TRUE) : 
>  missing value where TRUE/FALSE needed

You wouldn't happen ot have the "Spot" package installed, would you?

> Which bails out of library(reposTools), preventing the loading of libraries
> depending on reposTools.   Perhaps it would be good to store a version
> number in the "liblisting.Rda" file so that an obsolete one can be ignored &
> a new one regenerated?

The problem here is that the format of the liblisting.Rda file has not
changed, ever.  So tagging it with a version isn't going to help in
that respect.  The problem is that there have been bugs in reposTools
which *could* lead to corruption in one's liblisting.Rda file - we could
say that tehre's a certain minimum version of reposTools that a
liblisting.Rda must be associated with if we come across something that
leads to liblisting corruption -> but an older liblisting is not (and
probably not for most people) going to be corrupted.

(btw, the short term solution here for you in particular right now, is to
remove the liblisting.Rda file)

> I got this problem with 1.1.37, using install.packages, and had to manually
> install affy and affydata to fix the problem.

I've run install.packages2 on affy using BIOCDevel from multiple installs
of R w/ varying degrees of cleanliness and do not get this problem
whatsoever.  Does anyone else get still have this problem?

-J