[BioC] [AnnBuilder] How to use/load generated annotation packages

[Rainer Grohmann]

Hi All!

I'm really new to bioconductor, so may this is a dumb question...

So, I went through the AnnBuilder vignette, added my own data -- no
problem. As a result, I get a directory with three sub-dirs (data, man,
R), with some .rda-files in the data directory (the others are empty).

The vignette says, that this is package may be installed as any other
package. Now this is where my problems start.

If I try to install it, the following happens:

$ R CMD INSTALL -d tmp/R/myPkg
WARNING: invalid package 'tmp/R/myPkg'
'Rcmd INSTALL': in startdir= /home/rainer with tmpdir= /tmp/R.INSTALL.IjH8U0
   lib= '/usr/local/lib/R/site-library', pkgs= ''
ERROR: no packages specified

I also tried to tar the dir, with the following result:
$ R CMD INSTALL -d tmp/R/myPkg.tar.gz
ERROR: cannot extract package from 'tmp/R/myPkg.tar.gz'

Finally, I tried to check the package:
$ R CMD check tmp/R/myPkg
* checking for working latex ... OK
* using log directory '/home/rainer/myPkg.Rcheck'
* using R version 2.1.1, 2005-06-20
* checking for file 'myPkg/DESCRIPTION' ... NO

So what to do?

By the way, I installed bioconductor just this week using the biocLite.R
script from the web. However, a very old version of Annbuilder was
installed, which was in bioconductor 1.6. I upgraded it manually to
1.8.0. Still, all other packages seem to be bioconductor 1.6 versions.
Does that cause problems? How to upgrade to 1.7?


Thanks a lot in advance,

  Rainer