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

[Ting-Yuan Liu]

Hi, Rainer,

On Fri, 25 Nov 2005, Rainer Grohmann wrote:

> 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?
> 

Your package is not completed.  You still need to provide a file called 
"DESCRIPTION" in your package.  This is why you got such a error message.  
Please refer to the "Writing R Extensions" manual for more information.  

> 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?
> 
> 

Do you notice that you are using R 2.1.1?  The latest version of R is 
2.2.0.  biocLite will get the suitable version of BioConductor for your 
R.  BioC 1.6 is for R 2.1.x, and BioC 1.7 is for R 2.2.x.  You have to 
upgrade your R to version 2.2.0 so that biocLite can install BioC 1.7 for 
you.

> Thanks a lot in advance,
> 
>   Rainer
> 
> _______________________________________________
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> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> 

While your package is completed, use "R CMD build" to build the source 
package (*.tar.gz) and you can install it by "R CMD INSTALL *.tar.gz".  
You can also use "R CMD check *.tar.gz" to see if you have any problem in 
your package.

HTH,
Ting-Yuan