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

[Rainer Grohmann]

Hi Ting-Yuan,

Thanks a lot for your directions -- I've never had contact with creating
packages so far. Creating a proper DESCRIPTION file did help indeed.

Rainer

Ting-Yuan Liu wrote:
> 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
>>
>>_______________________________________________
>>Bioconductor mailing list
>>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
>