[BioC] Annbuilder for chicken data

Seth Falcon sfalcon at fhcrc.org
Tue May 15 00:06:44 CEST 2007

"Bart Buitenhuis" <Bart.Buitenhuis at agrsci.dk> writes:
> Thank you for your reply. I have studied the suggestions in the manual
> you suggested, but now I'm at a stage I'm not quite sure how to proceed
> further.
> This is what I have done so far:
> 1: I have downloaded all the suggested programmes and files from the
> http://www.murdoch-sutherland.com/Rtools/ webside

It might make sense at this point to verify that your tool chain is
working properly by dowloading a source package from the BioC package
repository and running build and check to verify that you can generate
valid packages.

> 2: Used the Annbuilder package to make an annotation package for chicken
> data with R 2.5.0 under windows XP (see script in the bottom of this
> mail)... OK
> (a directory "bartkip" is generated with 3 sub-directories "data" ,
> "man", "R")
> Now I'd like to make this Annotation package suitable to be read in R
> 2.5.0 under windows.
> 3: Set the dos prompt to the directory where 'bartkip' is situated.
> 4:  R CMD build --binary bartkip
> This gives the following message:
> * checking for file 'bartkip/DESCRIPTION' ... OK
> * preparing 'bartkip'
> * checking DESCRIPTION meta-information ... OK
> * remove junk files
> * checking for LF line-endings in source files
> * checking for empty and unneeded directories
> * building binary distribution
> * some HTML links may not be found
> installing R.css in c:/TEMP/Rinst333285638
> Using auto-selected zip options 'bartkip-HELP=ziponly'
> make[2]: *** [zzzfirst] Error 57
> make[1]: *** [All] Error 2
> *** installation of bartkip failed ***
> Removing 'c:/TEMP/Rinst333285638/bartkip'
> *installation failed

The HTML links not found is just a warning and I don't think that is the

The problem I don't recognize is "Error 57" and zzzfirst.  I would
recommend testing a package that is known to build on Windows and see
what happens.

+ seth

Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center

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