[BioC] missing AnnBuilder parser

Francois Pepin fpepin at cs.mcgill.ca
Tue Apr 12 03:17:00 CEST 2005

On Mon, 2005-04-11 at 14:49, John Zhang wrote:
> I have checked in the bug fixes. Please look for a new build (1.1.1) of 
> Resourcerer in the next few days. Meanwhile, you may try to fix the bug yourself 
> by changing the argument baseMapType = c("gb", "ug", "ll") to baseMapType = 
> c("gbNRef", "gb", "ug") of resourcerer2BioC and call the function by setting 
> baseMapType = "gbNRef" (resourcerer2BioC("Agilent_HumanGenome.zip", organism = 
> "human", baseMapType = "gbNRef"))  
> Let me know if you run into any problem. 

With a lot of begging and pleading, it ends up working:

getProbe2ID (in Resourcerer) also has to be changed, but it doesn't know how to deal
with gbNRef. It seems to be happy if I just give it 'gb'.

ABPkgBuilder (in AnnBuilder) also needs to be changed to accept 'gbNRef'.

But at the end (sending 'gbNRef to 'resourcerer2BioC', 'gb' to getProbe2ID
and 'gbNRef' to ABPkgBuilder), there is the same error as before:

[22] "/usr/local/lib/R/library/Resourcerer/temp/AgilentHsWg/data/AgilentHsWgSYMBOL.rda"
[23] "/usr/local/lib/R/library/Resourcerer/temp/AgilentHsWg/data/AgilentHsWgUNIGENE.rda"
exiting from: ABPkgBuilder(baseFile, srcUrls, baseMapType, otherSrc, pkgName,
    pkgPath, organism, version, makeXML, author, fromWeb)
Warning: cannot open compressed file `/usr/local/lib/R/library/Resourcerer/temp/AgilentHsWg/data/AgilentHsWgLOCUSID.rda'
Error in open.connection(con, "rb") : unable to open connection

> traceback()
5: open.connection(con, "rb")
4: open(con, "rb")
3: load(llRda)
2: checkMapping(pkgName, tempOther, file.path(pkgPath, pkgName,
       "data", paste(pkgName, "LOCUSID.rda", sep = "")))
1: resourcerer2BioC("Agilent_HumanGenome.zip", organism = "human", baseMapType = "gbNRef"))

Building it with check=FALSE (along with the modifications above) seems to work
fine, and I can install the package. The number of annotation has slightly
increased since the last time I build it which is expected. The few mappings that
I checked seem manually match. to show it working. I'd feel a bit better if the 
"checkMapping" function could confirm that the package was built properly.


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