[BioC] load the annotation package generated by AnnBuilder

[Martin Morgan]

Hi Di -- 

"Di Wu" <di.wu at med.monash.edu.au> writes:

> Dear list,
>
> I am using BrainArray CDF in my microarray data analysis. I am interested to
> look at the GO information from my top list. But it has no this information.
> So I am using AnnBuilder to build my mm430mmRS package with GO and other
> information. I successfully build the package as a folfer "mm430mmRS". There
> are 3 folders inside: data, man, R. And two files: DESCRIPTION and
> NAMESPACE.
>
> Here is my code:
>
> library(AnnBuilder)
> read.table(file.path(.path.package("AnnBuilder"), "data",
> "mm430mmrefseq_ID"),
> sep = "\t", header = FALSE, as.is = TRUE)[100:115, ]
>
> myBase <- file.path(.path.package("AnnBuilder"), "data", "mm430mmrefseq_ID")
> myBaseType <- "refseq"
> mySrcUrls <- getSrcUrl("all", "Mus musculus")
> mySrcUrls
>
> myDir <- c("C:\\Documents and Settings\\dwu\\My Documents\\Di PhD\\R")
>
> ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType =
> myBaseType, pkgName = "mm430mmRS",
> pkgPath = myDir, organism = "Mus musculus", version = "2.5.0",
> author = list(authors = "Di Wu", maintainer =
> "myname at myemail."), fromWeb = TRUE)
>
> I zipped the fold and install it. It looks fine, listed in the library
> available.

Did you

cd C:\\Documents and Settings\\dwu\\My Documents\\Di PhD\\R
R CMD INSTALL mm430mmRS

? Although the files end with '.zip', they are processed before being
zipped. Additional tools are needed to use R CMD INSTALL, see

http://cran.r-project.org/bin/windows/base/rw-FAQ.html#Packages

where the instructions have to be followed carefully; a good good idea
is to make sure your toolchain works by trying to download the source
version of an existing annotation package, and installing that with R
CMD INSTALL.

Hope that helps,

Martin

> Then, I wanted to load it by library(mm430mmRS)
>
> The error is:
> Error in library(package, lib.loc = lib.loc, character.only = TRUE, logical
> = TRUE,  :
>         'mm430mmRS' is not a valid package -- installed < 2.0.0?
>
>
> I tried make "version=1.1.0". It does not solve it . I don't know if that's
> the problem.
>
> But I am thinking maybe there are some other ways to load the packages
> generated by AnnBuilder to avoid the error since my package do es not have
> the full contents as normal packages, such as "meta" package.
>
> Please give me some opinions. Thanks in advance.
>
> Di
>
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>
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-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org