Hi, Eric,
The "error" messages about KEGG urls are not really errors, so you can
ignore
them. And the information about removing datasets are normal messages
as well.
Could you please try:
ABPkgBuilder(baseName="keyp.txt", baseMapType="gb", pkgName="vaimm06",
pkgPath="./", organism="Mus musculus", version="0.1",
author=list(author="Eric
J. Kort", maintainer="Eric J. Kort"))
It is the same as your code except that "srcUrls" is removed. Let me
know if it
doesn't work
thanks
Nianhua Li
Computational Biology, PHS, FHCRC
Hi Nianhua.
No...the syntax you suggested resulted in the same set of annotation
objects being built, with no GO annotation.
Any other thoughts?
Thanks,
-Eric
>From: Nianhua Li [mailto:nli at fhcrc.org]
>Sent: Friday, July 21, 2006 12:09 PM
>To: bioconductor at stat.math.ethz.ch
>Subject: Re: [BioC] ABPackageBuilder not building GO package?
>
>Hi, Eric,
>
>The "error" messages about KEGG urls are not really errors, so you
can ignore
>them. And the information about removing datasets are normal messages
as well.
>Could you please try:
>
>ABPkgBuilder(baseName="keyp.txt", baseMapType="gb",
pkgName="vaimm06",
>pkgPath="./", organism="Mus musculus", version="0.1",
author=list(author="Eric
>J. Kort", maintainer="Eric J. Kort"))
>
>It is the same as your code except that "srcUrls" is removed. Let me
know if it
>doesn't work
>
>thanks
>
>Nianhua Li
>Computational Biology, PHS, FHCRC
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor
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http://news.gmane.org/gmane.science.biology.informatics.conductor
>
Hi, Eric,
I used a baseFile to test the script, and got a perfectly valid
package.
Maybe your base file "keyp.txt" or your network configuration have
some
problem? The script I used is :
vaimm06 <- function(pkgPath, version) {
ABPkgBuilder(baseName="mouse4302.GeneBankID",
baseMapType="gb",
pkgName="vaimm06",
pkgPath=pkgPath,
organism="Mus musculus",
version=version,
author=list(authors="Eric J. Kort", maintainer="Eric
J.
Kort <eric.kort at="" exsilico.biz="">")
)
}
vaimm06(getwd(), "0.1")
And the base file "mouse4302.GeneBankID" looks like:
41484_r_at X56681
41485_at X02152
41486_at U82396
41487_at W72400
41488_at AC002394
41489_at M99435
41490_at Y00971
41491_s_at AB028944
41492_r_at AB028944
41493_at AI094610
41494_at X99802
41495_at W37606
41496_at AL050189
41497_at AI401296
41498_at AB020718
41499_at X15218
414_at X59373
41500_at AI761818
41501_at AF004849
41502_at AI523538
41503_at AB020661
41504_s_at AF055376
...
And my environment is (I don't think it is important for this problem
though):
> sessionInfo()
R version 2.4.0 Under development (unstable) (2006-05-19 r38133)
x86_64-unknown-linux-gnu
attached base packages:
[1] "tools" "methods" "stats" "graphics" "grDevices"
"utils"
[7] "datasets" "base"
other attached packages:
AnnBuilder RSQLite DBI annotate XML Biobase
"1.11.4" "0.4-1" "0.1-10" "1.9.6" "0.99-8" "1.9.28"
good luck
nianhua
