[BioC] Resourcerer, UniGene and getSrcUrl

Morten morten.mattingsdal at student.uib.no
Tue Jul 12 12:46:56 CEST 2005


Hello everyone.

Im puzzled (and maybe abit stupid). When i try to use Resourcerer with:

resourcerer2BioC("Agilent_HumanGenome.zip",organism="human",destDir=file.path(.path.package("Resourcerer"),"temp"),
pkgName=("AgilentHumanGenome"), srcUrls=getSrcUrl("all","Homo sapiens"),
pkgPath=file.path(.path.package("Resourcerer"),"temp"),otherSrc=NULL,baseMapType="gbNRef",
version="1.0.0",fromWeb=True,baseUrl="ftp://ftp.tigr.org/pub/data/tgi/Resourcerer",
check=TRUE,author=list(author="Anonymous",maintainer="<morten.mattingsdal at medisin.uio.no>"))

i get:
Error in loadFromUrl(srcUrls[i]) : URL
ftp://ftp.ncbi.nih.gov/repository/UniGene/Hs.data.gz is incorrect or the target
site is not responding!
[1] "Unsuccessful"

After trying the ftp adress above, Resourcerer is correct cause there is no
Hs.data.gz there. The correct one is

ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/

Have ncbi recently moved their data or am I just confused? Is this a way to
surpass this? i have tried to manualy set the url by:

mySrcUrls <- c(
GP="ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Homo_sapiens/database/",
UG="ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/",
KEGG="ftp://ftp.genome.ad.jp/pub/kegg/pathways",
EG="ftp://ftp.ncbi.nlm.nih.gov/gene/DATA",
HG="ftp://ftp.ncbi.nih.gov/pub/HomoloGene/old/hmlg.ftp",
GO="http://www.godatabase.org/dev/database/archive/latest/go_200506-termdb.rdf-xml.gz",
YG="ftp://genome-ftp.stanford.edu/pub/yeast/data_download/")

but i still get 
Error in loadFromUrl(srcUrls[i]) : URL
ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/ is incorrect or the
target site is not responding!

anyone got any hints ?

morten


with:
R 2.1.0
Resourcerer 1.1.2
AnnBuilder  1.5.31



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