[BioC] Resourcerer, UniGene and getSrcUrl

[John Zhang]

Yes, NCBI has moved files around. The fix will be included in a new version of 
AnnBuilder. Meanwhile, if you replace srcUrls of resourcer2BioC with mySrcUrls 
that has the correct urls, the code should work.

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>Date: Tue, 12 Jul 2005 12:46:56 +0200
>From: Morten <morten.mattingsdal at student.uib.no>
>To: Bioconductor at stat.math.ethz.ch
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>Subject: [BioC] Resourcerer, UniGene and getSrcUrl
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>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,baseMapTyp
e="gbNRef",
>version="1.0.0",fromWeb=True,baseUrl="ftp://ftp.tigr.org/pub/data/tgi/Resourcer
er",
>check=TRUE,author=list(author="Anonymous",maintainer="<morten.mattingsdal at medis
in.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/databa
se/",
>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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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084