[BioC] Resourcerer, UniGene and getSrcUrl

[Morten Mattingsdal]

Hi..

yes, I saw I was using the wrong:
ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/

instead of the correct
ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.data.gz
in mySrcUrls

when i do, everything goes fine for a while but then i get:
Error in readURL(infoURL): Can't read from 
ulr:ftp://ftp.ncbi.nih.gov/repository/UniGene/Hs.info
[1] Unsuccessful

Which is abit strange since I have already specified the correct url 
where both Hs.data.gz and Hs.info is located.
Ill just wait for the new realease of AnnBuilder :)
morten

>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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>>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
>
>  
>