[BioC] AnnBuilder URL
tliu at fhcrc.org
Tue Dec 20 19:11:38 CET 2005
First, your R is version 2.1.0 which is out-of-dated. Please update it to
the latest version, 2.2.0.
Second, one suggestion I gave to Anja regarding to the post on Dec 7 is
removing the argument "srcUrls=mySrcUrls" because AnnBuilder will do this
for you automatically.
Third, you have a typo in the argument "author". It should be
author=list(authors="Toni Juli", maintainer="Toni
See the typo? (There could be more than one author for a package.) If
this is a typo somewhere in the examples/vignettes, please let me know
and I will fix them in the next release.
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
Seattle, WA, USA
On Mon, 19 Dec 2005, Toni Julià wrote:
> Ive been trying to create an annotation package using AnnBuilder but an
> error keeps appearing:
> Warning message:
> Built for UCSC is not valid! in: getUCSCBuilt(organism)
> Error in loadFromUrl(srcUrls[i]) : URL
> ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.data.gz is
> incorrect or the target site is not responding!
> On Wed, 7 Dec 2005, Anja Schiel also posted the same problem using mouse
> annotation. At that time the unavailability of the Unigene site was the
> problem but in this case the URL can be directly accessed with no problem.
> My ABPkgBuilder function and system info are:
> mySrcUrls <- getSrcUrl("all", "Homo sapiens")
> ABPkgBuilder(baseName = myBase, baseMapType = myBaseType, srcUrls =
> mySrcUrls, pkgName = "Human.annot" , pkgPath = mydir, organism ="Homo
> sapiens", version = "1.1.0", author = list(author= "Toni Juli", maintainer
> = "ajulia[AT]vhebron.net"), fromWeb=T)
> R version 2.1.0, 2005-04-18, i386-pc-mingw32
> attached base packages:
>  "tools" "methods" "stats" "graphics" "grDevices" "utils"
>  "datasets" "base"
> other attached packages:
> GO AnnBuilder annotate XML Biobase
> "1.8.2" "1.8.0" "1.5.16" "0.97-8" "1.5.12"
> What could be going wrong?
> Thanks for your help!
> Antonio Juli
> Unitat de Recerca de Reumatologia (URR)
> Hospital Universitari Vall d'Hebron
> Pg Vall d'Hebron, 119-129
> 08035, Barcelona, SPAIN
> Tel: + 34 93 274 6200
> e-mail: ajulia at vhebron.net
> [[alternative HTML version deleted]]
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