[BioC] AnnBuilder and Kegg

[Paola Pedotti]

Hi everybody, 
I am trying to annotate my dataset (home spotted array, two colors,
mice) using AnnBuilder. 
Every time I run the program the connection with the kegg
website is not working, so I am able to build the annotation
package but not for the kegg pathways. Does anybody know how to
fix this problem or did anybody find a way to by pass it (like
downloading a list of accession numbers  and corresponding pathways)?
here my script:

*****************************************************************************************************

library(AnnBuilder)
#Loading required package: Biobase
#Loading required package: tools
#Welcome to Bioconductor
#         Vignettes contain introductory material.  To view,
#         simply type: openVignette()
#         For details on reading vignettes, see
#         the openVignette help page.
#Loading required package: annotate

library(GO)

sessionInfo()

#Version 2.3.1 (2006-06-01)
#i386-pc-linux-gnu
#
#attached base packages:
#[1] "splines"   "tools"     "methods"   "stats"     "graphics"
#"grDevices"
#[7] "utils"     "datasets"  "base"
#
#other attached packages:
#  
#       globaltest               vsn             limma          multtest
#          "4.2.0"          "1.10.0"           "2.7.3"          "1.10.2"
#         survival          affydata              affy            affyio
#           "2.20"           "1.8.0"          "1.10.0"           "1.0.0"
#           KEGG            GO        AnnBuilder           RSQLite
#         "1.12.0"          "1.12.0"          "1.10.0"           "0.4-1"
#              DBI          annotate               XML           Biobase
#         "0.1-10"          "1.10.0"          "0.99-7"          "1.10.0"
       

mySrcUrls <- getSrcUrl("all", organism="Mus Musclusus")

base<- file.path(.path.package("AnnBuilder"), "data", "lgtc.ids.1.txt")

myBaseType<- "gbNRef"
ABPkgBuilder(baseName=base, 
                      srcUrls = mySrcUrls,
                      baseMapType = myBaseType, 
                      pkgName = "lgtc201106",
                      pkgPath = ".", 
                      organism ="Mus Musclusus", 
                      version ="1.1.0", 
                      author = list(author = "Paola Pedotti", 
                      maintener ="Paola Pedotti <p.pedotti at lumc.nl>")
                      ) 
                       
                       
#Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways//07214.gene
#Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways//07215.gene
#Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways//07216.gene
#Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways//07217.gene
#Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways//07218.gene
#[1] "0 2 2"
#Warning message:
#cannot open file
'/usr/local/lib/R/site-library/AnnBuilder/templates/PKGNAMEGO.1.Rd',
reason 'No such file or directory'
#The following data sets have been added to the database and will be
removed:
# [1] "./lgtc161106/data/lgtc161106ACCNUM.rda"
# [2] "./lgtc161106/data/lgtc161106CHR.rda"
# [3] "./lgtc161106/data/lgtc161106ENZYME.rda"
# [4] "./lgtc161106/data/lgtc161106GENENAME.rda"
# [5] "./lgtc161106/data/lgtc161106GO.1.rda"
# [6] "./lgtc161106/data/lgtc161106GO2ALLPROBES.rda"
# [7] "./lgtc161106/data/lgtc161106GO2PROBE.rda"
# [8] "./lgtc161106/data/lgtc161106GO.rda"
# [9] "./lgtc161106/data/lgtc161106LOCUSID.rda"
#[10] "./lgtc161106/data/lgtc161106MAPCOUNTS.rda"
#[11] "./lgtc161106/data/lgtc161106MAP.rda"
#[12] "./lgtc161106/data/lgtc161106OMIM.rda"
#[13] "./lgtc161106/data/lgtc161106ORGANISM.rda"
#[14] "./lgtc161106/data/lgtc161106PATH.rda"
#[15] "./lgtc161106/data/lgtc161106PMID2PROBE.rda"
#[16] "./lgtc161106/data/lgtc161106PMID.rda"
#[17] "./lgtc161106/data/lgtc161106QCDATA.rda"
#[18] "./lgtc161106/data/lgtc161106QC.rda"
#[19] "./lgtc161106/data/lgtc161106REFSEQ.rda"
#[20] "./lgtc161106/data/lgtc161106SUMFUNC.rda"
#[21] "./lgtc161106/data/lgtc161106SYMBOL.rda"
#[22] "./lgtc161106/data/lgtc161106UNIGENE.rda"
#Warning message:
#Can't
copy /usr/local/lib/R/site-library/AnnBuilder/templates/PKGNAMEGO.1.Rd
in: copyTemplates(repList, pattern, pkgName, pkgPath)

*****************************************************************************************************


thank you in advance

Paola



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