[BioC] AnnBuilder and Kegg

[John Zhang]

>
>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:

I guess the best thing for you to do is to update your R and BioC packages. The 
released version of AnnBuilder is 1.12.0 while you have 1.10.0 on your machine. 



>
>*******************************************************************************
**********************
>
>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
>
>
>
>_______________________________________
>Center for Human and Clinical Genetics
>Leiden University Medical Center      
>Postzone: S-04-P, Postbus 9600        
>2300 RC Leiden, The Netherlands 
>Telephone: +31 71 526 9440 
>Fax: +31 71 526 8285
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor
>Search the archives: 
http://news.gmane.org/gmane.science.biology.informatics.conductor

Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084