Dear list.

I have ran into trouble when I was re-annotating some in-house  
arrays. Although I do not get any errors I have trouble due to that:
1) the environments created are empty
2) the GO-environemnts are missing

Is the GO-annotation moved to another function/package within the  
Bioconductor?

I would really appreciate any tips of what has gone wrong.

Best regards

// Johan Lindberg

#############################
#My file with identifiers looks like this, it is tab-separated:
RG3-B1	R45056
RG3-F1	AA031514
RG3-B4	AA428335
RG3-F4	AA143331
RG3-B7	N52474
.
.
.
#############################
#The package contains the following:
ls("package:Hum30kbatch1to5")
[1] "Hum30kbatch1to5"           "Hum30kbatch1to5ACCNUM"
[3] "Hum30kbatch1to5CHRLENGTHS" "Hum30kbatch1to5CHRLOC"
[5] "Hum30kbatch1to5ENTREZID"   "Hum30kbatch1to5ENZYME"
[7] "Hum30kbatch1to5LOCUSID"    "Hum30kbatch1to5MAPCOUNTS"
[9] "Hum30kbatch1to5ORGANISM"   "Hum30kbatch1to5PATH"
[11] "Hum30kbatch1to5PFAM"       "Hum30kbatch1to5PROSITE"
[13] "Hum30kbatch1to5QC"         "Hum30kbatch1to5QCDATA"
#Where is the GO-environments?

#############################
#My code and sessionInfo:
 > AnnWd <- "/Volumes/Cartman_2/forAnnbuilder/GBbatch1to5.txt"
 > AnnWd2 <- "/Volumes/Cartman_2/forAnnbuilder/hum30k1to5"
 > mySrcUrls <- getSrcUrl("all", organism = "Homo sapiens")
 > ABPkgBuilder(baseName=AnnWd, srcUrls=mySrcUrls, baseMapType =  
"gb",pkgName="Hum30kbatch1to5", pkgPath=AnnWd2, organism = "Homo  
sapiens", version = "1.1.1", author = list(author = "Johan Lindberg",  
maintainer = "johanl@biotech.kth.se"), fromWeb = TRUE)
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
	LC_ALL = (unset),
	LANG = "en_SE.UTF-8"
     are supported and installed on your system.
Read 1 item
Read 1 item
Failed to get data from URL: ftp://ftp.genome.ad.jp/pub/kegg/pathways/ 
hsa/hsa00195.gene
Failed to get data from URL: ftp://ftp.genome.ad.jp/pub/kegg/pathways/ 
hsa/hsa00196.gene
Failed to get data from URL: ftp://ftp.genome.ad.jp/pub/kegg/pathways/ 
hsa/hsa00231.gene
#I get this for many genes....
.
.
.
.
[1] "4085 2 2"
The following data sets have been added to the database and will be  
removed:
[1] "/Volumes/Cartman_2/My documents/Microarray stuff/Genlistor/ 
forAnnbuilder/hum30k1to5/Hum30kbatch1to5/data/Hum30kbatch1to5ACCNUM.rda"
[2] "/Volumes/Cartman_2/My documents/Microarray stuff/Genlistor/ 
forAnnbuilder/hum30k1to5/Hum30kbatch1to5/data/ 
Hum30kbatch1to5CHRLENGTHS.rda"
[3] "/Volumes/Cartman_2/My documents/Microarray stuff/Genlistor/ 
forAnnbuilder/hum30k1to5/Hum30kbatch1to5/data/Hum30kbatch1to5CHRLOC.rda"
[4] "/Volumes/Cartman_2/My documents/Microarray stuff/Genlistor/ 
forAnnbuilder/hum30k1to5/Hum30kbatch1to5/data/ 
Hum30kbatch1to5ENTREZID.rda"
[5] "/Volumes/Cartman_2/My documents/Microarray stuff/Genlistor/ 
forAnnbuilder/hum30k1to5/Hum30kbatch1to5/data/Hum30kbatch1to5ENZYME.rda"
[6] "/Volumes/Cartman_2/My documents/Microarray stuff/Genlistor/ 
forAnnbuilder/hum30k1to5/Hum30kbatch1to5/data/ 
Hum30kbatch1to5MAPCOUNTS.rda"
[7] "/Volumes/Cartman_2/My documents/Microarray stuff/Genlistor/ 
forAnnbuilder/hum30k1to5/Hum30kbatch1to5/data/ 
Hum30kbatch1to5ORGANISM.rda"
[8] "/Volumes/Cartman_2/My documents/Microarray stuff/Genlistor/ 
forAnnbuilder/hum30k1to5/Hum30kbatch1to5/data/Hum30kbatch1to5PATH.rda"
[9] "/Volumes/Cartman_2/My documents/Microarray stuff/Genlistor/ 
forAnnbuilder/hum30k1to5/Hum30kbatch1to5/data/Hum30kbatch1to5PFAM.rda"
[10] "/Volumes/Cartman_2/My documents/Microarray stuff/Genlistor/ 
forAnnbuilder/hum30k1to5/Hum30kbatch1to5/data/ 
Hum30kbatch1to5PROSITE.rda"
[11] "/Volumes/Cartman_2/My documents/Microarray stuff/Genlistor/ 
forAnnbuilder/hum30k1to5/Hum30kbatch1to5/data/Hum30kbatch1to5QC.rda"
[12] "/Volumes/Cartman_2/My documents/Microarray stuff/Genlistor/ 
forAnnbuilder/hum30k1to5/Hum30kbatch1to5/data/Hum30kbatch1to5QCDATA.rda"
Warning message:
Some rda files were not removed, be sure to check the data dir before  
building in: makeLLDB(file.path(pkgPath, pkgName), compress = TRUE)

#Then I check and compile the package:
  R CMD check Hum30kbatch1to5
  R CMD build Hum30kbatch1to5
#Everything seems to be fine

 > sessionInfo()
R version 2.4.1 (2006-12-18)
i386-apple-darwin8.8.1

locale:
C

attached base packages:
[1] "splines"   "tools"     "stats"     "graphics"  "grDevices"
[6] "utils"     "datasets"  "methods"   "base"

other attached packages:
         GOstats        Category      genefilter        survival
         "2.0.4"         "2.0.3"        "1.12.0"          "2.30"
            KEGG            RBGL              GO           graph
        "1.14.1"        "1.10.0"        "1.14.1"        "1.12.0"
Hum30kbatch1to5      AnnBuilder         RSQLite             DBI
         "1.1.1"        "1.12.0"        "0.4-19"        "0.1-12"
        annotate             XML         Biobase
        "1.12.1"         "1.4-1"        "1.12.2"
*********************************************
Johan Lindberg
Royal Institute of Technology
AlbaNova University Center
Stockholm Center for Physics, Astronomy and Biotechnology
School of Molecular Biotechnology
Department of Gene Technology
Visiting address:
Roslagstullsbacken 21, Floor 3
106 91 Stockholm, Sweden
Delivering address:
Roslagstullsbacken 30B
104 06 Stockholm, Sweden
Phone (office) +46 8 553 783 44
Fax + 46 8 553 784 81
http://www.ktharray.se/
http://www.arrayadvice.se/
*********************************************



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