[BioC] AnnBuilder problem with CHR slot

[Nianhua Li]

Dear Dario,

Please upgrade AnnBuilder to 1.11.6 and rebuild your package with this script:

library(AnnBuilder)
mypkg <- function(pkgPath, version) {
    ABPkgBuilder(baseName="mybase.txt",
                 baseMapType="ll",
                 pkgName="mypkg",
                 pkgPath=pkgPath,
                 organism="Homo sapiens",
                 version=version,
                 author=list(
                   authors="Dario Greco",
                   maintainer="Dario Greco <email at email.com>"
                   )
                 )
}
mypkg(getwd(), "1.0.0")

Here is the result I got by using your sample baseFile:
Quality control information for  mypkg
Date built: Created: Mon Aug  7 09:17:36 2006

Number of probes: 20
Probe number missmatch: None
Probe missmatch: None
Mappings found for probe based rda files:
         mypkgACCNUM found 0 of 20
         mypkgCHRLOC found 18 of 20
         mypkgCHR found 18 of 20
         mypkgENZYME found 4 of 20
         mypkgGENENAME found 18 of 20
         mypkgGO found 16 of 20
         mypkgLOCUSID found 18 of 20
         mypkgMAP found 18 of 20
         mypkgOMIM found 16 of 20
         mypkgPATH found 7 of 20
         mypkgPMID found 18 of 20
         mypkgREFSEQ found 18 of 20
         mypkgSUMFUNC found 0 of 20
         mypkgSYMBOL found 18 of 20
         mypkgUNIGENE found 18 of 20
Mappings found for non-probe based rda files:
         mypkgCHRLENGTHS found 25
         mypkgENZYME2PROBE found 3
         mypkgGO2ALLPROBES found 274
         mypkgGO2PROBE found 89
         mypkgORGANISM found 1
         mypkgPATH2PROBE found 13
         mypkgPFAM found 16
         mypkgPMID2PROBE found 349
         mypkgPROSITE found 14

mget(ls(mypkgCHR), mypkgCHR)
$`10000_spt`
[1] "14"

$`10001_spt`
[1] "12"

$`10002_spt`
[1] "20"

$`10003_spt`
[1] "12"

$`10004_spt`
[1] "22"

$`10005_spt`
[1] "10"

$`10006_spt`
[1] "1"

$`10007_spt`
[1] "6"

$`10008_spt`
[1] "11"

$`10009_spt`
[1] NA

$`1000_spt`
[1] "17"

$`10010_spt`
[1] "6"

$`10011_spt`
[1] NA

$`10012_spt`
[1] "X"

$`10013_spt`
[1] "7"

$`10014_spt`
[1] "3"

$`1001_spt`
[1] "4"

$`100_spt`
[1] "8"

$`10_spt`
[1] "7"

$`1_spt`
[1] "7"

Hope it is helpful. Thanks

nianhua