  HI, Nianhua:

Thanks so much for your suggestions, but I tried several things following
your instructions, unfortunately there are still some problems with GO
annotation data, such as RosettaGO2PROBE are all NULL.
the following is what I was doing:

1. downloaded and installed R-2.4.0
2. installed package
getBioC()

3. Installed AnnBuilder package and then GO
4. got rid of basefil01.txt colnames, no blank line left.
5. Runing my code once again!
          myBase <- "d:/Shiliang/result/limma/basefile01.txt"
          myBaseType <- "ll"
          myDir <- "d:/Shiliang/temp"
          myPkgName <- "Rosetta"
          ABPkgBuilder(baseName = myBase, baseMapType = myBaseType,
         pkgName = myPkgName, pkgPath = myDir,
         organism = "Mus musculus", version = "2.3.0",
         author = list(author = "Shiliang Wang<swang@email.unc.edu>",
         maintainer = "Shiliang Wang<swang@email.unc.edu>"),
         fromWeb = TRUE)
6. some of my basefile:(left:Rosetta reporterid;Right:LocusLinkID)
10024407494 11307
10024401025 11308
10024394441 11370
10024403966 11409
10024409675 11416
10024409230 11418
10024409230 11418
10024410196 11419
10024397993 11421

7. the whole information is the following :



R version 2.4.0 Under development (unstable) (2006-07-25 r38698)
Copyright (C) 2006 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(GO)
> library(AnnBuilder)
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

Loading required package: XML
Loading required package: annotate
Loading required package: RSQLite
Loading required package: DBI

Attaching package: 'AnnBuilder'


        The following object(s) are masked from package:GO :

         GO

Warning message:
'symbol.C' is deprecated in: symbol.C("sqlite3_libversion")

>  myBase <- "d:/Shiliang/result/limma/basefile01.txt"
>  myBaseType <- "ll"
>  myDir <- "d:/Shiliang/temp"
>  myPkgName <- "Rosetta"
>  ABPkgBuilder(baseName = myBase, baseMapType = myBaseType,
+  pkgName = myPkgName, pkgPath = myDir,
+  organism = "Mus musculus", version = "2.3.0",
+  author = list(author = "Shiliang Wang<swang@email.unc.edu>",
+  maintainer = "Shiliang Wang<swang@email.unc.edu>"),
+  fromWeb = TRUE)
Read 1 item
Read 1 item
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu00195.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu00231.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu00253.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu00311.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu00312.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu00331.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu00473.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu00513.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu00522.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu00523.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu00540.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu00621.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu00622.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu00627.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu00631.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu00641.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu00901.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu00902.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu00941.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu01010.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu01020.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu01021.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu01022.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu01023.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu01024.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu01025.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu01026.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu01051.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu01052.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu01053.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu01054.gene
Warning message:
failed to create a data connection
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu01055.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu01056.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu01057.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu01100.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu01110.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu01120.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu01130.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu01140.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu01150.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu01160.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu01170.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu01190.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu01195.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu01196.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu01330.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu02011.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu02020.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu02021.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu02030.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu02031.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu02040.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu02060.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu03070.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu03080.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu03090.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu04120.gene
Warning message:
failed to create a data connection
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu04630.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu04914.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu05110.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu05111.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu05112.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu05113.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu05114.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu05120.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu05130.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu05131.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07011.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07012.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07013.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07014.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07015.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07016.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07017.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07018.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07019.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07020.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07021.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07022.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07023.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07024.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07025.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07026.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07027.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07028.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07029.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07030.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07031.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07032.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07033.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07034.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07035.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07036.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07110.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07111.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07112.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07113.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07114.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07115.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07116.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07117.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07211.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07212.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07213.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07214.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07215.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07216.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07217.gene
[1] "3824 2 2"
The following data sets have been added to the database and will be removed:
 [1] "d:/Shiliang/temp/Rosetta/data/RosettaACCNUM.rda"
 [2] "d:/Shiliang/temp/Rosetta/data/RosettaCHR.rda"
 [3] "d:/Shiliang/temp/Rosetta/data/RosettaCHRLENGTHS.rda"
 [4] "d:/Shiliang/temp/Rosetta/data/RosettaCHRLOC.rda"
 [5] "d:/Shiliang/temp/Rosetta/data/RosettaENZYME.rda"
 [6] "d:/Shiliang/temp/Rosetta/data/RosettaENZYME2PROBE.rda"
 [7] "d:/Shiliang/temp/Rosetta/data/RosettaGENENAME.rda"
 [8] "d:/Shiliang/temp/Rosetta/data/RosettaGO.rda"
 [9] "d:/Shiliang/temp/Rosetta/data/RosettaGO2ALLPROBES.rda"
[10] "d:/Shiliang/temp/Rosetta/data/RosettaGO2PROBE.rda"
[11] "d:/Shiliang/temp/Rosetta/data/RosettaLOCUSID.rda"
[12] "d:/Shiliang/temp/Rosetta/data/RosettaMAP.rda"
[13] "d:/Shiliang/temp/Rosetta/data/RosettaMAPCOUNTS.rda"
[14] "d:/Shiliang/temp/Rosetta/data/RosettaORGANISM.rda"
[15] "d:/Shiliang/temp/Rosetta/data/RosettaPATH.rda"
[16] "d:/Shiliang/temp/Rosetta/data/RosettaPATH2PROBE.rda"
[17] "d:/Shiliang/temp/Rosetta/data/RosettaPFAM.rda"
[18] "d:/Shiliang/temp/Rosetta/data/RosettaPMID.rda"
[19] "d:/Shiliang/temp/Rosetta/data/RosettaPMID2PROBE.rda"
[20] "d:/Shiliang/temp/Rosetta/data/RosettaPROSITE.rda"
[21] "d:/Shiliang/temp/Rosetta/data/RosettaQC.rda"
[22] "d:/Shiliang/temp/Rosetta/data/RosettaQCDATA.rda"
[23] "d:/Shiliang/temp/Rosetta/data/RosettaREFSEQ.rda"
[24] "d:/Shiliang/temp/Rosetta/data/RosettaSUMFUNC.rda"
[25] "d:/Shiliang/temp/Rosetta/data/RosettaSYMBOL.rda"
[26] "d:/Shiliang/temp/Rosetta/data/RosettaUNIGENE.rda"
> library(Rosetta)
> Rosetta()


Quality control information for  Rosetta
Date built: Created: Thu Jul 27 16:38:20 2006

Number of probes: 20466
Probe number missmatch: RosettaACCNUM; RosettaCHR; RosettaCHRLOC;
RosettaENZYME; RosettaGENENAME; RosettaGO; RosettaLOCUSID; RosettaMAP;
RosettaPATH; RosettaPMID; RosettaREFSEQ; RosettaSUMFUNC; RosettaSYMBOL;
RosettaUNIGENE
Probe missmatch: None
Mappings found for probe based rda files:
         RosettaACCNUM found 0 of 20466
         RosettaCHR found 18659 of 20466
         RosettaCHRLOC found 15939 of 20466
         RosettaENZYME found 1683 of 20466
         RosettaGENENAME found 17924 of 20466
         RosettaGO found 14402 of 20466
         RosettaLOCUSID found 18883 of 20466
         RosettaMAP found 17745 of 20466
         RosettaPATH found 3568 of 20466
         RosettaPMID found 18060 of 20466
         RosettaREFSEQ found 18223 of 20466
         RosettaSUMFUNC found 0 of 20466
         RosettaSYMBOL found 18671 of 20466
         RosettaUNIGENE found 18363 of 20466
Mappings found for non-probe based rda files:
         RosettaCHRLENGTHS found 21
         RosettaENZYME2PROBE found 753
         RosettaGO2ALLPROBES found 0
         RosettaGO2PROBE found 0
         RosettaORGANISM found 1
         RosettaPATH2PROBE found 174
         RosettaPFAM found 14431
         RosettaPMID2PROBE found 86785
         RosettaPROSITE found 9754

> sessionInfo()
R version 2.4.0 Under development (unstable) (2006-07-25 r38698)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

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

other attached packages:
   Rosetta AnnBuilder    RSQLite        DBI   annotate        XML
Biobase         GO
   "2.3.0"   "1.11.5"    "0.4-1"   "0.1-10"   "1.11.2"   "0.99-8"  "1.11.22"
"1.12.0"
>


Hi, Shiliang,

I didn't run your example file. But I think AnnBuilder should work for your
case. A
couple of suggestions:

1. I saw a lot of environments have probe number missmatch in your output.
This is
abnormal. Could you remove the header line:
probe_id    LocusLinkID
and all the blank lines in basefile01.txt, and run AnnBuilder one more time?
Let me know
if you still see probe number missmatch.

2. The GO mapping problem:

The screen print for "library(AnnBuilder)" is abnormal:
--------------------------------------------
Attaching package: 'annotate'

      The following object(s) are masked *_by_* .GlobalEnv :

       getGO
--------------------------------------------
Did you define a "getGO" function in .GlobalEnv? If you do
"library(AnnBuilder)" from a
fresh R session, you shouldn't get any warning about "getGO". If you have
loaded package
"GO" before "AnnBuilder", you should get a warning like this:
-------------------------------------------
library(GO)
library(AnnBuilder)

Loading required package: Biobase Loading required package: tools
Welcome to Bioconductor

   Vignettes contain introductory material.
   To view, simply type 'openVignette()' or start with 'help(Biobase)'.
   For details on reading vignettes, see the openVignette help page.

Loading required package: XML
Loading required package: annotate
Loading required package: RSQLite
Loading required package: DBI

Attaching package: 'AnnBuilder'

       The following object(s) are masked from package:GO :

        GO
---------------------------------------------------

So, please make sure your R environment is clean before you run AnnBuilder.
For example,
if you are using linux, you can use
"R --no-restore" or "R --vanilla" (use "R --help" to see commandline
options).

3. I encourage you to post questions to the mailing-list next time, so that
you can get
suggestions from many experts and other users can also benefit from the
answer.

Hope this is useful. Please let me know if you still have problem using
AnnBuilder.

good luck

nianhua

==================================================================
HI, Nianhua:

Sorry to bother you, I tried to build an annotation data package for Rosetta
chip. I am
pretty new to R language. Problem is that I cannot get Go annotation worked,
the follwing
is my summary:
library(Rosetta)
Rosetta()


Quality control information for  Rosetta Date built: Created: Wed Jul 26
17:04:08 2006
Number of probes: 20467 Probe number missmatch: RosettaACCNUM; RosettaCHR;
RosettaCHRLOC;
RosettaENZYME; RosettaGENENAME; RosettaGO; RosettaLOCUSID; RosettaMAP;
RosettaPATH;
RosettaPMID; RosettaREFSEQ; RosettaSUMFUNC; RosettaSYMBOL; RosettaUNIGENE
Probe
missmatch: None Mappings found for probe based rda files:
 RosettaACCNUM found 0
of 20467
       RosettaCHR found 18659 of 20467
       RosettaCHRLOC found 15939 of 20467
       RosettaENZYME found 1685 of 20467
       RosettaGENENAME found 17923 of 20467
       RosettaGO found 14402 of 20467
       RosettaLOCUSID found 18883 of 20467
       RosettaMAP found 17745 of 20467
       RosettaPATH found 3588 of 20467
       RosettaPMID found 18060 of 20467
       RosettaREFSEQ found 18223 of 20467
       RosettaSUMFUNC found 0 of 20467
       RosettaSYMBOL found 18671 of 20467
       RosettaUNIGENE found 18363 of 20467 Mappings found for non-probe
based rda files:
       RosettaCHRLENGTHS found 21
       RosettaENZYME2PROBE found 753
       RosettaGO2ALLPROBES found 0
       RosettaGO2PROBE found 0
       RosettaORGANISM found 1
       RosettaPATH2PROBE found 174
       RosettaPFAM found 14431
       RosettaPMID2PROBE found 86663
       RosettaPROSITE found 9754

I tried to use RosettaGO2PROBE, but it is all NULL, I built binary package
without any
problem. the following is my code to built the package:

myBase <- "d:/Shiliang/result/limma/basefile01.txt"
myBaseType <- "ll"
myDir <- "d:/Shiliang/temp"
myPkgName <- "Rosetta"
ABPkgBuilder(baseName = myBase, baseMapType = myBaseType,
pkgName = myPkgName, pkgPath = myDir,
organism = "Mus musculus", version = "2.3.0",
author = list(author = "Shiliang
Wang<swang@email.unc.edu<javascript:open_compose_win('to=swang%40email.unc.edu&thismailbox=INBOX');>
>",
maintainer = "Shiliang
Wang<swang@email.unc.edu<javascript:open_compose_win('to=swang%40email.unc.edu&thismailbox=INBOX');>
>"),
fromWeb = TRUE)

It runs with a lots of warning like "fail to get data from kegg...."
the attached is my basefile for Rosetta chip.

the following is my sessionInfo
library(AnnBuilder)

Loading required package: Biobase Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()' or start with 'help(Biobase)'. For details
  on reading vignettes, see the openVignette help page.

Loading required package: XML
Loading required package: annotate

Attaching package: 'annotate'


      The following object(s) are masked *_by_* .GlobalEnv :

       getGO

Loading required package: RSQLite
Loading required package: DBI
Warning message:
package 'AnnBuilder' was built under R version 2.4.0
sessionInfo()

Version 2.3.1 (2006-06-01) i386-pc-mingw32
attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
[7] "datasets"
 "base"

other attached packages:
AnnBuilder    RSQLite        DBI   annotate        XML    Biobase  "1.11.4"
  "0.4-1"
"0.1-10"   "1.10.0"   "0.99-8"   "1.10.1"



Do you know what is the problem with my code, I saw you answer lots of
question in the
mailing list, one of them is similiar with mine, I read your answer and
tried your code
for vaimm06( pkgname), probably you can find it.
it works for GB basemaptype but for my case I used "ll", it seems the
package has some
bugs inside.

Thanks a lot

Best
Shiliang Wang

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