Hi,:

Thanks a lot to John and Nianhua. thanks for your guys help!
I tried to use Annbuilder 1.11.6 (that I checked out using SVN in
bioconductor and build the package by myself) to build annotation package
again, it still does't work out. this is the information I got.
what should I do?

I noticed several issues:

1.    Warning message:
'symbol.C' is deprecated in: symbol.C("sqlite3_libversion")
2.    Error in gzfile(file, "wb") : unable to open connection
In addition: Warning message:
cannot open compressed file
'C:/Shiliang/temp/Rosetta/data/RosettaLOCUSID.rda'
3.     there are still no data for GO2Probe ?




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(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
Warning message:
'symbol.C' is deprecated in: symbol.C("sqlite3_libversion")
>  myBase <- "d:/Shiliang/result/limma/basefile01.txt"
>  myBaseType <- "ll"
>  myDir <- "C:/Shiliang/temp"
>  myPkgName <- "Rosetta"
>  ABPkgBuilder(baseName = myBase, baseMapType = myBaseType,
+  pkgName = myPkgName, pkgPath = myDir,
+  organism = "Mus musculus", version = "1.0.0",
+  author = list(author = "Shiliang Wang<swang@email.unc.edu>",
+  maintainer = "Shiliang Wang<swang@email.unc.edu>"),
+  fromWeb = TRUE)

Attaching package: 'GO'


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

         GO

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
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
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
Warning message:
failed to create a data connection
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] "3850 2 2"
Error in gzfile(file, "wb") : unable to open connection
In addition: Warning message:
cannot open compressed file
'C:/Shiliang/temp/Rosetta/data/RosettaLOCUSID.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

> temp <- as.list( RosettaGO2PROBE)
> temp
list()
> 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         GO AnnBuilder    RSQLite        DBI   annotate
XML    Biobase
   "2.3.0"   "1.12.0"   "1.11.6"    "0.4-1"   "0.1-10"   "1.11.2"   "0.99-8"
"1.11.22"








On 7/28/06, John Zhang <jzhang@jimmy.harvard.edu> wrote:
>
>
> >Also, I found I cannot use some of function in AnnBuilder, I don't know
> why?
> >I used it because I want to reproduce the result from AnnBuilder.pdf from
> >the package review. it always give me error.
>
> It is a name space issue. Try AnnBuilder:::functionName
>
>
> >
> >Best
> >
> >Shiliang
> >
> >
> >
> >
> >R : Copyright 2006, The R Foundation for Statistical Computing
> >Version 2.3.1 (2006-06-01)
> >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.
> >
> >[Previously saved workspace restored]
> >
> >> library(AnnBUilder)
> >Error in library(AnnBUilder) : there is no package called 'AnnBUilder'
> >> 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
> >> writeAnnData2Pkg
> >Error: object "writeAnnData2Pkg" not found
> >> getChroLocation
> >Error: object "getChroLocation" not found
> >>
> >
> >
> >
> >On 7/27/06, Nianhua Li <nli@fhcrc.org> wrote:
> >>
> >> Hi, Shiliang,
> >>
> >> You were right that AnnBuilder did have a bug. Thanks for the report!
> >>
> >> The bug is related to Weijun's question:
> >>
> >>
>
> http://thread.gmane.org/gmane.science.biology.informatics.conductor/9227/focus=9
> 232
> >> When baseType is "ll", the baseFile can't be parsed correctly because
> >> some parsers assume Entrez Gene is at the 3rd column of the base file.
> >> Thanks for John's patch, AnnBuilder just quietly converts the base file
> >> into three columns when baseType is "ll". So, weijun's problem got
> >> solved. Unfortunately, the parser used for "go2probe" mapping assumes a
> >> two-column setting for baseType "ll", therefore can't work correctly
> >> with the patch.
> >>
> >> Now the problem has been solved. You can either get the up-to-date
> >> AnnBuilder (v 1.11.6) from svn or wait still Saturday noon to download
> >> it using biocLite or from website. You can also modify your local
> source
> >> AnnBuilder/R/ABPkgBuilder.R if you are in a hurry:
> >> ===================================================================
> >> --- ABPkgBuilder.R      (v1.11.5 or before)
> >> +++ ABPkgBuilder.R      (v1.11.6)
> >>
> >> # Map GO ids to probe ids that are directly associated with the GO ids
> >> mapGO2Probe <- function(eg, baseMapType){
> >> -     if(baseMapType == "ll"){
> >> -            parser(eg) <- file.path(.path.package("AnnBuilder"),
> >> -                                    "scripts", "GO2ProbeParser4LL")
> >> -        }else{
> >> -            parser(eg) <- file.path(.path.package("AnnBuilder"),
> >> +        parser(eg) <- file.path(.path.package("AnnBuilder"),
> >>                                     "scripts", "GO2ProbeParser")
> >> -        }
> >>         options(show.error.messages = FALSE)
> >>         go2Probe <- try(parseData(eg, eg@go, ncol = 3))
> >>         options(show.error.messages = TRUE)
> >> ====================================================================
> >>
> >> Also the probe number mismatch is because your base file has duplicated
> >> probeset identifiers.
> >>
> >> help it works this time :)
> >>
> >> nianhua
> >>
> >>
> >
> >       [[alternative HTML version deleted]]
> >
> >_______________________________________________
> >Bioconductor mailing list
> >Bioconductor@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
>
>

	[[alternative HTML version deleted]]

