[BioC] Error while using AnnBuilder

[Ting-Yuan Liu]

Hi Julien,

> What does it mean "The following object(s) are masked from
> package:AnnBuilder :" ?

This is not the reason why you cannot run ABPkgBuilder successfully.  The 
function GO in the GO package is used to display some descriptive 
statistics for the environments, and the GO function in AnnBuilder is to 
define a new object of class "GO".  It is OK to see this message.

> Erreur dans all(is.na(annotation[, "GO"])) : indice hors limites
> $>

I think this bug has been fixed.  Could you try the developmental version 
of AnnBuilder and see if you still get the same error message?

> $> mySrcUrls <-
> 
c(EG="ftp://ftp.ncbi.nih.gov/gene/DATA",UG="ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_s$
>

This setting is not necessary.  If you ignore the srcUrls argument, 
AnnBuilder will determine it for you.  

HTH,
Ting-Yuan
______________________________________
Ting-Yuan Liu
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
Seattle, WA, USA
______________________________________

On Sat, 28 Jan 2006, TEXTORIS Julien wrote:

> Hi, 
> 
> We are currently trying to develop a library to deal with nylon arrays.
> 
> I wanted to build an annotation package for our chip, but i have an error with 
> GO. Here is the log :
> 
> $> mySrcUrls <- 
> c(EG="ftp://ftp.ncbi.nih.gov/gene/DATA",UG="ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.data.gz")
> $> myBase <- "/home/jtextori/Documents/DEA/bioc/MC0311.txt.csv"
> $> myBaseType <- "image"
> $> myDir <-  tempdir()
> $> ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = 
> myBaseType, otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir, 
> organism = "Homo sapiens", version = "1.1.0", makeXML = FALSE, author = 
> list(author = "Julien TEXTORIS", maintainer = "Julien.Textoris at gmail.com"), 
> fromWeb = TRUE)
> Erreur : impossible de trouver la fonction "ABPkgBuilder"
> $> library(AnnBuilder)
> Le chargement a nécessité le package : Biobase
> Le chargement a nécessité le 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.
> 
> Le chargement a nécessité le package : XML
> Le chargement a nécessité le package : annotate
> $> ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = 
> myBaseType, otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir, 
> organism = "Homo sapiens", version = "1.1.0", makeXML = FALSE, author = 
> list(author = "Julien TEXTORIS", maintainer = "Julien.Textoris at gmail.com"), 
> fromWeb = TRUE)
> Erreur dans ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = 
> myBaseType,  : 
> 	argument(s) inutilisé(s) (makeXML ...)
> $> ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = 
> myBaseType, , pkgName = "myPkg", pkgPath = myDir, organism = "Homo sapiens", 
> version = "1.1.0", author = list(author = "Julien TEXTORIS", maintainer = 
> "Julien.Textoris at gmail.com"), fromWeb = TRUE)
> 
> Attachement du package : 'GO'
> 
> 
> 	The following object(s) are masked from package:AnnBuilder :
> 
> 	 GO 
> 
> 
> Erreur dans all(is.na(annotation[, "GO"])) : indice hors limites
> $>
> 
> The file is a text file with two columns, separated by a tabulation. First is 
> the identifier from the chip, seond is the cloneId in the form IMAGE:nnnnn
> 
> I had the same error when i specified an URL for GO ?
> 
> What does it mean "The following object(s) are masked from 
> package:AnnBuilder :" ?
> 
> Thanks in advance for any help,
> 
> Julien
> 
> PS, sessionInfo() follows :
> 
> > sessionInfo()
> R version 2.2.1, 2005-12-20, i686-pc-linux-gnu 
> 
> attached base packages:
> [1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"    
> [7] "datasets"  "base"     
> 
> other attached packages:
>         GO AnnBuilder   annotate        XML    Biobase 
>   "1.10.0"    "1.8.0"    "1.8.0"   "0.99-6"    "1.8.0" 
> >
> 
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