[BioC] AnnBuilder error

[Aedin Culhane]

Hi
I'd be grateful for your help. I am having problems with creating an 
annotation packages.  The errors are:

gunzip: /tmp/RtmpQ29612/file66334873Hs.data.gz: invalid compressed 
data--crc error
gunzip: /tmp/RtmpQ29612/file66334873Hs.data.gz: invalid compressed 
data--length error
Can not open /tmp/RtmpQ29612/file66334873Hs.data at 
/tmp/RtmpQ29612/tempPerl238e1f29.pl line 6.
Warning messages:
1: Built for UCSC is not valid! in: getUCSCBuilt(organism)
2: cannot open file '/tmp/RtmpQ29612/tempOut625558ec', reason 'No such 
file or directory'
Error in if (!is.null(ug) && nrow(ugMapping) > 0) { :
        missing value where TRUE/FALSE needed
In addition: Warning message:
Failed to get or parse UniGene data becaus of:

 Error in file(file, "r") : unable to open connection
 in: unifyMappings(base, eg, ug, otherSrc)


 > traceback()
6: unifyMappings(base, eg, ug, otherSrc)
5: getUniMappings(baseName, srcObjs[["eg"]], srcObjs[["ug"]], NULL,
       baseMapType)
4: ABPkgBuilder(baseName = mybaseName, srcUrls = mySrcUrls, baseMapType 
= myBaseType,
       otherSrc = NULL, pkgName = "TIGR40K.mapGB", pkgPath = myDir,
       organism = "Homo sapiens", version = "1.1.0", author = myauthor,
       fromWeb = TRUE)
3: eval.with.vis(expr, envir, enclos)
2: eval.with.vis(ei, envir)
1: source("AnnBuilder.R")


My basefile looks like.  V2 are genbank accesssion numbers

        V1       V2
1   489567 AA099162
2    46105   H09322
3   396145 AA757917
4  1755589 AI204424
5  1690935 AI091817
6   504207 AA132086
7    33150   R43822
8  1690655 AI143430
9   809876 AA455126
10   32175   R43463


 > mySrcUrls
                                                                                 
GP
   
"ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Homo_sapiens/database/"
                                                                                 
UG
                
"ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.data.gz"
                                                                                 
GO
"http://www.godatabase.org/dev/database/archive/latest/go_200602-termdb.rdf-xml.gz"
                                                                                 
HG
                               
"ftp://ftp.ncbi.nih.gov/pub/HomoloGene/old/hmlg.ftp"
                                                                                 
EG
                                             
"ftp://ftp.ncbi.nlm.nih.gov/gene/DATA"



Session Info
R version 2.2.0, 2005-10-06, i686-redhat-linux-gnu

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

other attached packages:
hgu133plus2          GO  AnnBuilder    annotate         XML     Biobase
   "1.10.0"     "1.7.1"     "1.8.0"     "1.8.0"    "0.99-6"     "1.8.0"


Thanks for your help
Aedin