[BioC] AnnBuilder error

[Ting-Yuan Liu]

Hi Aedin,

It seems that your gunzip function cannot unzip the Hs.data.gz file 
correctly.  It could be (1) the gunzip function didn't work well, or (2) 
the Hs.data.gz is not compressed well.  According to the website 
ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/, the file 
Hs.data.gz is put on Dec 30, 2005.  When I was building packages between 
Dec 30, 2005, and today, I don't have any problem in this file.  
Therefore, I think the file Hs.data.gz is OK.

Here is my gunzip version:
tliu at gopher1:~/tmp> gunzip --version
gunzip 1.3.5
(2002-09-30)

This one works on the Hs.data.gz file.  Today I used "wget" to download 
ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.data.gz and I 
can unzip it without any error messages.  

Could you also try
wget ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.data.gz
and
gunzip Hs.data.gz
to see if your gunzip function works?

Could you also try to build the package again to see if you will have the 
same problem?  It is also possible that the Hs.data.gz file was not 
downloaded completely (due to the network connection problem) so that the 
file cannot be uncompressed successfully.  

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

On Fri, 24 Feb 2006, Aedin Culhane wrote:

> 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
> 
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