[BioC] RE : RE : RE : RE : maping SNPs

[Simon Noël]

Hi

As you can see, the package GenomicRanges and IRanges  don't have the same version as yours on the supercomputer.  I will ask our informaticien to update them to the version you have and will see if now  makeTranscriptDbFromUCSC works.  I will let you know of any positive or negative result.    

> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
 [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8    
 [5] LC_MONETARY=C              LC_MESSAGES=en_CA.UTF-8   
 [7] LC_PAPER=en_CA.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C       
 attachedbase packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     
 otherattached packages:
[1] GenomicFeatures_1.2.3                 
[2] SNPlocs.Hsapiens.dbSNP.20101109_0.99.2
[3] GenomicRanges_1.2.2                   
[4] IRanges_1.8.7                         
 loadedvia a namespace (and not attached):
 [1] Biobase_2.10.0     biomaRt_2.6.0      Biostrings_2.18.2  BSgenome_1.18.2   
 [5] DBI_0.2-5          RCurl_1.5-0        RSQLite_0.9-4      rtracklayer_1.10.6
 [9] tools_2.12.0       XML_3.2-0  


Simon Noël
CdeC
________________________________________
De : Hervé Pagès [hpages at fhcrc.org]
Date d'envoi : 11 janvier 2011 21:05
À : Simon Noël
Cc : Valerie Obenchain; bioconductor at r-project.org
Objet : Re: [BioC] RE : RE :  RE :  maping SNPs

>     On     the    super    computer, it still doesn't work    and    on my
>     computer, it still taking a lot of time.  What isn't working is
>
>     >  txdb<- makeTranscriptDbFromUCSC(genome="hg19", tablename="refGene")
>      Downloadthe refGene table ... OK
>      Downloadthe refLink table ... OK
>      Extractthe 'transcripts' data frame ... OK
>      Extractthe 'splicings' data frame ... OK
>      Downloadand preprocess the 'chrominfo' data frame ... OK
>      Preparethe 'metadata' data frame ... OK
>      Makethe TranscriptDb object  ... Error  in  .writeMetadataTable(conn,
>     metadata) : subscript out of bounds
>     In addition: There were 50 or more warnings (use warnings() to see the first
>     50)

 Probablybecause some of the packages need to be updated on this machine
(as you are already aware). See my sessionInfo below.

Cheers,
H.

R version 2.12.0 (2010-10-15)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
  [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
  [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
  [7] LC_PAPER=en_US.utf8       LC_NAME=C
  [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

 attachedbase packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

 otherattached packages:
[1] GenomicFeatures_1.2.3
[2] SNPlocs.Hsapiens.dbSNP.20101109_0.99.2
[3] GenomicRanges_1.2.3
[4] IRanges_1.8.8

 loadedvia a namespace (and not attached):
[1] Biobase_2.10.0     biomaRt_2.6.0      Biostrings_2.18.2
BSgenome_1.18.2
[5] DBI_0.2-5          RCurl_1.5-0        RSQLite_0.9-4
rtracklayer_1.10.6
[9] XML_3.2-0


>
>
>     Simon Noël
>     CdeC
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--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
 P.O.Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319