Hi,

here is my sessionInfo:

> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] GenomicFeatures_1.8.0 AnnotationDbi_1.18.0  Biobase_2.16.0       
[4] GenomicRanges_1.8.1   IRanges_1.14.2        BiocGenerics_0.2.0   

loaded via a namespace (and not attached):
 [1] biomaRt_2.12.0     Biostrings_2.24.0  bitops_1.0-4.1     BSgenome_1.24.0   
 [5] DBI_0.2-5          RCurl_1.91-1       Rsamtools_1.8.0    RSQLite_0.11.1    
 [9] rtracklayer_1.16.0 stats4_2.15.0      tools_2.15.0       XML_3.9-4         
[13] zlibbioc_1.2.0  

I updated GenomicFeatures to 1.8.1, but unfortunately did not help.


BUT:  makeTranscriptDbFromUCSC did work :)

> txdb <- makeTranscriptDbFromUCSC(genome="hg19", tablename="ensGene")
Download the ensGene table ... OK
Extract the 'transcripts' data frame ... OK
Extract the 'splicings' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Prepare the 'metadata' data frame ... metadata: OK
Make the TranscriptDb object ... OK
There were 50 or more warnings (use warnings() to see the first 50)

> txdb
TranscriptDb object:
| Db type: TranscriptDb
| Supporting package: GenomicFeatures
| Data source: UCSC
| Genome: hg19
| Genus and Species: Homo sapiens
| UCSC Table: ensGene
| Resource URL: http://genome.ucsc.edu/
| Type of Gene ID: Ensembl gene ID
| Full dataset: yes
| miRBase build ID: NA
| transcript_nrow: 181648
| exon_nrow: 541825
| cds_nrow: 278798
| Db created by: GenomicFeatures package from Bioconductor
| Creation time: 2012-06-07 17:48:45 +0200 (Thu, 07 Jun 2012)
| GenomicFeatures version at creation time: 1.8.1
| RSQLite version at creation time: 0.11.1
| DBSCHEMAVERSION: 1.0

> warnings()
Warning messages:
1: In .extractUCSCCdsStartEnd(cdsStart[i], cdsEnd[i], exon_locs$start[[i]],  ... :
  UCSC data anomaly in transcript ENST00000513161: the cds cumulative length is not a multiple of 3
2: In .extractUCSCCdsStartEnd(cdsStart[i], cdsEnd[i], exon_locs$start[[i]],  ... :
  UCSC data anomaly in transcript ENST00000417833: the cds cumulative length is not a multiple of 3
3: In .extractUCSCCdsStartEnd(cdsStart[i], cdsEnd[i], exon_locs$start[[i]],  ... :
  UCSC data anomaly in transcript ENST00000450884: the cds cumulative length is not a multiple of 3


Best,
Stefanie

Am 07.06.2012 um 16:25 schrieb Steve Lianoglou:

> Hi Stefanie,
> 
> On Thu, Jun 7, 2012 at 5:16 AM, Stefanie Tauber
> <stefanie.tauber@univie.ac.at> wrote:
>> Hi
>> 
>> I just tried it with R 2.15, I get the same error.
>> 
>> If I follow your suggestion:
>> 
>> txdb <- makeTranscriptDbFromUCSC(genome="hg19", tablename="ensGene")
>> 
>> 
>> I get:
>> 
>> Download the ensGene table ... OK
>> Extract the 'transcripts' data frame ... OK
>> Extract the 'splicings' data frame ... OK
>> Download and preprocess the 'chrominfo' data frame ... Error in
>> download.file(url, destfile, quiet = TRUE) :
>>   cannot open URL
>> 'http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz'
>> In addition: There were 50 or more warnings (use warnings() to see the first
>> 50)
> [snip]
> 
> Strange ... I also get the same warnings you get (the "cds cumulative
> length is not a multiple of 3") for some transcripts, but I think this
> is something beyond our control. I don't get any error(s) when
> downloading and building the TxDB, so it completes fine for me.
> 
> I'm actually running the *-devel versions of the bioc packages w/
> R-2.15.x so it's not very easy for me to check the current released
> GenomicFeatures package, but I'd be a bit surprised if the error is
> there.
> 
> Could you paste the output of `sessionInfo()` after you call
> `library(GenomicFeatures)` when running your new R-2.15.x install?
> 
> -steve
> 
> 
> -- 
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact

DI Stefanie Tauber

Center for Integrative Bioinformatics Vienna (CIBIV)
(CIBIV is a joint institute of Vienna University, Medical University, and University of Veterinary Medicine, Vienna, Austria)
Max F. Perutz Laboratories (MFPL)
Campus Vienna Biocenter 5 (VBC5), Ebene 1, Room 1812.2
Dr. Bohr Gasse 9
A-1030 Wien, Austria
Phone: ++43 +1 / 42772-4030
Fax:     ++43 +1 / 42772-4098
email:   stefanie.tauber@univie.ac.at
www.cibiv.at


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