[BioC] error of makeTranscriptDbFromGFF

[DL Guo [guest]]

Hi, 
   I have run the function,makeTranscriptDbFromGFF, of the GenomicFeatures package with the simplest way （txdb <- makeTranscriptDbFromGFF(file = "Vitis_vinifera.IGGP_12x.gtf", format = "gtf")）or other complicate way and always got the following errors:
Warning messages:
1: In .deduceExonRankings(exs, format = "gtf") :
  Infering Exon Rankings.  If this is not what you expected, then please be sure that you have provided a valid attribute for exonRankAttributeName
2: In matchCircularity(chroms, circ_seqs) :
  None of the strings in your circ_seqs argument match your seqnames.
 I got the gtf file of vitis vinefera from here:
http://plants.ensembl.org/info/data/ftp/index.html.
  
    And I also tried the instructions of makeTranscriptDbFromGFF on the website as the following:
gtfFile <- system.file("extdata","Aedes_aegypti.partial.gtf", package="GenomicFeatures")
txdb <- makeTranscriptDbFromGFF(file = gtfFile, format= "gtf").
   Unfortunately, I got the same error as the vitis gtf file was used.
   So I am confused. Why did the errors happen even if I use the sample file?
    Thank you!

 -- output of sessionInfo(): 

output
txdb <- makeTranscriptDbFromGFF(file = "Vitis_vinifera.IGGP_12x.gtf", format = "gtf")
extracting transcript information
Estimating transcript ranges.
Extracting gene IDs
Processing splicing information for gtf file.
Deducing exon rank from relative coordinates provided
Prepare the 'metadata' data frame ... metadata: OK
Now generating chrominfo from available sequence names. No chromosome length information is available.
Warning messages:
1: In .deduceExonRankings(exs, format = "gtf") :
  Infering Exon Rankings.  If this is not what you expected, then please be sure that you have provided a valid attribute for exonRankAttributeName
2: In matchCircularity(chroms, circ_seqs) :
  None of the strings in your circ_seqs argument match your seqnames.

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936 
[2] LC_CTYPE=Chinese (Simplified)_China.936   
[3] LC_MONETARY=Chinese (Simplified)_China.936
[4] LC_NUMERIC=C                              
[5] LC_TIME=Chinese (Simplified)_China.936    

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

other attached packages:
[1] GenomicFeatures_1.14.3 AnnotationDbi_1.24.0  
[3] Biobase_2.22.0         GenomicRanges_1.14.4  
[5] XVector_0.2.0          IRanges_1.20.7        
[7] BiocGenerics_0.8.0     BiocInstaller_1.12.0  

loaded via a namespace (and not attached):
 [1] biomaRt_2.18.0     Biostrings_2.30.1  bitops_1.0-6      
 [4] BSgenome_1.30.0    DBI_0.2-7          RCurl_1.95-4.1    
 [7] Rsamtools_1.14.3   RSQLite_0.11.4     rtracklayer_1.22.4
[10] stats4_3.0.2       tools_3.0.2        XML_3.98-1.1      
[13] zlibbioc_1.8.0 

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