Hi Murli,

I just now saw that your email went to not only my inbox, but also to 
the bioconductor mailing list as well.  I will now answer it here so 
that others who may have similar questions can benefit:

Those are not actually errors.  They are warnings.  An error means 
something severe went wrong and the code cannot (or should not) 
continue.  A warning means you should look at this message in case this 
detail might affect you.

The 1st of these warning messages is telling you that your file did not 
contain exon ranking information (and so the order is being inferred by 
the order that the exons are present in the source file).  You may or 
may not feel comfortable with that inference.  Frankly, it depends on 
the file (and the species of organism) whether or not its a fair thing 
to assume and we expect that you will know whether or not you need to 
worry about it.

The other warning says that your the code was unable to guess about 
which (if any) of your chromosomes were circular.

Whether any of that is a problem or not will entirely depend on you and 
what you want (and what you want to do next).  It's not possible for us 
to know whether or not these circumstances are a problem for you or not, 
so we issue a warning (instead of an error).


  Marc



On 03/12/2014 02:27 PM, Maintainer wrote:
> Hi,
>     I have run the function,makeTranscriptDbFromGFF, of the GenomicFeatures package with the simplest way пј^txdb <- makeTranscriptDbFromGFF(file = "Vitis_vinifera.IGGP_12x.gtf", format = "gtf")пј0/00or 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
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
>
>
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