Hello All,

I am trying to load E. coli genes from a gff3 with makeTranscriptDbFromGff but am getting the following error:

> chrominfo <- data.frame(chrom=c('ecoli'), length=c(4639675), is_circular=c(NA))
> txdb <- makeTranscriptDbFromGFF("ecoli.gff", format="gff3", chrominfo=chrominfo)
Prepare the 'metadata' data frame ... metadata: OK
Error in is.data.frame(arg) : object 'tables' not found
In addition: Warning message:
In if is.na(chrominfo)) { :
  the condition has length > 1 and only the first element will be used

I have seen posts from others with similar issues but have been unable to find a solution. I have a hunch that the problem may be with my gff input file but it passes validation at http://genometools.org/cgi-bin/gff3validator.cgi, so I'm not sure what is amiss. Hopefully someone can give me some insight into what's going wrong.

The gff file was constructed from a .ptt file using a simple script and my first thought was that it was a problem with the gff format and it's possible I'm missing some component(s) I need or something is out of place. First ten lines of the file are below...

##gff-version 3
##sequence-region ecoli    1    4639675
ecoli    pttToGff    gene    190    255    .    +    .    gene_name="thrL"
ecoli    pttToGff    gene    337    2799    .    +    .    gene_name="thrA"
ecoli    pttToGff    gene    2801    3733    .    +    .    gene_name="thrB"
ecoli    pttToGff    gene    3734    5020    .    +    .    gene_name="thrC"
ecoli    pttToGff    gene    5234    5530    .    +    .    gene_name="yaaX"
ecoli    pttToGff    gene    5683    6459    .    -    .    gene_name="yaaA"
ecoli    pttToGff    gene    6529    7959    .    -    .    gene_name="yaaJ"
ecoli    pttToGff    gene    8238    9191    .    +    .    gene_name="talB"

And for completeness (and to address the very real possibility that my very old computer is at issue), here's the output form sessionInfo()... On that note, it may be worth mentioning that I was unable to install the most recent versions of certain dependencies for the rnaseqGene workflow because they just would not compile on my machine. Suffice it to say, I'm stuck with the hardware I have, so if it's just not going to work, then it is what it is!

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: i386-apple-darwin10.8.0 (32-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base     

other attached packages:
 [1] ecoliK12.db0_3.0.0     GenomicFeatures_1.18.2 AnnotationDbi_1.28.1  
 [4] Biobase_2.26.0         Rsamtools_1.18.2       Biostrings_2.34.0     
 [7] XVector_0.6.0          GenomicRanges_1.18.3   GenomeInfoDb_1.2.3    
[10] IRanges_2.0.0          S4Vectors_0.4.0        BiocGenerics_0.12.1   
[13] BiocInstaller_1.16.1  

loaded via a namespace (and not attached):
 [1] base64enc_0.1-2         BatchJobs_1.5           BBmisc_1.8             
 [4] BiocParallel_1.0.0      biomaRt_2.22.0          bitops_1.0-6           
 [7] brew_1.0-6              checkmate_1.5.0         codetools_0.2-9        
[10] DBI_0.3.1               digest_0.6.4            fail_1.2               
[13] foreach_1.4.2           GenomicAlignments_1.2.1 iterators_1.0.7        
[16] RCurl_1.95-4.4          RSQLite_1.0.0           rtracklayer_1.26.2     
[19] sendmailR_1.2-1         stringr_0.6.2           tools_3.1.2            
[22] XML_3.98-1.1            zlibbioc_1.12.0        

At any rate, I'm hoping someone can shed some light on the issue and get me back on track with this. Thanks!

Adam