Dear all,

I encountered a really long elapsed time for importing a small toy gff3 file 
when using `import.gff3()`, here is what I did:

> library(rtracklayer)
> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
> txdb = TxDb.Hsapiens.UCSC.hg19.knownGene
> grl.exons = exonsBy(txdb, by = 'tx')[1:42]

> export.gff3(grl.exons, 'test.gff3')

> system.time(import.gff3('test.gff3'))

   user  system elapsed
  0.892   0.092  60.428 

It takes about one minute to import it, and the time varies a lot when I repeat.
I don't understand what's going on in this case, and I don't know if it can apply 
to you or just on my system.

Any suggestion?

> sessionInfo()

R version 3.3.2 (2016-10-31)
Platform: x86_64-suse-linux-gnu (64-bit)
Running under: openSUSE Tumbleweed

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=en_US.UTF-8       LC_NAME=C                 
[9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[2] GenomicFeatures_1.26.0                 
[3] AnnotationDbi_1.36.0                   
[4] Biobase_2.34.0                         
[5] rtracklayer_1.34.1                     
[6] GenomicRanges_1.26.1                   
[7] GenomeInfoDb_1.10.1                    
[8] IRanges_2.8.1                          
[9] S4Vectors_0.12.0                       
[10] BiocGenerics_0.20.0                    

loaded via a namespace (and not attached):
[1] XVector_0.14.0             zlibbioc_1.20.0           
[3] GenomicAlignments_1.10.0   BiocParallel_1.8.1        
[5] BSgenome_1.42.0            lattice_0.20-34           
[7] tools_3.3.2                SummarizedExperiment_1.4.0
[9] grid_3.3.2                 DBI_0.5-1                 
[11] Matrix_1.2-7.1             bitops_1.0-6              
[13] RCurl_1.95-4.8             biomaRt_2.30.0            
[15] RSQLite_1.0.0              BiocInstaller_1.24.0      
[17] Biostrings_2.42.0          Rsamtools_1.26.1          
[19] XML_3.98-1.4             

This takes <1s for me, but after running this I see in sessionInfo()

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg19_1.4.0      
 [2] BSgenome_1.42.0                       
...

I'm guessing that import.gff3 is consulting a source to correctly populate the seqinfo of the returned value. For me it sees that I have an appropriate BSgenome package installed, but for you it runs off to the UCSC and incurs latency. So you could try installing the BSgenome package.