Error in gtf2sqlite

[mlist]

gtf2sqlite( assembly = "hg19",
            db.file  = system.file("~/human_hg19_ens75_txdb.sqlite",
                                   package="ciRcus"))

snapshotDate(): 2016-11-13
loading from cache ‘/home/mlist//.AnnotationHub/10684’
using guess work to populate seqinfo
Error in sqliteCopyDatabase(dbconn(x), file) : 
  'to' must be SQLiteConnection object or a non-empty string

Here is my sessionInfo()

R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               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    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] GenomicRanges_1.26.1 GenomeInfoDb_1.10.1  IRanges_2.8.1        S4Vectors_0.12.0     BiocGenerics_0.20.0 
[6] ciRcus_0.1.2        

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.7                   RColorBrewer_1.1-2            plyr_1.8.4                   
 [4] BiocInstaller_1.24.0          AnnotationHub_2.6.1           XVector_0.14.0               
 [7] GenomicFeatures_1.26.0        bitops_1.0-6                  tools_3.3.1                  
[10] zlibbioc_1.20.0               biomaRt_2.30.0                digest_0.6.10                
[13] tibble_1.2                    gtable_0.2.0                  lattice_0.20-34              
[16] RSQLite_1.0.0                 Matrix_1.2-7.1                shiny_0.14.1                 
[19] DBI_0.5-1                     curl_2.1                      stringr_1.1.0                
[22] rtracklayer_1.34.0            httr_1.2.1                    Biostrings_2.42.0            
[25] grid_3.3.1                    data.table_1.9.6              Biobase_2.34.0               
[28] R6_2.2.0                      hash_2.2.6                    AnnotationDbi_1.36.0         
[31] RMySQL_0.10.9                 XML_3.98-1.4                  BiocParallel_1.8.0           
[34] magrittr_1.5                  ggplot2_2.2.0                 scales_0.4.1                 
[37] Rsamtools_1.26.0              htmltools_0.3.5               GenomicAlignments_1.10.0     
[40] assertthat_0.1                SummarizedExperiment_1.4.0    colorspace_1.2-7             
[43] mime_0.5                      interactiveDisplayBase_1.12.0 xtable_1.8-2                 
[46] httpuv_1.3.3                  stringi_1.1.2                 lazyeval_0.2.0               
[49] munsell_0.4.3                 RCurl_1.95-4.8                chron_2.3-47    

---

edit (@mschilli87): formatting

[mschilli87]

The system.file function is currently broken returning an empty string (""). If you specify a valid file name as db.file parameter, it should work.

[mschilli87]

I have to correct myself. The call in the README is currently wrong. @retaj is working on a fix right now.