SRAdb: could not find function "sqliteTableFields"
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@darioberaldi-6991
Last seen 6 weeks ago
United Kingdom

Hello,

I just installed SRAdb. I get the error "could not find function "sqliteTableFields" when executing getSRA. Any idea what's wrong?

Many thanks!

Dario

library(SRAdb)
sra_dbname <- 'SRAmetadb.sqlite'      
sra_con <- dbConnect(dbDriver("SQLite"), sra_dbname)
rs <- getSRA (search_terms ='breast cancer', out_types=c('run','study'), sra_con=sra_con)
#Error in getSRA(search_terms = "breast cancer", out_types = c("run", "study"),  :
#  could not find function "sqliteTableFields"
    
sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-redhat-linux-gnu (64-bit)

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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] SRAdb_1.18.0   RCurl_1.95-4.3 bitops_1.0-6   graph_1.42.0   RSQLite_1.0.0
[6] DBI_0.3.1     

loaded via a namespace (and not attached):
[1] Biobase_2.24.0      BiocGenerics_0.10.0 GEOquery_2.30.1    
[4] parallel_3.1.1      stats4_3.1.1        tools_3.1.1        
[7] XML_3.98-1.1       

 

sradb sqlite • 1.3k views
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@sean-davis-490
Last seen 23 days ago
United States

It looks like you are running an older version of Bioconductor.  An upgrade to the most recent version of SRAdb (1.20.1) and Bioconductor should fix the problem.

source("http://bioconductor.org/biocLite.R")
biocLite("BiocUpgrade")

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Done. Thanks a lot that fixed it!

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