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Question: SRAdb: could not find function "sqliteTableFields"
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gravatar for dario.beraldi
3.0 years ago by
United Kingdom
dario.beraldi0 wrote:

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       

 

ADD COMMENTlink modified 3.0 years ago by Sean Davis21k • written 3.0 years ago by dario.beraldi0
2
gravatar for Sean Davis
3.0 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:

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")

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Sean Davis21k

Done. Thanks a lot that fixed it!

ADD REPLYlink written 3.0 years ago by dario.beraldi0
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