SRAdb: Error downloading sqlite files
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Entering edit mode
arielle • 0
@arielle-12244
Last seen 2.2 years ago

 

I have successfully installed the SRAdb package. I am now trying to download and uncompress the files,

sqlfile <- 'SRAmetadb.sqlite'
if(!file.exists('SRAmetadb.sqlite')) sqlfile <<- getSRAdbFile()

But I get the following error:

downloaded 0 bytes

Error in download.file(url_sra, destfile = localfile, mode = "wb", method = method) : 
  cannot download all files

 

I have looked up this error but came up with nothing, could you help me find out what the problem is? Thank you!

> traceback()

2: download.file(url_sra, destfile = localfile, mode = "wb", method = method)
1: getSRAdbFile()


> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X El Capitan 10.11.6

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

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

other attached packages:
[1] SRAdb_1.32.0        RCurl_1.95-4.8      bitops_1.0-6        graph_1.52.0        BiocGenerics_0.20.0 RSQLite_1.1-2      

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12    XML_3.98-1.5    digest_0.6.12   R6_2.2.2        DBI_0.5-1       stats4_3.3.3    httr_1.2.1      tools_3.3.3     Biobase_2.34.0 
[10] memoise_1.0.0   GEOquery_2.40.0

 

 

 

 

 

 

 

sradb • 1.4k views
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Entering edit mode
arielle • 0
@arielle-12244
Last seen 2.2 years ago

It seems that the getSRAdbFile() function does not worked for me. This solved the problem:

system("wget https://s3.amazonaws.com/starbuck1/sradb/SRAmetadb.sqlite.gz")
system("gunzip SRAmetadb.sqlite.gz")
sqlfile <- 'SRAmetadb.sqlite'
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Entering edit mode

Newer versions of SRAdb have fixed this issue. Upgrading should allow the `getSRAdbFile()` function to work again. 

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