getSRAdbFile() does not work
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jfertaj ▴ 30
@jfertaj-8566
Last seen 11 weeks ago
United Kingdom

Hi,

I am trying to retrieve SRAmetadb and GEOmetadb databases but the links does not work


library(GEOmetadb)
library(SRAdb)

>  getSRAdbFile()
probando la URL 'https://gbnci-abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz'
Error in download.file(url_sra, destfile = localfile, mode = "wb", method = method) : 
  no fue posible abrir la URL 'https://gbnci-abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz'
> geometadbfile <- getSQLiteFile()
probando la URL 'http://starbuck1.s3.amazonaws.com/sradb/GEOmetadb.sqlite.gz'
Error in download.file(url_geo, destfile = localfile, mode = "wb") : 
  no fue posible abrir la URL 'http://starbuck1.s3.amazonaws.com/sradb/GEOmetadb.sqlite.gz'

sessionInfo( )
R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur/Monterey 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

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

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

other attached packages:
[1] GEOmetadb_1.58.0    GEOquery_2.64.2     Biobase_2.56.0     
[4] SRAdb_1.58.0        RCurl_1.98-1.8      graph_1.74.0       
[7] BiocGenerics_0.42.0 RSQLite_2.2.16      BiocManager_1.30.18

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.9        compiler_4.2.0    pillar_1.8.1      bitops_1.0-7     
 [5] tools_4.2.0       bit_4.0.4         memoise_2.0.1     lifecycle_1.0.1  
 [9] tibble_3.1.8      pkgconfig_2.0.3   rlang_1.0.4       DBI_1.1.3        
[13] cli_3.3.0         fastmap_1.1.0     xml2_1.3.3        dplyr_1.0.9      
[17] generics_0.1.3    vctrs_0.4.1       hms_1.1.2         stats4_4.2.0     
[21] bit64_4.0.5       tidyselect_1.1.2  glue_1.6.2        data.table_1.14.2
[25] R6_2.5.1          fansi_1.0.3       limma_3.52.2      tidyr_1.2.0      
[29] tzdb_0.3.0        purrr_0.3.4       readr_2.1.2       blob_1.2.3       
[33] magrittr_2.0.3    ellipsis_0.3.2    assertthat_0.2.1  utf8_1.2.2       
[37] cachem_1.0.6

I guess the files are not available anymore, anyone found another repository for this two sqlite databases?

Thanks

SRAdb GEOmetadb • 230 views
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Hi, i am getting the same error using the GEOmetadb package.

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It seems the objects were disables, I am not sure if the maintainer had more news about this...

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