getSRAdbFile() does not work
0
0
Entering edit mode
jfertaj ▴ 30
@jfertaj-8566
Last seen 2.2 years 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 • 1.2k views
ADD COMMENT
0
Entering edit mode

Hi, i am getting the same error using the GEOmetadb package.

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 940 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6