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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
Hi, i am getting the same error using the GEOmetadb package.
It seems the objects were disables, I am not sure if the maintainer had more news about this...