Error in import data directly from GEO（rnb.read.geo）

[mumdark]

Hello, I want to report that when I'm running example analysis, I'm getting the following error:

I use this code to import data directly from GEO. Example dataset: Nazor, et al. (2012). Cell Stem Cell, 10(5), 620–634

rnbs.geo <- rnb.execute.import(data.source="GSE31848", data.type="infinium.GEO")

Error in rnb.read.geo(data.source) : Could not download GEO Data Series, error code -99 In addition: Warning messages: 1: 'memory.size()' is no longer supported 2: 'memory.size()' is no longer supported 3: 'memory.size()' is no longer supported 4: In download.file(gse.url, fname, quiet = FALSE, mode = "wb") : URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE31nnn/GSE31848/matrix/GSE31848_series_matrix.txt.gz': status was 'Failure when receiving data from the peer' 5: In file.remove(fname) : cannot remove file 'C:\Users\30768\AppData\Local\Temp\Rtmpw9mEeU\gse4f9c730d413c.txt.gz', reason 'No such file or directory'

Thank you for your help!

[schmic05]

Hi! Unfortunately, I cannot reproduce and thus fix the issue that you are facing. I assume that this might be related to your configuration of R/RnBeads. Do you have a proper internet connection within R and can you download some file (using download.file())? Otherwise, it might also be that you don't have enough disk space or that R is not allowed to download and save a file. Hope you can figure it out!

[mumdark]

Hi! Unfortunately, I cannot reproduce and thus fix the issue that you are facing. I assume that this might be related to your configuration of R/RnBeads. Do you have a proper internet connection within R and can you download some file (using download.file())? Otherwise, it might also be that you don't have enough disk space or that R is not allowed to download and save a file. Hope you can figure it out!

Thanks for your reply！ On my computer, the following code does not work:

 download.file(
"ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE14nnn/GSE145745/matrix/GSE145745_series_matrix.txt.gz", 
tempfile("gse", tempdir(), ".txt. gz"), 
quiet = FALSE, 
mode = "wb")

It's not a big problem, I'll download it in geo database😁