Hi all,
I cant seem to use GEOquery::getGEO(). I get Error in open.connection(x, "rb") : HTTP error 403 . everything worked before the weekend but it seems now it doesn't
example:
> getGEO("GSE5364")
Error in open.connection(x, "rb") : HTTP error 403.
This happens for every accession number.
When i garbage collect with gc() i get:
> Warning messages: 1: In .Internal(gc(verbose, reset, full)) :
> closing unused connection 6
> (https://ftp.ncbi.nlm.nih.gov/geo/series/GSE5nnn/GSE5364/matrix/)
When trying to access this URL, it doesn't seem to exist anymore. The parent directory does however: https://ftp.ncbi.nlm.nih.gov/. Albeit it doesnt seem to have a subfolder for GEO anymore?
Alternatively, ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE5nnn/GSE5364/ does exist.
Question 1: Is anyone else having this issue and has something happened to the GEO directory within NCBI?
Question 2: Can i change the URL that GEOquery uses to pull the data to ftp://ftp.ncbi.nlm.nih.gov.
I know i can download them and access them locally but i will be using a lot of series and so wanted to use getGEO's ability to pull this information with just accession numbers.
Thanks in advance!
> sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8.1 x64 (build 9600)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] GEOquery_2.50.5 Biobase_2.42.0 BiocGenerics_0.28.0
I believe this is an issue with GEO, not the GEOquery package. Changing the URL within GEOquery to ftp://ftp.ncbi.nlm.nih.gov yielded a different error:
Error in open.connection(x, "rb") : Server denied you to change to the given directoryI am currently unable to access any sites on ftp.ncbi.nlm.nih.gov/geo/series/ either via https or ftp.
Yes, to be clear, this is a problem at NCBI. There is nothing to be done with the GEOquery package to fix this.
I just came to post about this, too. It is causing some Bioconductor packages to fail to build.
Also reported on Biostars: https://www.biostars.org/p/377082/#377212
This is a problem at NCBI. I've reported the issue and it will hopefully be resolved soon.
The problem, at least for now, appears to be resolved.