GEOquery: HTTP error 403
1
1
Entering edit mode
andy_shaps ▴ 10
@andy_shaps-20648
Last seen 2.2 years ago

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
GEOquery GEO HTTP error 403 • 1.0k views
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1
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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 directory

I am currently unable to access any sites on ftp.ncbi.nlm.nih.gov/geo/series/ either via https or ftp.

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1
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Yes, to be clear, this is a problem at NCBI. There is nothing to be done with the GEOquery package to fix this.

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0
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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

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This is a problem at NCBI. I've reported the issue and it will hopefully be resolved soon.

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The problem, at least for now, appears to be resolved.

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andy_shaps ▴ 10
@andy_shaps-20648
Last seen 2.2 years ago

This seems to be fixed now. Thank you all for your comments and for reporting the issue.

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