Question

Internet connection for Bioconductor packages in Rstudio in Iran...

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needNGS • 0

@b518f35f

Last seen 8 months ago

United States

Hello all!

I have internet problem running the Bioconductor packages like GEOquery or getGEO command in Rstudio inside IRAN...(Iranian ip)

There is no connection problem as other packages get installed flawlessly..

If anyone has a solution or a working proxy it would be appreciated...

Some examples of problem:

> if (!require("BiocManager", quietly = TRUE))
+     install.packages("BiocManager")
Bioconductor version cannot be validated; no internet
  connection?  See #troubleshooting section in vignette
Warning messages:
1: In file(con, "r") :
  URL 'https://bioconductor.org/config.yaml': status was 'SSL connect error'
2: In file(con, "r") :
  cannot open URL 'http://bioconductor.org/config.yaml': HTTP status was '503 Service Unavailable'
> BiocManager::install(version = "3.18")
Error: Bioconductor version cannot be validated; no internet
  connection?  See #troubleshooting section in vignette


> getGEO("GSExxxxx")
Error in open.connection(x, "rb") : 
  cannot open the connection to 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSExxxxx/matrix/'
>

No_internet_connection_Packages Proxy Bioconductor GEOquery Internet_connection_problem • 1.2k views

ADD COMMENT • link 8 months ago needNGS • 0

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How long ago did you try this? We were updating some configurations that might have caused the temporary issue with validating Bioconductor. It should be resolved now if you try again. As far as the getGEO query error, you would have to replace GSExxxx with a valid query argument.

ADD REPLY • link 8 months ago shepherl 4.1k

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Hi!

Sure I used a valid GSE number, that xxxxx was just for showing that pattern...

For example I just now tried it:

getGEO("GSE232205") Error in open.connection(x, "rb") : cannot open the connection to 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE232nnn/GSE232205/matrix/'

ADD REPLY • link 8 months ago needNGS • 0

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It will likely be very difficult for anybody outside Iran to help you diagnose this issue, as it may be some sort of blocking that we won't encounter. For example

> z <- getGEO("GSE232205")
Found 1 file(s)
GSE232205_series_matrix.txt.gz
> z[[1]]
ExpressionSet (storageMode: lockedEnvironment)
assayData: 768 features, 24 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: GSM7319660
    GSM7319662 ... GSM7319689
    (24 total)
  varLabels: title geo_accession
    ... tissue:ch1 (40 total)
  varMetadata: labelDescription
featureData
  featureNames: NM_001001152.2
    NM_001001303.1 ...
    XM_897036.2 (768 total)
  fvarLabels: ID GB_ACC
  fvarMetadata: Column
    Description labelDescription
experimentData: use 'experimentData(object)'
  pubMedIds: 38500536 
Annotation: GPL30588

There is no apparent issue for me to access that FTP site from within the US. The fact that you cannot open the connection appears to be connection issue, rather than an issue with the GEOquery package.

ADD REPLY • link 8 months ago James W. MacDonald 67k

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Thanks

Sure it is a connection problem...

My speculation is that some ports are blocked...since some other packages could be installed....

ADD REPLY • link 8 months ago needNGS • 0

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And your speculation is probably correct. For someone living in Iran. But not for somebody living in the US.

ADD REPLY • link 8 months ago James W. MacDonald 67k

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Deadend of inter(a)net!

ADD REPLY • link 8 months ago needNGS • 0

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Will this script work?

Sys.setenv(http_proxy = "http://proxy.yourorganization.com:port") Sys.setenv(https_proxy = "https://proxy.yourorganization.com:port")

Do you know any working proxy?

ADD REPLY • link 8 months ago needNGS • 0