Question

installing bioconductor packages with DNS problem

1

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PabloR ▴ 10

@pablor-12233

Last seen 4.4 years ago

Hi,

I'm having DNS problems in my server (where Rstudio is installed). For instance, if I ping bioconductor.org I get a fail response, but if I ping its IP, 13.227.106.21, I have a return.

Is there a way to install a Bioconductor package by adding the direct IP of bioconductor.org (or some mirror) to try to avoid the DNA failures I'm experiencing (and hope to solve soon), in order to temporarily circumvent this issue?

I tried setRepositories(addURLs = c(IPbioconductor = "13.227.106.21")) as well as BiocManager::install("GEOquery", site_repository = "13.227.106.21") but none worked.

bioconductor biocmanager installing packages dns • 3.6k views

ADD COMMENT • link updated 4.4 years ago by Martin Morgan 25k • written 4.4 years ago by PabloR ▴ 10

Martin Morgan · Answer 1 · 2020-08-03

0

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Martin Morgan 25k

@martin-morgan-1513

Last seen 5 months ago

United States

You can set the option BioC_mirror

> options(BioC_mirror = "https://13.227.106.21")
> BiocManager::repositories()
                                     BioCsoft
           "https://13.227.106.21/packages/3.12/bioc"
                                      BioCann
"https://13.227.106.21/packages/3.12/data/annotation"
                                      BioCexp
"https://13.227.106.21/packages/3.12/data/experiment"
                                BioCworkflows
      "https://13.227.106.21/packages/3.12/workflows"
                                         CRAN
                   "https://cran.rstudio.com"

Note that we use Amazon Cloudfront, and the IP address you identify is likely geo-local and perhaps not even permanent. A better choice would be https://master.bioconductor.org 52.71.54.154, but an even better choice (e.g., because package installations will always occur from North America) would be to engage your system administrator to investigate why bioconductor.org does not resolve; a problem might be that your institute has blacklisted the address, perhaps because other domains directed to the same CloudFront edge node have mis-behaved. The solution is then to convince your administrator to white-list bioconductor.org.

It would also be helpful if you could add a comment indicating where you are trying to connect from, and if you do speak with your system administrator what the problem / solution was.

ADD COMMENT • link 4.4 years ago Martin Morgan 25k

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Thank you Martin. I tried using the options parameter you passed, but once I try to BiocManager::repositories() I get Error: Bioconductor version cannot be validated; no internet connection? In addition: Warning messages: 1: In file(con, "r") : URL 'https://bioconductor.org/config.yaml': status was 'Couldn't resolve host name' 2: In file(con, "r") : URL 'http://bioconductor.org/config.yaml': status was 'Couldn't resolve host name'

ADD REPLY • link 4.4 years ago PabloR ▴ 10

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Also create this option

options(
    BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS = FALSE
)

There are additional notes in the vignette https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html in the 'Offline use' section.

But the underlying problem should be investigated...

ADD REPLY • link 4.4 years ago Martin Morgan 25k

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I completely agree. But there is overall DNS failure in our institution (not bioconductor-specific) due to a firewall mess. I just wanted to get things done without having to wait for sysadmins to resolve the issue. I've followed the Offline use section of the vignette to no avail:

> options(
  repos = "https://52.71.54.154",
  BioC_mirror = "https://52.71.54.154"
)
options(
  BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS = FALSE
)
install.packages(c("BiocManager", "BiocVersion"))
BiocManager::repositories()

still gives me

>Error: Bioconductor version cannot be validated; no internet connection?
In addition: Warning message:
Bioconductor online version validation disabled; see
  ?BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS 

>

ADD REPLY • link updated 4.4 years ago by Martin Morgan 25k • written 4.4 years ago by PabloR ▴ 10

0

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What does traceback() say after the error?

ADD REPLY • link 4.4 years ago Martin Morgan 25k

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``
> BiocManager::repositories()
Error: Bioconductor version cannot be validated; no internet connection?
In addition: Warning message:
Bioconductor online version validation disabled; see
  ?BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS 
> traceback()
4: stop(.msg(...), call. = call.)
3: .stop(txt)
2: .version_validate(version)
1: BiocManager::repositories()
``

ADD REPLY • link updated 4.4 years ago by Martin Morgan 25k • written 4.4 years ago by PabloR ▴ 10