unable to access index for repository
3
0
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@88dc9bc0
Last seen 11 months ago
Norway

Hi, I`m trying to download the package Consensusclusterplus after R was updated to version 4.2 on my computer (Windows 10). But no I just get errors when computing the code for Biomanager 3.16.

 BiocManager::install("ConsensusClusterPlus")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.uib.no/

Warning: unable to access index for repository https://bioconductor.org/packages/3.16/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/workflows/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/workflows/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/books/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/books/src/contrib/PACKAGES'
Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31 ucrt)
Installing package(s) 'BiocVersion', 'ConsensusClusterPlus'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/workflows/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/workflows/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/books/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/books/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/annotation/bin/windows/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.16/data/annotation/bin/windows/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/experiment/bin/windows/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.16/data/experiment/bin/windows/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/workflows/bin/windows/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.16/workflows/bin/windows/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/books/bin/windows/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.16/books/bin/windows/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/workflows/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/workflows/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/books/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/books/src/contrib/PACKAGES'
Installation paths not writeable, unable to update packages
  path: C:/Program Files/R/R-4.2.2/library
  packages:
    Matrix, boot, foreign, nlme
Warning messages:
1: In file(con, "r") :
  URL 'https://bioconductor.org/config.yaml': status was 'SSL connect error'
2: packages ‘BiocVersion’, ‘ConsensusClusterPlus’ are not available for Bioconductor version '3.16'

Versions of these packages for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages

Please help me, were publishing a paper on these results and Im missing just a few details but cant run anything now...
Bioconductor ConsensusClusterPlus • 11k views
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were you connected to the internet? It looks like perhaps there might have been intermittent connection issues?

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Try setting the environment variable BIOCONDUCTOR_CONFIG_FILE="http://bioconductor.org/config.yaml" before loading the BiocManager package. I'm not sure about current practices for setting environment variables in R for Windows; it might be possible to Sys.setenv(BIOCONDUCTOR_CONFIG_FILE="http://bioconductor.org/config.yaml") but some alternative steps might be necessary.

Try also using a non-https mirror with chooseBiocMirror() then '(other mirrors)' then '0-Bioconductor'.

These are both work-arounds, really you would like to use https and thus figure out why readLines('https://bioconductor.org/config.yaml') generates a warning; there might be some hints on the help page ?download.file

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@88dc9bc0
Last seen 11 months ago
Norway

Yes, I was connected to the internet. Can it be that there are not available binaries? errormessage -->"packages ‘BiocVersion’, ‘ConsensusClusterPlus’ are not available as a binary package for Bioconductor version '3.16' is in the bottom...
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did you try again? if wget https://bioconductor.org/config.yaml is failing you have a connectivity problem.

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If you go to the website you can see that the binary does in fact exist.

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@88dc9bc0
Last seen 11 months ago
Norway

Ok thank you very much for the feedback! I tried both Sys.setenv(BIOCONDUCTOR_CONFIG_FILE="http://bioconductor.org/config.yaml"). Didn`t work.

And chooseBiocMirror(), got this error:

Warning message: In download.file(url, destfile = f, quiet = TRUE) : URL 'https://bioconductor.org/BioC_mirrors.csv': status was 'SSL connect error'

I`m connected to a workdesktop and the new Rstudio version had to be updated by people from internal security department. There might be any walls that preventing me from connecting to other webpages? I have internet connection, so nothing wrong with that. Can I possibly change anything in the Rprofile that might work? I will check with the security department, but usually there is not much help from them..

Kristin
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I didn't realize that chooseBiocMirror() would try to download something from the https address; try instead options(BioC_mirror = "http://bioconductor.org").

If there is a general firewall issue then pasting https://bioconductor.org/config.yaml will fail.

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To be really clear about this: try to open https://bioconductor.org/config.yaml in your browser (Chrome, Firefox, Microsoft Edge, etc...)

If that doesn't work, then there's a network access problem on your side.

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It worked!! Tried options(BioC_mirror = "http://bioconductor.org"). What a relief, have been working on this for over a week!! thank you so much!!

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0
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Glad you have it working. Can you report what happens when you try to access https://bioconductor.org/config.yaml in your web browser?

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It just opens a new window with a lot of text... wasn`t sure how to use it...

Kristin

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So long as the text looks something like

---
## Lines that must be updated when we release a new software version are 
## indicated in comments below

output_dir: output
staging_deploy_root: biocadmin@staging.bioconductor.org:/loc/www/bioconductor-test.fhcrc.org
production_deploy_root: webadmin@master.bioconductor.org:/extra/www/bioc

## CHANGE THIS WHEN WE RELEASE A VERSION:
release_version: "3.16"
r_version_associated_with_release: "4.2.0"
r_version_associated_with_devel: "4.2.0"
...

then your report is very helpful -- it says that the correct data is on the Bioconductor server, the data is being 'served' correctly, your institution doesn't block https access to bioconductor.org, and at least your browser is configured to navigate proxies or other obstacles that your local institution might be using to moderate web access.

So the problem is likely with your R configuration, rather than anywhere else. The problem is likely to be a 'proxy' setting. This is not something I know a lot about, but google points me to this Posit / RStudio support article as a place to start. I'd also be tempted to reach out to my support desk, with that article in hand; they will know about proxy details that are required to configure R correctly; they might also realize that whatever they are doing is likely to cause problems for all R users, so might modify policies.

It is worth while to figure this out, since you'll likely want to access other internet resources from within R, and you won't want to have to figure out workarounds each time.

I'd use as a 'test' case trying to download that config.yaml file within R -- when things are configured correctly, readLines("https://bioconductor.org/config.yaml") will return the same information you see in the web browser.

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Mehdi • 0
@mehdi-16509
Last seen 8 months ago
United States

I had the same problem. There was no right repository/mirror to download packages. options(BioC_mirror = "http://bioconductor.org" solved the problem for me too.
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