Version map cannot be validated - not mapping to new bioconductor website #183
Comments
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I am not sure what to say about your internet issue. I find the following succeeds, while browsing to the config.yaml does not. |
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@vjcitn If you browse in a web broswer it likely downloaded the config to your computer if you did not get an error. I also cannot produce this. If you run the code above that vince ran what do you get @aehrenberg ? |
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When I ran the code suggested by @vjcitn : I got the following: I thought to try the url to the new bioconductor website as follows and got the following: Again, it seems like there is an issue with referencing the old bioconductor website, no? |
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For what it's worth, BiocManager is using download.file() (to avoid a dependency on httr). So one would like to look at
```
download.file("https://bioconductor.org/config.yaml", fl <- tempfile())
```
and then validate the content of fl.
The vignette has a section 'Offline config.yaml' that would allow you to continue working while this issue gets resolved https://bioconductor.github.io/BiocManager/articles/BiocManager.html#offline-config-yaml.
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This is helpful info. I got the same result using the download.file function as before (didn't work with the regular url but did seem to work for the new url. I was able to get the config.yaml offline, but am getting hit with a ton of errors when I try to do basic things like install Deseq... |
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What specifically is the output with ? Solving this problem will, I bet, solve all your problems. It is not likely an issue with bioconductor.org per se. What is |
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When I put that in, I get the following error and the tempfile path, fl, maps to a file that doesn't exist: Session info is as follows: I tried running the following: on all download.file.method options ("internal", "libcurl", "wget", "curl" and "wininet") and got the same error each time: |
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Did you say that you were behind a firewall? If so, what specifically have you done to set up a proxy? If this is at an institution or company and you cannot browse to https://bioconductor.org, I would suggest contacting your local tech support with that request 'help me connect to...' If this were a general problem, then likely there would have been much more gnashing of teeth on the support site / mailing list / slack. |
Restart R. Enjoy! |
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Submitting the basic installation command for Bioconductor:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install(version = "3.18")in R (version 4.3.0) returns the following error:
Error: Bioconductor version cannot be validated; no internet connection? See #troubleshooting section in vignetteNone of the suggested solutions I've found online (adjusting the proxy/firewall settings, ensuring internet connection, etc) have helped.
The documentation suggests that the version map can be found at https://bioconductor.org/config.yaml which, as of today (11/13/2023), cannot be reached. There is a version map I can reach through the new bioconductor website at this link, though, https://new.bioconductor.org/config.yaml.
It seems like the version map cannot be validated because the bioconductor.org/config.yaml is a broken link, whereas the new.bioconductor.org/config.yaml would work. Can this be fixed?
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