News:PLEASE READ: devel packages in release channel
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 8 months ago
United States

Hi Bioconductors,

Due to a human error (mine) our release build machines were building and propagating devel packages for a short period today.

This has been corrected; however, if you installed/updated any Bioconductor packages in the last say 8 hours, and you were using the release version of Bioconductor (3.2) you should do the following steps to make sure you don't have any packages that are 'too new' for your release and may cause issues.

First, start R with the --vanilla flag so as to make sure no packages are loaded:

R --vanilla

Then inside R, remove the BiocInstaller package:

remove.packages("BiocInstaller")

Then reinstall the release version of Bioconductor:

source("https://bioconductor.org/biocLite.R")

(If this causes an error saying https:// is not supported, try again without the 's' in 'https").

Now run biocValid() to see if there are any packages that are too new:

biocValid()

If there are, this command will tell you and provide instructions for how to fix the issue.

It's important to fix this, because having packages that are 'too new' can prevent necessary updates from happening. But again, it's only necessary if you are using Bioconductor 3.2 and installed packages today.

I apologize for the problem. Please reply here if you have any questions.

Dan

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Would this explain why, for instance, the S4Vectors source download link isn't working for me currently, at least for the 0.8.0 version?

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The appropriate package versions are currently being copied back and will be available in a few minutes.

Dan

 

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Yes, that explains it. But please, only download if you have a good reason to not install with biocLite(). Using biocLite() should always be your first choice.

Thanks,

H.

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