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Today I've discovered that there is another repository except CPAN. This repository is Bioconductor. So far I've noticed that Bioconductor's installation process is slightly different compared to classic CRAN's install.packages(). Should I worry when I want to use some packages from Bioconductor? Is it possible to get into some dependencies problems (as when you are mixing e.g. ubuntu/debian repositories etc.) etc.? I'm asking because e.g. this says:

If you dont mind using bioconductor packages, then, You can use...

What is wrong with Bioconductor or potentially another repositories?

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Wakan Tanka
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    please clarify why I get downwote, thanks – Wakan Tanka Apr 24 '16 at 21:47
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    good question but off-topic IMO. bioc or any public repo will share the same advantages and disadvantages as cran. I would judge the packages/authors themselves as there is a lot of garbage on cran as well as bioc. I think you have misinterpreted arun's comment as "bioconductor is a risky repo, use at own risk" which I do not think he was implying – rawr Apr 24 '16 at 22:06
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    In the linked question, I specifically asked for base, recommend, or CRAN-available modules for the solution. That's why Arun included that comment. Why I needed to restrict the source of any code is not important here. If you can use Bioconductor packages, go for it. – Matthew Lundberg Apr 24 '16 at 22:22
  • @MatthewLundberg now I did and and I've end up with error `Failed with error: ‘package ‘Rlibstree’ was built before R 3.0.0: please re-install it’ ` any ideas? – Wakan Tanka Apr 24 '16 at 22:24
  • @WakanTanka https://github.com/omegahat/Rlibstree – rawr Apr 24 '16 at 22:46
  • @rawr yes I've checked it but last commit was 4 years ago so it looks like same version as in Bioconductor. – Wakan Tanka Apr 24 '16 at 22:55
  • I'm saying that you can use those instructions to install it from source – rawr Apr 24 '16 at 22:58
  • @WakanTanka if you're having problems installing a Bioconductor package, ask on the [Bioconductor support site](https://support.bioconductor.org). – Martin Morgan Apr 25 '16 at 09:15

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BioConductor is very well structured, tested and operating. There is nothing wrong with it. Please just read up on it yourself.

And please do understand there is practically no limit to the number of different repositories you can use. 'Base R' already knows about CRAN, BioConductor and OmegaHat (though I am unsure how active it currently is, it too has a proud 15 year history).

Lastly, you easily build / host / use your own repositories using drat.

Dirk Eddelbuettel
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