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Question: How to permanently add custom repositories to BiocLite
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gravatar for arnau.bria
7 weeks ago by
arnau.bria0
arnau.bria0 wrote:

Dear all,

I have a local repository that I'd like to permanently add to the list of repositories that biocLite uses when looking for packages.

I've seen that biocLite has the option "siteRepos" but it does not make the configuration permanent.

Is there any way to add a custom repository in the default list of repositories?

(I've tried to add in the "repositories" file but it did not work )

 

TIA

ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by arnau.bria0
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gravatar for JackieMe
7 weeks ago by
JackieMe0
JackieMe0 wrote:

Do you mean a local repo on your own computer? That I don't know, maybe this thread is helpful. In case you mean another Bioconductor website, put the something like following line in your <font face="monospace">~/.Rprofile :</font>
 

options(BioC_mirror="https://mirrors.tuna.tsinghua.edu.cn/bioconductor")

 

This sets the Bioconductor repo to the website after Bioc_mirror.

ADD COMMENTlink written 7 weeks ago by JackieMe0
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gravatar for arnau.bria
7 weeks ago by
arnau.bria0
arnau.bria0 wrote:

Hi,

first of all, thanks for your answer.

I already have the repository ready. But what I want is biocLite to look into it for packages. IOW, when you run biocinstallRepos() I want it to know that it has to look into my repo aswell.

> biocinstallRepos();
                                               BioCsoft
           "https://bioconductor.org/packages/3.5/bioc"
                                                BioCann
"https://bioconductor.org/packages/3.5/data/annotation"
                                                BioCexp
"https://bioconductor.org/packages/3.5/data/experiment"
                                              BioCextra
          "https://bioconductor.org/packages/3.5/extra"
                                                   MyRepo
                             "https://myURL.bogus.com"

 

I can do that if I call biocLite with siteRepos, but it is a temporary switch and I want it to be permanent.

Best, Arnau

ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by arnau.bria0
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