How to permanently add custom repositories to BiocLite
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arnau.bria • 0
@arnaubria-14041
Last seen 3.8 years ago

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

bioclite repository repos • 897 views
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JackieMe • 0
@jackieme-14035
Last seen 2.1 years ago

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.

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arnau.bria • 0
@arnaubria-14041
Last seen 3.8 years ago

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

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