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I'm trying to install Bioconductor packages with Microsoft R Open 3.5.0 seems to fail not sure what is the issue.

This is what I'm trying to do 

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

But I keep getting an error about "curl" had non-zero exit. How can I install the packages of Bioconductor?

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    $\begingroup$ Please edit your question and clarify. Your first paragraph seems to be about installing R but the last one suggests you have already installed it. Please don't ask multiple questions in a single post, edit and ask one, specific and clear question. Thanks! $\endgroup$
    – terdon ♦
    Sep 11, 2018 at 12:01
  • $\begingroup$ updated my question ..iim getting this "curl' non-zero exit which wanted to post the error but closed my terminal so lost the exact error message $\endgroup$
    – kcm
    Sep 11, 2018 at 13:02
  • $\begingroup$ Then please run the command again and then add the error message to the your question. We can't help you solve an error if you don't show it. $\endgroup$
    – terdon ♦
    Sep 11, 2018 at 13:56

1 Answer 1

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I can't comment yet but from what you said it seems that you need to install additional libraries like the one you mentioned: "curl".

from the R terminal you should type:

install.packages("curl")

then R will install the package. Not sure if there are some other dependencies. If yes R will return you some error message in which there are some package names you need to install.

EDIT:

of course, after installing all the required packages you should be able to install biocLite too.

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  • $\begingroup$ cd /opt/microsoft/ropen/3.5.1/lib64/R/library/ inside the path i can see the curl so why still i get the error i'm not sure $\endgroup$
    – kcm
    Sep 11, 2018 at 13:18
  • $\begingroup$ try loading the curl package from the R terminal and see if it actually works (library(curl)). Maybe some libraries are missing. I use linux and curl requires additional libraries that are not installed by R but are system's libraries. $\endgroup$
    – gabt
    Sep 11, 2018 at 13:24
  • $\begingroup$ yeah i did check the system level libraries as i can see using this "locate libcurl "so still not sure why the non-zero exit $\endgroup$
    – kcm
    Sep 11, 2018 at 13:32
  • $\begingroup$ finally after some time it did work. $\endgroup$
    – kcm
    Sep 12, 2018 at 7:16
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    $\begingroup$ sorry for not replying! if you solved the issue just post how you did it. This will help other people having the same problems! $\endgroup$
    – gabt
    Sep 12, 2018 at 8:16

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