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I am trying to install DESeq2 in my Ubuntu with R version 3.5.1. According to the package repository in Bioconductor the version should be 3.5.

> R.version

platform       x86_64-pc-linux-gnu         
arch           x86_64                      
os             linux-gnu                   
system         x86_64, linux-gnu           
status                                     
major          3                           
minor          5.1                         
year           2018                        
month          07                          
day            02                          
svn rev        74947                       
language       R                           
version.string R version 3.5.1 (2018-07-02)
nickname       Feather Spray

then I attempt to install DESeq2, following the instructions in Bioconductor:

> if (!requireNamespace("BiocManager", quietly = TRUE))
       install.packages("BiocManager")
   BiocManager::install("DESeq2", version = "3.8"

and at the end I get:

Warning messages:
1: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘RCurl’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘GenomeInfoDb’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘annotate’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘GenomicRanges’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘genefilter’ had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘geneplotter’ had non-zero exit status
7: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘SummarizedExperiment’ had non-zero exit status
8: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘DESeq2’ had non-zero exit status

I have visited $2*10^{9999}$ discussions on this issue and none of them helped me solving the problem. In addition, I didn't have any problem installing other packages like limma and edgeR, so I assume that this might be specific to DESeq2 or one of it's dependencies.

Thank you for the help!

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  • $\begingroup$ I used to have an issue where I had to run R-studio with sudo or my OS wouldn't allow me to install packages. $\endgroup$
    – Pallie
    Feb 11, 2019 at 9:36
  • $\begingroup$ @Pallie, thanks! I had similar issues with other packages but in this case I run rstudio with sudo and it didn't help. $\endgroup$
    – aerijman
    Feb 12, 2019 at 14:23

2 Answers 2

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First I installed this libraries:

sudo apt-get install libcurl4-openssl-dev libxml2-dev

I then installed RCurl: 

BiocManager::install("RCurl")

and lastly:

BiocManager::install("DESeq2", version = "3.8")
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Have you tried just typing,

install.packages("BiocManager")

Without all the proceeding if statement? If this doesn't install correctly nothing else will. Personally I would be tempted install each of the named libraries independently. If that works okay, e.g. its not a problem with the mirrors then I'd contact the developer michaelisaiahlove at gmail.com

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  • $\begingroup$ BiocManager is successfully installed. The problem is with DESeq2... $\endgroup$
    – aerijman
    Feb 11, 2019 at 1:36
  • 1
    $\begingroup$ Thanks it worked! I will post the answer for others with the same problem $\endgroup$
    – aerijman
    Feb 11, 2019 at 1:46
  • $\begingroup$ Cool, happy to hear! Systems admin is the bane of every bioinformatician. $\endgroup$
    – M__ ♦
    Feb 11, 2019 at 11:24
  • $\begingroup$ I noticed that some packages sometimes failed to compile depending on the version of gcc present on the system. So far, most of my problems were solved using a minimal R 3.5 installation, gcc 4.9 and trying to install everything using Bioconductor. $\endgroup$
    – bli
    Feb 25, 2019 at 16:07

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