<p>First I installed this libraries:</p>

<pre><code>sudo apt-get install libcurl4-openssl-dev libxml2-dev
</code></pre>

<p>I then installed RCurl: </p>

<pre><code>BiocManager::install("RCurl")
</code></pre>

<p>and lastly:</p>

<pre><code>BiocManager::install("DESeq2", version = "3.8")
</code></pre>

CC BY-SA 4.0
2019-02-11T01:47:18.953Z
2019-02-11T01:47:18.953Z
aerijman
<p>Have you tried just typing,</p>

<pre><code>install.packages("BiocManager")
</code></pre>

<p>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</p>

CC BY-SA 4.0
2019-02-11T01:36:30.993Z
BiocManager is successfully installed. The problem is with DESeq2...
aerijman
CC BY-SA 4.0
2019-02-11T01:46:56.523Z
Thanks it worked! I will post the answer for others with the same problem
aerijman
CC BY-SA 4.0
2019-02-11T11:24:09.487Z
Cool, happy to hear! Systems admin is the bane of every bioinformatician.
M__
CC BY-SA 4.0
2019-02-25T16:07:25.063Z
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.
bli
CC BY-SA 4.0
2019-02-10T23:11:40.113Z
2019-02-10T23:11:40.113Z
M__
<p>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.</p>

<pre><code>&gt; 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
</code></pre>

<p>then I attempt to install DESeq2, following the instructions in Bioconductor:</p>

<pre><code>&gt; if (!requireNamespace("BiocManager", quietly = TRUE))
       install.packages("BiocManager")
   BiocManager::install("DESeq2", version = "3.8"
</code></pre>

<p>and at the end I get:</p>

<pre><code>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
</code></pre>

<p>I have visited <span class="math-container">$2*10^{9999}$</span> 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.</p>

<p>Thank you for the help!</p>

<deseq2><software-installation><linux>
Installing DESeq2 in Ubuntu
# Installing DESeq2 in Ubuntu

(Asked by: username_0 on 2019-02-10)

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!

**Tags:** deseq2, software-installation, linux

---

## 2 answers

### Answer by username_0 on 2019-02-11. Score: 4

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")


---

### Answer by username_1 on 2019-02-10. Score: 1

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

> **Comments:**
> **username_0**: BiocManager is successfully installed. The problem is with DESeq2...  
> **username_0**: Thanks it worked! I will post the answer for others with the same problem  
> **username_1**: Cool, happy to hear! Systems admin is the bane of every bioinformatician.  
> **username_2**: 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.  

---

