Hi, I'm having some troubles when installing DESeq2 both in Ubuntu 14.04 LTS and also in Linux Mint 18.1. In both cases, when running biocLite and also package installation from source DESeq2 shows an error (non-zero exit status).

Please, can you help to me?

Warning messages:

1: In install.packages(pkgs = doing, lib = lib, ...) :

  installation of package ‘DESeq2’ had non-zero exit status

2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :

  installation of package ‘cairoDevice’ had non-zero exit status

3: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :

  installation of package ‘littler’ had non-zero exit status

4: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :

  installation of package ‘RcppArmadillo’ had non-zero exit status

5: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :

  installation of package ‘rgl’ had non-zero exit status

6: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :

  installation of package ‘tkrplot’ had non-zero exit status

7: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :

  installation of package ‘mgcv’ had non-zero exit status

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0

locale:
 [1] LC_CTYPE=es_ES.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=es_ES.UTF-8     LC_MONETARY=en_GB.UTF-8   
 [6] LC_MESSAGES=es_ES.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.26.1

loaded via a namespace (and not attached):
[1] compiler_3.4.1 tools_3.4.1  

I don't think this is an issue with DESeq2 per se, but more likely that some of those packages you are unable to install are missing system libraries, and when those packages fail installation DESeq2 fails too.  

My advice would be too try installing each of the failing packages seperately, and look closely at the error message that gets printed out.  This often tells you the missing system library, but it is likely buried in a wall of text.  You can then search for the appropriate library in the Ubuntu package manager, and install the developmental version using that.  Then try installing the R package again to check it worked.

For example, if I try to install tkrplot it throws an error:

BiocInstaller::biocLite("tkrplot")

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.6 (BiocInstaller 1.27.4), R 3.4.1 (2017-06-30).
Installing package(s) ‘tkrplot’
trying URL 'https://cran.rstudio.com/src/contrib/tkrplot_0.0-23.tar.gz'
Content type 'application/x-gzip' length 39037 bytes (38 KB)
==================================================
downloaded 38 KB

* installing *source* package ‘tkrplot’ ...
** package ‘tkrplot’ successfully unpacked and MD5 sums checked  

...

checking for tcl.h... no
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I/home/msmith/Applications/R/R-3.4.1/include -DNDEBUG   -I/usr/local/include   -fpic  -mtune=native -O2  -c tcltkimg.c -o tcltkimg.o
tcltkimg.c:2:16: fatal error: tk.h: No such file or directory
compilation terminated.
/home/msmith/Applications/R/R-3.4.1/etc/Makeconf:159: recipe for target 'tcltkimg.o' failed
make: *** [tcltkimg.o] Error 1
ERROR: compilation failed for package ‘tkrplot’
* removing ‘/home/msmith/Applications/R/R-3.4.1/library/tkrplot’
The downloaded source packages are in
    ‘/tmp/RtmpCVDuVR/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘tkrplot’ had non-zero exit status

For me the important parts are highlighted in yellow, and let me know we're missing things to do with the tcltk library.  I happen to know what package needs to be installed to fix this and would run:

sudo apt-get install tk-dev tcl-dev

but you might also just search for 'tk dev' in the Ubuntu package manager.