Hi I am trying to install DESeq2 on Google Cloud Platform (Ubuntu 18.04.2 LTS; 4 CPUs; 15 GB RAM; sessionInfo() below) and get the following non-zero exit status. R appears to be installed correctly, it is started with sudo -i R, and I was able to install BiocManager (see below). Non-zero exits are also returned when installing XML, annotate, genefilter, or geneplotter individually.

I successfully install DESeq2 on macOS 10.14.4 (Mojave). Any suggestions?

Thank you Emilio

BiocManager Installed

BiocManager::valid() 
[1] TRUE

DESeq2 Install Command

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

DESeq2 Install Error (returned at the end)

ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
* removing ‘/usr/local/lib/R/site-library/DESeq2’
The downloaded source packages are in
        ‘/tmp/Rtmpurxecw/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘XML’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘annotate’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘genefilter’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘geneplotter’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘DESeq2’ had non-zero exit status

Session Information

> sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

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

other attached packages:
[1] BiocManager_1.30.4

loaded via a namespace (and not attached):
[1] compiler_3.5.3 tools_3.5.3

It's better if you give all of the R output rather than what you think might be useful. This error often comes up if you are missing the xml headers, so you probably have to install libxml2-devel. Often there is something like

checking for pkg-config... 
/usr/bin/pkg-config checking for xml2-config... no 
Cannot find xml2-config

during the attempt to install XML, which would be instructive, and indicates that you need to install libxml2-devel.