Hello everybody,

I'm quite new to both Linux and R but would like to use both for analysis of RNA-Seq data.

I desperately would like to install R package DESeq2 but always get a error message whatever the way i try to install it :

> source("http://bioconductor.org/biocLite.R")

Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
> biocLite("DESeq2")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘DESeq2’
also installing the dependencies ‘RCurl’, ‘annotate’, ‘genefilter’, ‘geneplotter’

trying URL 'https://cran.rstudio.com/src/contrib/RCurl_1.95-4.8.tar.gz'
Content type 'application/x-gzip' length 916934 bytes (895 KB)
==================================================
downloaded 895 KB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/annotate_1.52.1.tar.gz'
Content type 'application/x-gzip' length 1860820 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/genefilter_1.56.0.tar.gz'
Content type 'application/x-gzip' length 1407436 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/geneplotter_1.52.0.tar.gz'
Content type 'application/x-gzip' length 1426298 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/DESeq2_1.14.1.tar.gz'
Content type 'application/x-gzip' length 1406022 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/home/rwillamme/R/x86_64-pc-linux-gnu-library/3.3/RCurl’
ERROR: dependency ‘RCurl’ is not available for package ‘annotate’
* removing ‘/home/rwillamme/R/x86_64-pc-linux-gnu-library/3.3/annotate’
ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
* removing ‘/home/rwillamme/R/x86_64-pc-linux-gnu-library/3.3/genefilter’
ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’
* removing ‘/home/rwillamme/R/x86_64-pc-linux-gnu-library/3.3/geneplotter’
ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
* removing ‘/home/rwillamme/R/x86_64-pc-linux-gnu-library/3.3/DESeq2’

The downloaded source packages are in
    ‘/tmp/RtmpRxerxe/downloaded_packages’
installation path not writeable, unable to update packages: survival
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘RCurl’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘annotate’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘genefilter’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘geneplotter’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘DESeq2’ had non-zero exit status

I also tried to install the package via the package menu but I got this :

>  install.packages("DESeq2")

Installing package into ‘/home/rwillamme/R/x86_64-pc-linux-gnu-library/3.3’ (as ‘lib’ is unspecified)

Warning in install.packages :  package ‘DESeq2’ is not available (for R version 3.3.2)

Finally i downloaded the package archive file (.tar.gz) and tried once again but without success :

> install.packages("~/Downloads/DESeq2_1.14.1.tar.gz", repos = NULL, type = "source")
Installing package into ‘/home/rwillamme/R/x86_64-pc-linux-gnu-library/3.3’ (as ‘lib’ is unspecified)
ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
* removing ‘/home/rwillamme/R/x86_64-pc-linux-gnu-library/3.3/DESeq2’
Warning in install.packages :
  installation of package ‘/home/rwillamme/Downloads/DESeq2_1.14.1.tar.gz’ had non-zero exit status 

I tried to solve it myself by checking the already existing posts, and made 

$ sudo apt-get install libxml2-dev

And got this for an answer :

sudo: unable to resolve host gene-remi
[sudo] password for rwillamme: 
Reading package lists... Done
Building dependency tree       
Reading state information... Done
libxml2-dev is already the newest version (2.9.3+dfsg1-1ubuntu0.1).
The following packages were automatically installed and are no longer required:
  linux-headers-4.4.0-47 linux-headers-4.4.0-47-generic linux-headers-4.4.0-51
  linux-headers-4.4.0-51-generic linux-image-4.4.0-47-generic
  linux-image-4.4.0-51-generic linux-image-extra-4.4.0-47-generic
  linux-image-extra-4.4.0-51-generic
Use 'sudo apt autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

But it didn't help...

> sessionInfo()

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] BiocInstaller_1.24.0

loaded via a namespace (and not attached):
[1] tools_3.3.2

Any help would be sooo welcome!

Thanks already!

Solve the first problem -- RCurl -- first. You're on the right track with the system dependency; you'll also need, e.g.,

$ sudo apt-get install libcurl4-openssl-dev

and then

> biocLite("RCurl")