Error message

source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help
> biocLite("Rsubread")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
Installing package(s) ‘Rsubread’
Package which is only available in source form, and may need compilation of
  C/C++/Fortran: ‘Rsubread’
  These will not be installed
Old packages: 'foreign', 'lattice', 'Matrix', 'mgcv', 'survival'
Update all/some/none? [a/s/n]: 
a

Warning in install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  'lib = "C:/Program Files/R/R-3.3.1/library"' is not writable

Hi,

Looks like you are working in windows OS. Check if you have read/write permission for the directory C:/Program Files/R/R-3.3.1/library.

To set read/write permission:

1. Right-click the folder (C:/Program Files/R/R-3.3.1/library) , click Properties, and then click the Security tab.

2. Click Edit to open the Permissions for <Object> dialog box.

3. To allow  a permission, in the Permissions for <User or Group> box, select the Allow check box.

Let me know if this helps.