title: installation path not writable R, unable to update packages
body: <p>I am trying to install Bioconductor into R, using the code on their website. When I type in the code (see bellow) I get an error message saying that some packages can't be updated, the installation path is unwriteable.</p>
  
  <pre><code>&gt; ## try http:// if https:// URLs are not supported
  &gt; source("https://bioconductor.org/biocLite.R")
  Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
  &gt; biocLite()
  BioC_mirror: https://bioconductor.org
  Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
  installation path not writeable, unable to update packages: Matrix, mgcv,
  </code></pre>
  
  <p>survival</p>
  
  <p>I can install these package by going to packages/install packages.</p>
  
  <pre><code>&gt; utils:::menuInstallPkgs()
  trying URL    'https://www.stats.bris.ac.uk/R/bin/windows/contrib/3.3/Matrix_1.2-8.zip'
  Content type 'application/zip' length 2775038 bytes (2.6 MB)
  downloaded 2.6 MB
  
  trying URL 'https://www.stats.bris.ac.uk/R/bin/windows/contrib/3.3/mgcv_1.8-  16.zip'
  Content type 'application/zip' length 2346257 bytes (2.2 MB)
  downloaded 2.2 MB
  
  trying URL     'https://www.stats.bris.ac.uk/R/bin/windows/contrib/3.3/survival_2.40-1.zip'
  Content type 'application/zip' length 5109948 bytes (4.9 MB)
  downloaded 4.9 MB
  
  package ‘Matrix’ successfully unpacked and MD5 sums checked
  package ‘mgcv’ successfully unpacked and MD5 sums checked
  package ‘survival’ successfully unpacked and MD5 sums checked
  
  The downloaded binary packages are in
      C:\Users\stxeb8\AppData\Local\Temp\Rtmp2tQZ4v\downloaded_packages
  </code></pre>
  
  <p>I can then go to packages/ load packages and load them succesfully and search and see that the packages are there.</p>
  
  <pre><code>&gt; local({pkg &lt;- select.list(sort(.packages(all.available =   TRUE)),graphics=TRUE)
  + if(nchar(pkg)) library(pkg, character.only=TRUE)})
  Loading required package: nlme
  This is mgcv 1.8-16. For overview type 'help("mgcv-package")'.
  &gt; local({pkg &lt;- select.list(sort(.packages(all.available = TRUE)),graphics=TRUE)
  + if(nchar(pkg)) library(pkg, character.only=TRUE)})
  &gt; local({pkg &lt;- select.list(sort(.packages(all.available = TRUE)),graphics=TRUE)
  + if(nchar(pkg)) library(pkg, character.only=TRUE)})
  &gt; local({pkg &lt;- select.list(sort(.packages(all.available =     TRUE)),graphics=TRUE)
  + if(nchar(pkg)) library(pkg, character.only=TRUE)})
  &gt; search()
  [1] ".GlobalEnv"            "package:survival"      "package:mgcv"         
  [4] "package:nlme"          "package:Matrix"        "package:BiocInstaller"
  [7] "package:stats"         "package:graphics"      "package:grDevices"    
  [10] "package:utils"         "package:datasets"      "package:methods"      
  [13] "Autoloads"             "package:base"         
  </code></pre>
  
  <p>But then when I go to install bioconductor it gives me the same error message that Matrix, mgcv and survival aren't able to be updated.</p>
  
  <pre><code>&gt; ## try http:// if https:// URLs are not supported
  &gt; source("https://bioconductor.org/biocLite.R")
  Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
  &gt; biocLite()
  BioC_mirror: https://bioconductor.org
  Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
  installation path not writeable, unable to update packages: Matrix, mgcv,
    survival
  </code></pre>
  
  <p>What can I do to be able to update these packages so I can install bioconductor?</p>