title: installing dada2 into a version of R that was installed through condas
body: <p>I have an environment with R installed through condas (I currently use R with jupyter notebook, so this made sense at one point). I would like to use dada2 with this version of R.</p>
  
  <p>As per this site <a href="https://anaconda.org/bioconda/bioconductor-dada2" rel="nofollow noreferrer">https://anaconda.org/bioconda/bioconductor-dada2</a> the correct command to make this happen is</p>
  
  <pre><code> conda install -c bioconda bioconductor-dada2 
  </code></pre>
  
  <p>which gives me the following error</p>
  
  <p>Fetching package metadata .............
  Solving package specifications: .</p>
  
  <blockquote>
    <p>UnsatisfiableError: The following specifications were found to be in
    conflict:
      - bioconductor-dada2 -> bioconductor-biostrings >=2.32.1 -> bioconductor-biocgenerics >=0.15.6 -> r 3.3.1* -> r-base 3.3.1
      - r-glue Use "conda info " to see the dependencies for each package.</p>
  </blockquote>
  
  <p>If I run <code>conda info package r-glue</code> I can see that it depends on r-base 3.4.1.</p>
  
  <p><em>Alternative approach that also doesn't work:</em></p>
  
  <p>I also tried going into R and installing from there, but I can't get any packages to install with R packages</p>
  
  <pre><code> source("https://bioconductor.org/biocLite.R")
   biocLite("dada2")
  </code></pre>
  
  <p>Gives me a really long output, but the short of it is that a bunch of the dependencies return errors </p>
  
  <blockquote>
    <p>ERROR: compilation failed for package ‘RcppParallel’
    * removing ‘/home/jacob/anaconda3/lib/R/library/RcppParallel’ ERROR: dependency ‘S4Vectors’ is not available for package ‘IRanges’
    * removing ‘/home/jacob/anaconda3/lib/R/library/IRanges’ ERROR: dependencies ‘S4Vectors’, ‘IRanges’, ‘matrixStats’ are not available
    for package ‘DelayedArray’</p>
  </blockquote>
  
  <p>and then more stuff and at the end</p>
  
  <p>ERROR: dependencies ‘Biostrings’, ‘ShortRead’, ‘RcppParallel’ are not available for package ‘dada2’
  * removing ‘/home/jacob/anaconda3/lib/R/library/dada2’</p>
  
  <blockquote>
    <p>The downloaded source packages are in
      ‘/tmp/Rtmptx8OqE/downloaded_packages’ Updating HTML index of packages
    in '.Library' Making 'packages.html' ... done Old packages: 'curl',
    'dplyr', 'foreign', 'haven', 'httpuv', 'mgcv', 'purrr',   'Rcpp',
    'TTR', 'xts' Update all/some/none? [a/s/n]:</p>
  </blockquote>
  
  <p>and then all of the updates fail too.</p>
  
  <p>Is the correct answer to not try to use dada2 with condas in R and rather just use a condas independent version of R, or is there some way that I am missing?</p>
  
  <p>I am running R version 3.4.1 on ubuntu linux 16.04 and conda 3.2.23 for what that is worth.</p>