title: Clustering by M3C package : Error in `[.data.frame`(df, neworder2) : undefined columns selected
body: <p>I had a similar problem to what posted <a href="https://stackoverflow.com/questions/60896731/r-m3c-library-duplicate-row-names-error-message">here</a>. To resolve the issue,  followed the answer by @Jack Gisby there. Now a new error showed up:</p>
  <p>Working on TCGA data , I am getting the same error (first error):</p>
  <pre><code>Error in `.rowNamesDF&lt;-`(x, value = value) : 
    duplicate 'row.names' are not allowed
  </code></pre>
  <p>running <code>duplicated()</code> on each relevant field returned <code>FALSE</code>.</p>
  <p>Her is the second error (just after trimming identifiers to not start with a common string like &quot;TCGA-&quot;):</p>
  <pre><code>Error in `[.data.frame`(df, neworder2) : undefined columns selected
  &gt; traceback()
  5: stop(&quot;undefined columns selected&quot;)
  4: `[.data.frame`(df, neworder2)
  3: df[neworder2]
  2: M3Creal(as.matrix(mydata), maxK = maxK, reps = repsreal, pItem = pItem, 
         pFeature = 1, clusterAlg = clusteralg, distance = distance, 
         title = &quot;/home/christopher/Desktop/&quot;, des = des, lthick = lthick, 
         dotsize = dotsize, x1 = pacx1, x2 = pacx2, seed = seed, removeplots = removeplots, 
         silent = silent, fsize = fsize, method = method, objective = objective)
  1: M3C(pro.vst, des = clin, removeplots = FALSE, iters = 25, objective = &quot;PAC&quot;, 
         fsize = 8, lthick = 1, dotsize = 1.25)
  </code></pre>
  <p>I've added to an opened issue on the M3C GitHub.</p>