title: R session aborts when using vcf2geno code
body: <p>I'm beyond frustrated trying to get this code to run again. This code worked before and I submitted the assignment in full, but I am trying to use it for my project and now running this code causes R to abort the session. </p>
  
  <p>The code is as follow:</p>
  
  <pre><code>library(LEA)
  setwd("/Users/Changirwa/Desktop/COURSES/BIOL 468")
  
  vcf2geno(input.file = "data/pika_subset.vcf", output.file = "data/pika_subset.geno")
  
  geno2lfmm(input.file = "data/pika_subset.geno", output.file = "data/pika_subset.lfmm")
  </code></pre>
  
  <p>I attempted to knit the file to see what it would say and this is what it said:</p>
  
  <p><strong>* caught segfault *</strong></p>
  
  <p>address 0x0, cause 'memory not mapped'</p>
  
  <pre><code>Traceback:
  
  1: vcf2geno(input.file = "data/pika_subset.vcf", output.file = "data/pika_subset.geno")
  
  2: eval(expr, envir, enclos)
  
  3: eval(expr, envir, enclos)
  
  4: withVisible(eval(expr, envir, enclos))
  
  5: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,     error = eHandler, message = mHandler)
  
  6: handle(ev &lt;- withCallingHandlers(withVisible(eval(expr, envir,     enclos)), warning = wHandler, error = eHandler, message = mHandler))
  
  7: timing_fn(handle(ev &lt;- withCallingHandlers(withVisible(eval(expr,     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
  
  8: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,     debug = debug, last = i == length(out), use_try = stop_on_error !=         2L, keep_warning = keep_warning, keep_message = keep_message,     output_handler = output_handler, include_timing = include_timing)
  
  9: evaluate::evaluate(...)
  
  10: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),     keep_message = !isFALSE(options$message), stop_on_error = if (options$error &amp;&amp;        options$include) 0L else 2L, output_handler = knit_handlers(options$render,         options))
  
  11: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,     keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),     stop_on_error = if (options$error &amp;&amp; options$include) 0L else 2L,     output_handler = knit_handlers(options$render, options)))
  
  12: block_exec(params)
  
  13: call_block(x)
  
  14: process_group.block(group)
  
  15: process_group(group)
  
  16: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        setwd(wd)       cat(res, sep = "\n", file = output %n% "")        message("Quitting from lines ", paste(current_lines(i),             collapse = "-"), " (", knit_concord$get("infile"),             ") ")    })
  
  17: process_file(text, output)
  
  18: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
  
  19: rmarkdown::render("/Users/changirwa/Downloads/rlab3.Rmd", encoding = "UTF-8")
  An irrecoverable exception occurred. R is aborting now ...
  </code></pre>
  
  <p>Can anyone help me figure out what is going on so I can fix it?</p>