Error(s) in re-building vignettes:
  ...
--- re-building ‘rapidr-vignette.rnw’ using Sweave
/tmp/RtmpLVa4ee/working_dir/RtmpLla4GC/file390720f84504
Loading binned counts file
Checking every sampleID has an outcome
Finding bins to exclude in Chr Y 
... excluding 25 bins,  0.9 % of counts mapped to chrY in females.
Number of discarded samples: 0
Not doing PCA
Checking for outlier samples...
Samples with correlation to the mean bin counts of < 0.8. You may want to remove these from the reference set.
Summing counts per chromosome...
Finding baseline values...
Calling the unknowns 
Using zscore
Doing QC
Sample 1002 has 6 chromosome with counts outside the expected range
Calling the unknowns 
Using zscore
Error: processing vignette 'rapidr-vignette.rnw' failed with diagnostics:
Running 'texi2dvi' on 'rapidr-vignette.tex' failed.
LaTeX errors:
! Paragraph ended before \@tempa was complete.
<to be read again> 
                   \par 
l.31 
     
! Paragraph ended before \@tempa was complete.
<to be read again> 
                   \par 
l.260 
      
! LaTeX Error: \begin{center} on input line 26 ended by \end{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! You can't use `\end' in internal vertical mode.
\enddocument ... \endgroup \deadcycles \z@ \@@end 
                                                  
l.303 \end{document}
                    
! LaTeX Error: \begin{center} on input line 26 ended by \end{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Emergency stop.
<*> \nonstopmode \input ./rapidr-vignette.tex
                                             
*** (job aborted, no legal \end found)

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘rapidr-vignette.rnw’

SUMMARY: processing the following file failed:
  ‘rapidr-vignette.rnw’

Error: Vignette re-building failed.
Execution halted