Converting MultipleAlignments.Rnw to Rmarkdown

[BerylKanali]

@jwokaty
Take a look at the changes
PDF and HTML for comparison
Issues I have:

1. • In the description file when writing authors using this format

Authors@R: c(
  person("Hervé", "Pagès", role=c("aut", "cre"),

is it okay for the first name to be the intials as in the previous format.
2. Graph position not as exact as PDF
3. Size of graph(someone should not scroll to thee the whole graph)
6. The dev.off gives a different output when I knit

null device 
          1 

is the correct output but after in the HTML it shows

## png 
##   2

[jwokaty]

Let's follow the previous format using initials for the DESCRIPTION.

Looking at

Biostrings/vignettes/MultipleAlignments.Rnw

Lines 278 to 283 in c94e8fb

	\begin{figure}
	\begin{center}
	\includegraphics[width=0.6\textwidth]{goodTree}
	\caption{\label{f2} A tree produced by using strings with masked gaps.}
	\end{center}
	\end{figure}

, I suspect that the original authors moved the figure to waste less space on the pages of the PDF. Let's allow the figures to follow their code naturally since the HTML document will not have the same problem.

Since the PDF isn't displaying as nicely as we'd like, I'd like to ask @hpages if we can change pdf to png instead? Or if there's a way to make the PDF display nicely, that suggestion would be helpful.

Lastly, I think we don't have to worry about the value of dev.off() as this is turning off the device and returning the value of that device I believe (we can check with ?dev.off). dev.off is always the "stub", which is null device 1, on the build system, which will generate the vignettes available on bioconductor.org. For users running this code, it will almost always show something else.

[BerylKanali]

@jwokaty
This is ready for review apart from the graph issue talked about above. I did R CMD build and R CMD check and found no errors.

[jwokaty]

Thanks for working on this. I've marked a few items to correct; a few them, such as using back ticks (`) rather than asterisks (*) are repetitive but I marked them so that they can be checked again.

Before you ask for a review, make sure to review your knitted document against the current PDF that you find on the landing pages for each package.

@hpages Can we use .pngs for the figures rather than .pdfs since they don't format well? (If there's a better way to format them, please let us know.)

[hpages]

Can we use .pngs for the figures rather than .pdfs since they don't format well?

of course, thanks

[BerylKanali]

@jwokaty I made the requested changes.
Updated HTML for comparison with PDF

[hpages]

@BerylKanali @jwokaty Where are we standing with this PR?

[jwokaty]

I can check that the issues are resolved then notify @hpages.

[jwokaty]

@hpages This is ready for your review.