only rendering last X lines of chunk output in R Markdown - r

Question

I am calling a shell program from R Markdown like this
```{sh}
SomeShellProgram -options
```
and render the file as HTML. The calculation the program does take some time, wherefore the author included an self-updating progress "bar" which looks something like this:
45Mb 12.4% 935 OTUs, 3485 chimeras (6.7%)
However, especially if the progress is slow, it will update this line every 0.1% or so. And each line is rendered separately in the HTML, which can ad up to up to 1000 lines of progress bars.
I don't want to suppress the output completely , e.g. with echo=FALSE in the chunk options. I am producing a report and the information that is printed is important.
I am looking for a hack that would somehow only capture the last X lines and render these, or maybe using grep or something similar to only capture the lines that have 100% or so.
I tried redirecting the output with > output.txt but the progress wasn't printed to the file (although other information was).
I can't think of a way to provide a reproducible example without giving the full example, sorry for that.
For those that are interested: I am trying to produce a report on the analysis of 16S Illumina sequencing data and I'm using Usearch and the command that gives me the most headaches is the usearch -cluster_otus command.
UPDATE
There is an additional problem with rendering the last X lines: The progress bar in the output is delimited by ^M(carriage return characters) and not by line breaks, so lessonly recognises it as a single line. Therefore my final solution includes
redirecting the output from the progress bar with 2> into a file
replacing the ^Mcharacters with line breaks using sed
rendering the last X lines with less
My (pseudo)code to do this on mac osx is the following (where X = number of lines)
FunctionWithProgressBar -option 2> tempfile.tmp
sed -ibak $'s/\x0D/\\\n/g' tempfile.tmp
tail -nX tempfile.tmp
and in R Markdown:
```{sh, results="hide"}
FunctionWithProgressBar -option 2> tempfile.tmp
```
```{sh, echo=FALSE}
sed -ibak $'s/\x0D/\\\n/g' tempfile.tmp
tail -nX tempfile.tmp
```
note that matching the backspace is a pain in the butt (especially on osx) and changes between platforms.

Answer 1

The progress bar is probably in the sterr stream, so you capture it with "2>" and not ">" so you could capture stderr and stdout separately, e.g.:
usearch blablabla 2> only_err > only_stdout
Or if you want all of the output together, you have to redirect stderr to stdout, and do an append, as such:
usearch blablabla >> total_output 2>&1
As for the R-markdown part, I cannot really help, never used, sorry.
regards,
Moritz