Does not generate HTML or TSV files at all

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Hi

Thanks for the fantastic bit of software. I have aggregated ~250 Kraken2 reports, and it seems to visualise just fine. However trying to output a HTML file or TSV fails without any error message that I can see on the console.

i.e.

[Jan13 14:09] Started new shiny session #2 (2 session(s) running)
[Jan13 14:09] Exiting session #2
[Jan13 14:13] Writing RMD to /tmp/RtmplJQvv2/Uploaded_sample_set__-report.Rmd


processing file: Uploaded_sample_set__-report.Rmd
  |......                                                           |   9%
   inline R code fragments

  |............                                                     |  18%
label: setup (with options) 
List of 1
 $ include: logi FALSE

  |..................                                               |  27%
  ordinary text without R code

  |........................                                         |  36%
label: sample_summary (with options) 
List of 1
 $ message: logi FALSE

  |..............................                                   |  45%
  ordinary text without R code

  |...................................                              |  55%
label: classifications (with options) 
List of 3
 $ message: logi TRUE
 $ warning: logi TRUE
 $ eval   : logi TRUE

  |.........................................                        |  64%
  ordinary text without R code

  |...............................................                  |  73%
label: unnamed-chunk-1 (with options) 
List of 1
 $ eval: logi FALSE

  |.....................................................            |  82%
  ordinary text without R code

  |...........................................................      |  91%
label: sankey_vis
  |.................................................................| 100%
   inline R code fragments


output file: Uploaded_sample_set__-report.knit.md

/usr/bin/pandoc +RTS -K512m -RTS Uploaded_sample_set__-report.utf8.md --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output /tmp/RtmplJQvv2/file495d578f2e1.html --smart --email-obfuscation none --self-contained --standalone --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /home/beggsa/R/x86_64-pc-linux-gnu-library/3.4/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable 'theme:bootstrap' --include-in-header /tmp/RtmplJQvv2/rmarkdown-str495d22c196a1.html 

Output created: /tmp/RtmplJQvv2/file495d578f2e1.html