Error(s) in re-building vignettes:
--- re-building ‘Spectrum_vignette.Rmd’ using rmarkdown
tlmgr search --file --global '/framed.sty'
Trying to automatically install missing LaTeX packages...
tlmgr install framed
===============================================================================
tlmgr itself needs to be updated.
Please do this via either
  tlmgr update --self
or by getting the latest updater for Unix-ish systems:
  http://mirror.ctan.org/systems/texlive/tlnet/update-tlmgr-latest.sh
and/or Windows systems:
  http://mirror.ctan.org/systems/texlive/tlnet/update-tlmgr-latest.exe
Then continue with other updates as usual.
===============================================================================
tlmgr: Terminating; please see warning above!
tlmgr: package repository http://anorien.csc.warwick.ac.uk/mirrors/CTAN/systems/texlive/tlnet (verified)
tlmgr update --self
tlmgr: package repository http://anorien.csc.warwick.ac.uk/mirrors/CTAN/systems/texlive/tlnet (verified)
tlmgr: saving backups to /usr/local/texlive/2019/tlpkg/backups
[1/2, ??:??/??:??] update: texlive.infra [388k] (51545 -> 51561) ... done
[2/2, 00:02/00:02] update: texlive.infra.x86_64-linux [143k] (51539 -> 51563) ... done
running mktexlsr ...
done running mktexlsr.
running mtxrun --generate ...
done running mtxrun --generate.
tlmgr: package log updated: /usr/local/texlive/2019/texmf-var/web2c/tlmgr.log
fmtutil [WARNING]: double mention of mf/mf-nowin in /usr/share/texlive/texmf-dist/web2c/fmtutil.cnf
fmtutil [WARNING]: double mention of tex/tex in /usr/share/texlive/texmf-dist/web2c/fmtutil.cnf
fmtutil [ERROR]: format directory not writable: /usr/share/texlive/texmf-var/web2c
fmtutil: fmtutil is using the following fmtutil.cnf files (in precedence order):
fmtutil:   /usr/share/texlive/texmf-dist/web2c/fmtutil.cnf
fmtutil: fmtutil is using the following fmtutil.cnf file for writing changes:
fmtutil:   /usr/share/texlive/texmf-config/web2c/fmtutil.cnf
tlmgr install framed
tlmgr: package repository http://anorien.csc.warwick.ac.uk/mirrors/CTAN/systems/texlive/tlnet (verified)
tlmgr install: package already present: framed
tlmgr path add
add_link_dir_dir: /usr/local/share/info/dir exists; not making symlink.
tlmgr search --file --global '/framed.sty'
! LaTeX Error: File `framed.sty' not found.

! Emergency stop.
<read *> 

Error: processing vignette 'Spectrum_vignette.Rmd' failed with diagnostics:
Failed to compile Spectrum_vignette.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See Spectrum_vignette.log for more info.
--- failed re-building ‘Spectrum_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘Spectrum_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted