Error(s) in re-building vignettes:
--- re-building ‘Spectrum_vignette.Rmd’ using rmarkdown

kpathsea: Running mktexfmt pdftex.fmt
mktexfmt: mktexfmt is using the following fmtutil.cnf files (in precedence order):
mktexfmt:   /usr/share/texlive/texmf-dist/web2c/fmtutil.cnf
mktexfmt: mktexfmt is using the following fmtutil.cnf file for writing changes:
mktexfmt:   /data/gannet/ripley/.texlive2017/texmf-config/web2c/fmtutil.cnf
mktexfmt [WARNING]: double mention of mf/mf-nowin in /usr/share/texlive/texmf-dist/web2c/fmtutil.cnf
mktexfmt [WARNING]: double mention of tex/tex in /usr/share/texlive/texmf-dist/web2c/fmtutil.cnf
mktexfmt [INFO]: writing formats under /data/gannet/ripley/.texlive2017/texmf-var/web2c
mktexfmt [INFO]: --- remaking pdftex with pdftex
mktexfmt: running `pdftex -ini   -jobname=pdftex -progname=pdftex -translate-file=cp227.tcx *pdfetex.ini' ...
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017) (INITEX)
 restricted \write18 enabled.
 (/usr/share/texlive/texmf-dist/web2c/cp227.tcx)
entering extended mode
(/usr/share/texlive/texmf-dist/tex/plain/config/pdfetex.ini
(/usr/share/texlive/texmf-dist/tex/generic/tex-ini-files/pdftexconfig.tex)
(/usr/share/texlive/texmf-dist/tex/plain/etex/etex.src
(/usr/share/texlive/texmf-dist/tex/plain/base/plain.tex
Preloading the plain format: codes, registers, parameters, fonts, more fonts,
macros, math definitions, output routines, hyphenation
(/usr/share/texlive/texmf-dist/tex/generic/hyphen/hyphen.tex
[skipping from \patterns to end-of-file...]))
(/usr/share/texlive/texmf-dist/tex/plain/etex/etexdefs.lib
Skipping module "grouptypes"; Loading module "interactionmodes";
Skipping module "nodetypes"; Skipping module "iftypes";)
(/usr/share/texlive/texmf-dist/tex/generic/config/language.def
(/usr/share/texlive/texmf-dist/tex/generic/hyphen/hyphen.tex))
Augmenting the Plain TeX definitions: \tracingall;
Adding new e-TeX definitions: \eTeX, \loggingall, \tracingnone,
register allocation; extended register allocation; 
Recycling: \addlanguage, \@nswer (not defined), \@sk, \b@dresponsetrue,
\b@dresponsefalse, \ch@ckforyn, \mayber@cycle, \et@xabort, \et@xbuf,
\et@xfmtsrc, \et@xfilehdr, \et@xinf, \et@xpatterns, \l@ngdefnfile, \n@xt,
\p@rse (not defined), \pr@mpt (not defined), \pr@mptloop (not defined),
\forcer@cycle, \usef@llback, \usef@llbacktrue, \usef@llbackfalse, 
Retaining: \et@xerr, \et@xinput, \et@xlibhdr, \et@xmsg, \et@xtoks, \et@xwarn,
\et@xl@@d, \et@xl@ad, \et@xload, \et@xlang, \et@xhash, \eTeX, \etexhdrchk,
\etexstatus, \module, \uselanguage, \r@tain, \r@cycle,)
(/usr/share/texlive/texmf-dist/tex/plain/config/pdftexmagfix.tex) )
Beginning to dump on file pdftex.fmt
 (preloaded format=pdftex 2019.2.28)
2898 strings of total length 43224
7992 memory locations dumped; current usage is 203&7327
1265 multiletter control sequences
\font\nullfont=nullfont
\font\tenrm=cmr10
\font\preloaded=cmr9
\font\preloaded=cmr8
\font\sevenrm=cmr7
\font\preloaded=cmr6
\font\fiverm=cmr5
\font\teni=cmmi10
\font\preloaded=cmmi9
\font\preloaded=cmmi8
\font\seveni=cmmi7
\font\preloaded=cmmi6
\font\fivei=cmmi5
\font\tensy=cmsy10
\font\preloaded=cmsy9
\font\preloaded=cmsy8
\font\sevensy=cmsy7
\font\preloaded=cmsy6
\font\fivesy=cmsy5
\font\tenex=cmex10
\font\preloaded=cmss10
\font\preloaded=cmssq8
\font\preloaded=cmssi10
\font\preloaded=cmssqi8
\font\tenbf=cmbx10
\font\preloaded=cmbx9
\font\preloaded=cmbx8
\font\sevenbf=cmbx7
\font\preloaded=cmbx6
\font\fivebf=cmbx5
\font\tentt=cmtt10
\font\preloaded=cmtt9
\font\preloaded=cmtt8
\font\preloaded=cmsltt10
\font\tensl=cmsl10
\font\preloaded=cmsl9
\font\preloaded=cmsl8
\font\tenit=cmti10
\font\preloaded=cmti9
\font\preloaded=cmti8
\font\preloaded=cmti7
\font\preloaded=cmu10
\font\preloaded=cmmib10
\font\preloaded=cmbsy10
\font\preloaded=cmcsc10
\font\preloaded=cmssbx10
\font\preloaded=cmdunh10
\font\preloaded=cmr7 at 14.51799pt
\font\preloaded=cmtt10 at 14.4pt
\font\preloaded=cmssbx10 at 14.4pt
\font\preloaded=manfnt
14787 words of font info for 50 preloaded fonts
14 hyphenation exceptions
Hyphenation trie of length 6075 has 181 ops out of 35111
  181 for language 0
0 words of pdfTeX memory
0 indirect objects
No pages of output.
Transcript written on pdftex.log.
mktexfmt [INFO]: /data/gannet/ripley/.texlive2017/texmf-var/web2c/pdftex/pdftex.fmt installed.
mktexfmt [INFO]: Disabled formats: 32
mktexfmt [INFO]: Successfully rebuilt formats: 1
mktexfmt [INFO]: Not selected formats: 15
mktexfmt [INFO]: Total formats: 48
mktexfmt [INFO]: exiting with status 0
tlmgr search --file --global '/framed.sty'
TeX Live 2018 is frozen forever and will no
longer be updated.  This happens in preparation for a new release.

If you're interested in helping to pretest the new release (when
pretests are available), please read https://tug.org/texlive/pretest.html.
Otherwise, just wait, and the new release will be ready in due time.
Trying to automatically install missing LaTeX packages...
tlmgr install framed
TeX Live 2018 is frozen forever and will no
longer be updated.  This happens in preparation for a new release.

If you're interested in helping to pretest the new release (when
pretests are available), please read https://tug.org/texlive/pretest.html.
Otherwise, just wait, and the new release will be ready in due time.
tlmgr: package repository http://mirror.ox.ac.uk/sites/ctan.org/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'
TeX Live 2018 is frozen forever and will no
longer be updated.  This happens in preparation for a new release.

If you're interested in helping to pretest the new release (when
pretests are available), please read https://tug.org/texlive/pretest.html.
Otherwise, just wait, and the new release will be ready in due time.
! 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 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