2

Unfortunately, I am experiencing the same issue as reported in Compilation problem fontenc-Latex. I reinstalled my TeX installation and ran tlmgr update, all to no avail. I am using RStudio Version 1.3.820 (but also experience the same issue in RStudio Version 1.2.5033), with updates of all packages. I suspect the error lies in the use of an old LaTeX2e <2018-12-01> version, but I have no clue, why this version would be used, even though I have reinstalled my TeX installation with all sorts of different repositories.

I noticed that no matter what repository I use I get the following errors:

tlmgr install: package ifluatex not present in repository.
tlmgr install: package ifxetex not present in repository.

Am I right to suspect that this might cause the problem? Any suggestions how I could fix this? Again, running tlmgr update --all --self does not report any error or need to update.

When knitting my text in RStudio I get the following log:

/usr/local/bin/pandoc +RTS -K512m -RTS MODE_proposal_APA.utf8.md --to latex --from markdown+autolink_bare_uris+tex_math_single_backslash+raw_attribute --output MODE_proposal_APA.tex --self-contained --highlight-style tango --pdf-engine pdflatex --include-in-header /Library/Frameworks/R.framework/Versions/3.6/Resources/library/papaja/rmarkdown/templates/apa6/resources/apa6_header_includes.tex --variable graphics --lua-filter /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rmarkdown/rmd/lua/latex-div.lua --wrap preserve --csl /Library/Frameworks/R.framework/Versions/3.6/Resources/library/papaja/rmd/apa6.csl --filter /usr/local/bin/pandoc-citeproc --lua-filter /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rmdfiltr/replace_ampersands.lua --lua-filter /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rmdfiltr/wordcount.lua --variable 'classoption:,doc,a4paper' --variable 'lang:en-US' --variable 'subparagraph:yes' --variable 'block-headings:no' --include-in-header /var/folders/hh/vy5948dx2jv2v9qc_m2tbrx00000gn/T//Rtmp9tAYmU/includes_14464266266e.tex 
output file: MODE_proposal_APA.knit.md


! Undefined control sequence.
l.115 \xdef\@fontenc@load@list{\@fontenc@load@list

None of my documents render anymore. So using a different class makes no difference. I would very much appreciate any suggestions how to tackle this, since simply running tlmgr update did not solve it. (Sorry for posting this in an answer previously).

Here's the log file:

This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019) (preloaded format=pdflatex 2019.5.12)  21 FEB 2020 12:07
entering extended mode
 restricted \write18 enabled.
 %&-line parsing enabled.
**MODE_proposal_APA.tex
(./MODE_proposal_APA.tex
LaTeX2e <2018-12-01>
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/latex/apa7/apa7.cls
Document Class: apa7 2019/12/30 v1.04 APA formatting (7th edition)
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/latex/base/article.cls
Document Class: article 2019/12/20 v1.4l Standard LaTeX document class
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/latex/base/size11.clo
File: size11.clo 2019/12/20 v1.4l Standard LaTeX file (size option)
)
\c@part=\count80
\c@section=\count81
\c@subsection=\count82
\c@subsubsection=\count83
\c@paragraph=\count84
\c@subparagraph=\count85
\c@figure=\count86
\c@table=\count87
\abovecaptionskip=\skip41
\belowcaptionskip=\skip42
\bibindent=\dimen102
) (/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/latex/etoolbox/etoolbox.sty
Package: etoolbox 2019/09/21 v2.5h e-TeX tools for LaTeX (JAW)
\etb@tempcnta=\count88
)
Class apa7 Info: No bibliography package was specified; defaulting to (but not 
loading) Biblatex on input line 218.
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/latex/lm/lmodern.sty
Package: lmodern 2009/10/30 v1.6 Latin Modern Fonts
LaTeX Font Info:    Overwriting symbol font `operators' in version `normal'
(Font)                  OT1/cmr/m/n --> OT1/lmr/m/n on input line 22.
LaTeX Font Info:    Overwriting symbol font `letters' in version `normal'
(Font)                  OML/cmm/m/it --> OML/lmm/m/it on input line 23.
LaTeX Font Info:    Overwriting symbol font `symbols' in version `normal'
(Font)                  OMS/cmsy/m/n --> OMS/lmsy/m/n on input line 24.
LaTeX Font Info:    Overwriting symbol font `largesymbols' in version `normal'
(Font)                  OMX/cmex/m/n --> OMX/lmex/m/n on input line 25.
LaTeX Font Info:    Overwriting symbol font `operators' in version `bold'
(Font)                  OT1/cmr/bx/n --> OT1/lmr/bx/n on input line 26.
LaTeX Font Info:    Overwriting symbol font `letters' in version `bold'
(Font)                  OML/cmm/b/it --> OML/lmm/b/it on input line 27.
LaTeX Font Info:    Overwriting symbol font `symbols' in version `bold'
(Font)                  OMS/cmsy/b/n --> OMS/lmsy/b/n on input line 28.
LaTeX Font Info:    Overwriting symbol font `largesymbols' in version `bold'
(Font)                  OMX/cmex/m/n --> OMX/lmex/m/n on input line 29.
LaTeX Font Info:    Overwriting math alphabet `\mathbf' in version `normal'
(Font)                  OT1/cmr/bx/n --> OT1/lmr/bx/n on input line 31.
LaTeX Font Info:    Overwriting math alphabet `\mathsf' in version `normal'
(Font)                  OT1/cmss/m/n --> OT1/lmss/m/n on input line 32.
LaTeX Font Info:    Overwriting math alphabet `\mathit' in version `normal'
(Font)                  OT1/cmr/m/it --> OT1/lmr/m/it on input line 33.
LaTeX Font Info:    Overwriting math alphabet `\mathtt' in version `normal'
(Font)                  OT1/cmtt/m/n --> OT1/lmtt/m/n on input line 34.
LaTeX Font Info:    Overwriting math alphabet `\mathbf' in version `bold'
(Font)                  OT1/cmr/bx/n --> OT1/lmr/bx/n on input line 35.
LaTeX Font Info:    Overwriting math alphabet `\mathsf' in version `bold'
(Font)                  OT1/cmss/bx/n --> OT1/lmss/bx/n on input line 36.
LaTeX Font Info:    Overwriting math alphabet `\mathit' in version `bold'
(Font)                  OT1/cmr/bx/it --> OT1/lmr/bx/it on input line 37.
LaTeX Font Info:    Overwriting math alphabet `\mathtt' in version `bold'
(Font)                  OT1/cmtt/m/n --> OT1/lmtt/m/n on input line 38.
) (/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/latex/base/fontenc.sty
Package: fontenc 2020/02/11 v2.0o Standard LaTeX package
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/latex/base/t1enc.def
File: t1enc.def 2020/02/11 v2.0o Standard LaTeX file
LaTeX Font Info:    Redeclaring font encoding T1 on input line 48.
)
LaTeX Font Info:    Try loading font information for T1+lmr on input line 112.
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/latex/lm/t1lmr.fd
File: t1lmr.fd 2009/10/30 v1.6 Font defs for Latin Modern
)
! Undefined control sequence.
l.115 \xdef\@fontenc@load@list{\@fontenc@load@list

Here is how much of TeX's memory you used:
 865 strings out of 494553
 9932 string characters out of 6176313
 67509 words of memory out of 5000000
 4605 multiletter control sequences out of 15000+600000
 6930 words of font info for 16 fonts, out of 8000000 for 9000
 14 hyphenation exceptions out of 8191
 33i,0n,29p,804b,76s stack positions out of 5000i,500n,10000p,200000b,80000s

!  ==> Fatal error occurred, no output PDF file produced!

As requested the output of fmtutil-sys --byfmt pdflatex

(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/generic/dehyph-exptl/dehypht-
x-2019-04-04.pat
German Hyphenation Patterns (Traditional Orthography) `dehypht-x' 2019-04-04 (W
L)))
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/generic/dehyph-exptl/dehyphn-
x-2019-04-04.tex dehyph-exptl: using an 8-bit TeX engine.
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/generic/dehyph-exptl/dehyphn-
x-2019-04-04.pat
German Hyphenation Patterns (Reformed Orthography, 2006) `dehyphn-x' 2019-04-04
 (WL)))) (/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/latex/base/utf8.def
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/latex/base/omsenc.dfu)
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/latex/base/ot1enc.dfu)
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/latex/base/t1enc.dfu)
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/latex/base/ts1enc.dfu))
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/latex/base/ltexpl.ltx
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/latex/l3kernel/expl3.ltx
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/latex/l3kernel/expl3-code.tex

(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/latex/l3kernel/l3deprecation.
def))))
 ) )
Beginning to dump on file pdflatex.fmt
 (preloaded format=pdflatex 2020.2.21)
16842 strings of total length 286120
230907 memory locations dumped; current usage is 165&224195
15135 multiletter control sequences
\font\nullfont=nullfont
\font\OMX/cmex/m/n/10=cmex10
\font\tenln=line10
\font\tenlnw=linew10
\font\tencirc=lcircle10
\font\tencircw=lcirclew10
\font\OT1/cmr/m/n/5=cmr5
\font\OT1/cmr/m/n/7=cmr7
\font\OT1/cmr/m/n/10=cmr10
\font\OML/cmm/m/it/5=cmmi5
\font\OML/cmm/m/it/7=cmmi7
\font\OML/cmm/m/it/10=cmmi10
\font\OMS/cmsy/m/n/5=cmsy5
\font\OMS/cmsy/m/n/7=cmsy7
\font\OMS/cmsy/m/n/10=cmsy10
\font\c__fp_exp_intarray=cmr10 at 0.00002pt
\font\c__fp_trig_intarray=cmr10 at 0.00003pt
\font\g__regex_charcode_intarray=cmr10 at 0.00005pt
\font\g__regex_catcode_intarray=cmr10 at 0.00006pt
\font\g__regex_balance_intarray=cmr10 at 0.00008pt
\font\g__regex_state_active_intarray=cmr10 at 0.00009pt
\font\g__regex_thread_state_intarray=cmr10 at 0.0001pt
\font\g__regex_submatch_prev_intarray=cmr10 at 0.00012pt
\font\g__regex_submatch_begin_intarray=cmr10 at 0.00014pt
\font\g__regex_submatch_end_intarray=cmr10 at 0.00015pt
532331 words of font info for 24 preloaded fonts
14 hyphenation exceptions
Hyphenation trie of length 67075 has 1136 ops out of 35111
  475 for language 4
  478 for language 3
  2 for language 1
  181 for language 0
0 words of pdfTeX memory
0 indirect objects
No pages of output.
Transcript written on pdflatex.log.
fmtutil [INFO]: log file copied to: /Users/jrennstich/Library/TinyTeX/texmf-var/web2c/pdftex/pdflatex.log
fmtutil [INFO]: /Users/jrennstich/Library/TinyTeX/texmf-var/web2c/pdftex/pdflatex.fmt installed.
fmtutil [INFO]: --- remaking pdfetex with pdftex
fmtutil: running `pdftex -ini   -jobname=pdfetex -progname=pdfetex -translate-file=cp227.tcx *pdfetex.ini' ...
This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019) (INITEX)
 restricted \write18 enabled.
 (/Users/jrennstich/Library/TinyTeX/texmf-dist/web2c/cp227.tcx)
entering extended mode
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/plain/config/pdfetex.ini
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/generic/tex-ini-files/pdftexc
onfig.tex)
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/plain/etex/etex.src
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/plain/base/plain.tex
Preloading the plain format: codes, registers, parameters, fonts, more fonts,
macros, math definitions, output routines, hyphenation
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/generic/hyphen/hyphen.tex
[skipping from \patterns to end-of-file...]))
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/plain/etex/etexdefs.lib
Skipping module "grouptypes"; Loading module "interactionmodes";
Skipping module "nodetypes"; Skipping module "iftypes";)
(/Users/jrennstich/Library/TinyTeX/texmf-var/tex/generic/config/language.def
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/generic/hyphen/hyphen.tex)
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/generic/dehyph-exptl/dehypht-
x-2019-04-04.tex dehyph-exptl: using an 8-bit TeX engine.
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/generic/dehyph-exptl/dehypht-
x-2019-04-04.pat
German Hyphenation Patterns (Traditional Orthography) `dehypht-x' 2019-04-04 (W
L)))
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/generic/dehyph-exptl/dehypht-
x-2019-04-04.tex dehyph-exptl: using an 8-bit TeX engine.
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/generic/dehyph-exptl/dehypht-
x-2019-04-04.pat
German Hyphenation Patterns (Traditional Orthography) `dehypht-x' 2019-04-04 (W
L)))
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/generic/dehyph-exptl/dehyphn-
x-2019-04-04.tex dehyph-exptl: using an 8-bit TeX engine.
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/generic/dehyph-exptl/dehyphn-
x-2019-04-04.pat
German Hyphenation Patterns (Reformed Orthography, 2006) `dehyphn-x' 2019-04-04
 (WL)))
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/generic/dehyph-exptl/dehyphn-
x-2019-04-04.tex dehyph-exptl: using an 8-bit TeX engine.
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/generic/dehyph-exptl/dehyphn-
x-2019-04-04.pat
German Hyphenation Patterns (Reformed Orthography, 2006) `dehyphn-x' 2019-04-04
 (WL)))) 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,)
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/plain/config/pdftexmagfix.tex
) )
Beginning to dump on file pdfetex.fmt
 (preloaded format=pdfetex 2020.2.21)
2939 strings of total length 45509
8034 memory locations dumped; current usage is 203&7395
1282 multiletter control sequences
\font\nullfont=nullfont
\font\tenrm=cmr10
\font\preloaded=cmr9
\font\preloaded=cmr8
\font\sevenrm=cmr7
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\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
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\font\preloaded=cmssbx10
\font\preloaded=cmdunh10
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\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 67065 has 2087 ops out of 35111
  475 for language 4
  475 for language 3
  478 for language 2
  478 for language 1
  181 for language 0
0 words of pdfTeX memory
0 indirect objects
No pages of output.
Transcript written on pdfetex.log.
fmtutil [INFO]: log file copied to: /Users/jrennstich/Library/TinyTeX/texmf-var/web2c/pdftex/pdfetex.log
fmtutil [INFO]: /Users/jrennstich/Library/TinyTeX/texmf-var/web2c/pdftex/pdfetex.fmt installed.
fmtutil [INFO]: --- remaking dvilualatex with luatex
fmtutil: running `luatex -ini   -jobname=dvilualatex -progname=dvilualatex dvilualatex.ini' ...
This is LuaTeX, Version 1.10.0 (TeX Live 2019)  (INITEX)
 restricted system commands enabled.

(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/generic/tex-ini-files/dvilual
atex.ini
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/generic/tex-ini-files/lualate
x.ini
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/generic/tex-ini-files/luatexc
onfig.tex
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/generic/tex-ini-files/pdftexc
onfig.tex))
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/latex/base/latex.ltx
(/Users/jrennstich/Library/TinyTeX/texmf-dist/tex/latex/base/texsys.cfg)
./texsys.aux found
21
  • 2
    try to force the format to be rebuilt with fmtutil-sys --all you have incompatible files with the input files updated to 2020 versions but using a 2018 latex, that can not work. – David Carlisle Feb 21 '20 at 11:30
  • 1
    Have you tried the answer at the linked question, i.e. fmtutil-sys --all? – Ralf Stubner Feb 21 '20 at 11:31
  • Thank you for you suggestions. Yes, I ran fmtutil-sys -all. No changes, I still get that error. – JKR Feb 21 '20 at 12:01
  • 1
    Hello @JKR! There are two of - before all (--all) in the suggested command above. – Su-47 Feb 21 '20 at 12:09
  • Can you post the (first 100 lines of the) output of fmtutil-sys --byfmt pdflatex? Use sudo if needed. – Ralf Stubner Feb 21 '20 at 12:09

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