Cannot Knit

[ayodhyasovis]

When I try to knit a lot of error messages show.

[WARNING] Deprecated: --self-contained. use --embed-resources --standalone
tlmgr: package repository https://ctan.ebinger.cc/tex-archive/systems/texlive/tlnet (not verified: valid signature with expired key)
[1/1, ??:??/??:??] install: microtype [55k]
tlmgr: package log updated: /Users/ayodhyawickramasooriya/Library/TinyTeX/texmf-var/web2c/tlmgr.log
TeXLive::TLUtils::check_file_and_remove: checksums differ for /var/folders/fm/3zcm746j08z4q9qk4bl_9cp00000gn/T/_TYPapgQUM/0JDSBsIFb8/microtype.tar.xz:
TeXLive::TLUtils::check_file_and_remove:   tlchecksum=c80e6bb2c13432ecae2be22622e3bbfe82342ca138f61870cb8f3c2d7ec93f431bee5ae0a9619d4ad6a842b0752ecb73131452d6ac5c5fba7732ad4d5c979fa6, arg=62da418a9800c5f259ee607218e6eef9aad036f06245d5ae1a9d9bbd40a2972798cc07668d6ae7e518c49c5cf713033a67d7791b5b7a06428dcbd805aa8a9022
TeXLive::TLUtils::check_file_and_remove: backtrace:
 -> /Users/ayodhyawickramasooriya/Library/TinyTeX/tlpkg/TeXLive/TLUtils.pm:2590: TeXLive::TLUtils::check_file_and_remove
 -> /Users/ayodhyawickramasooriya/Library/TinyTeX/tlpkg/TeXLive/TLPDB.pm:1983: TeXLive::TLUtils::unpack
 -> /Users/ayodhyawickramasooriya/Library/TinyTeX/tlpkg/TeXLive/TLPDB.pm:1818: TeXLive::TLPDB::_install_data
 -> /Users/ayodhyawickramasooriya/Library/TinyTeX/tlpkg/TeXLive/TLPDB.pm:1734: TeXLive::TLPDB::not_virtual_install_package
 -> /Users/ayodhyawickramasooriya/Library/TinyTeX/bin/universal-darwin/tlmgr:3921: TeXLive::TLPDB::install_package
 -> /Users/ayodhyawickramasooriya/Library/TinyTeX/bin/universal-darwin/tlmgr:797: main::action_install
 -> /Users/ayodhyawickramasooriya/Library/TinyTeX/bin/universal-darwin/tlmgr:703: main::execute_action
 -> /Users/ayodhyawickramasooriya/Library/TinyTeX/bin/universal-darwin/tlmgr:366: main::main
TeXLive::TLUtils::check_file_and_remove:   removing /var/folders/fm/3zcm746j08z4q9qk4bl_9cp00000gn/T/_TYPapgQUM/0JDSBsIFb8/microtype.tar.xz, but saving copy in /var/folders/fm/3zcm746j08z4q9qk4bl_9cp00000gn/T/X0SDSOYlXw
TLPDB::_install_data: downloading did not succeed (check_file_and_remove failed) for https://ctan.ebinger.cc/tex-archive/systems/texlive/tlnet/archive/microtype.tar.xz
tlmgr update --self
tlmgr: package repository https://ctan.ebinger.cc/tex-archive/systems/texlive/tlnet (not verified: valid signature with expired key)
[1/1, ??:??/??:??] install: microtype [55k]
TeXLive::TLUtils::check_file_and_remove: checksums differ for /var/folders/fm/3zcm746j08z4q9qk4bl_9cp00000gn/T/msNMrmxa21/7hARXBn4mm/microtype.tar.xz:
TeXLive::TLUtils::check_file_and_remove:   tlchecksum=c80e6bb2c13432ecae2be22622e3bbfe82342ca138f61870cb8f3c2d7ec93f431bee5ae0a9619d4ad6a842b0752ecb73131452d6ac5c5fba7732ad4d5c979fa6, arg=62da418a9800c5f259ee607218e6eef9aad036f06245d5ae1a9d9bbd40a2972798cc07668d6ae7e518c49c5cf713033a67d7791b5b7a06428dcbd805aa8a9022
TeXLive::TLUtils::check_file_and_remove: backtrace:
 -> /Users/ayodhyawickramasooriya/Library/TinyTeX/tlpkg/TeXLive/TLUtils.pm:2590: TeXLive::TLUtils::check_file_and_remove
 -> /Users/ayodhyawickramasooriya/Library/TinyTeX/tlpkg/TeXLive/TLPDB.pm:1983: TeXLive::TLUtils::unpack
 -> /Users/ayodhyawickramasooriya/Library/TinyTeX/tlpkg/TeXLive/TLPDB.pm:1818: TeXLive::TLPDB::_install_data
 -> /Users/ayodhyawickramasooriya/Library/TinyTeX/tlpkg/TeXLive/TLPDB.pm:1734: TeXLive::TLPDB::not_virtual_install_package
 -> /Users/ayodhyawickramasooriya/Library/TinyTeX/bin/universal-darwin/tlmgr:3921: TeXLive::TLPDB::install_package
 -> /Users/ayodhyawickramasooriya/Library/TinyTeX/bin/universal-darwin/tlmgr:797: main::action_install
 -> /Users/ayodhyawickramasooriya/Library/TinyTeX/bin/universal-darwin/tlmgr:703: main::execute_action
 -> /Users/ayodhyawickramasooriya/Library/TinyTeX/bin/universal-darwin/tlmgr:366: main::main
TeXLive::TLUtils::check_file_and_remove:   removing /var/folders/fm/3zcm746j08z4q9qk4bl_9cp00000gn/T/msNMrmxa21/7hARXBn4mm/microtype.tar.xz, but saving copy in /var/folders/fm/3zcm746j08z4q9qk4bl_9cp00000gn/T/_6j0AColaO
TLPDB::_install_data: downloading did not succeed (check_file_and_remove failed) for https://ctan.ebinger.cc/tex-archive/systems/texlive/tlnet/archive/microtype.tar.xz
tlmgr: package log updated: /Users/ayodhyawickramasooriya/Library/TinyTeX/texmf-var/web2c/tlmgr.log
! LaTeX Error: File `microtype.sty' not found.

! Emergency stop.
<read *> 

Error: LaTeX failed to compile _main.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See _main.log for more info.
In addition: Warning message:
In do_once((if (is_R_CMD_check()) stop else warning)("The function xfun::isFALSE() will be deprecated in the future. Please ",  :
  The function xfun::isFALSE() will be deprecated in the future. Please consider using base::isFALSE(x) or identical(x, FALSE) instead.
Execution halted

[ulyngs]

Did you install the missing LaTeX packages as per the README?

missing_packages <- c(
  "appendix", "babel-english", "babel-greek", "babel-latin", 
  "biber", "biblatex", "caption", "cbfonts-fd", "colortbl", "csquotes", 
  "enumitem", "environ", "eso-pic", "fancyhdr", "greek-fontenc", 
  "grfext", "hyphen-greek", "hyphen-latin", "lineno", "logreq", 
  "makecell", "microtype", "minitoc", "multirow", "notoccite", 
  "oberdiek", "pdflscape", "pdfpages", "quotchap", "soul", "tabu", 
  "threeparttable", "threeparttablex", "titlesec", "tocbibind", 
  "trimspaces", "ulem", "units", "utopia", "varwidth", "wrapfig",
  "fvextra", "xurl"
  )
tinytex::tlmgr_install(missing_packages)