Install pdfcrop not working on Ubuntu 22

[dmkaplan2000]

I am trying to install pdfcrop using tinytex 0.37 in R 4.3.2 on Ubuntu 22.04.3 LTS. I get the following when I run tinytex::tlmgr_install("pdfcrop"):

tlmgr update --all --self
tlmgr install pdfcrop
tlmgr: package repository https://mirrors.rit.edu/CTAN/systems/texlive/tlnet/ (verified)
tlmgr install: package already present: pdfcrop
mkdir(/home/runner/) failed for tree /home/runner/bin: Permission denied
tlmgr: An error has occurred. See above messages. Exiting.
TLUtils::add_remove_symlinks: add of symlinks had 1 error(s), see messages above.

It seems it is trying to create a directory called /home/runner. If I create that directory myself outside of R and then rerun tinytex::tlmgr_install("pdfcrop"), I get:

tlmgr update --all --self
tlmgr install pdfcrop
tlmgr: package repository https://mirrors.rit.edu/CTAN/systems/texlive/tlnet/ (verified)
tlmgr install: package already present: pdfcrop
> Sys.which('pdfcrop')
pdfcrop 
     "" 
> knitr:::has_utility("pdfcrop")
[1] FALSE

Looking in /home/runner/bin I see that pdfcrop is indeed present, but this directory does not seem to be on the path, so has_utility cannot find it.

Cryptically, if has_utility fails to find pdfcrop, then knitr::plot_crop just returns the input filename with no message, which had me stumped for a bit.

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[yihui]

It seems there are at least two issues here. First, I wonder if /home/runner is really your HOME directory. It's the home directory of Github Action runners, but should be unlikely to be yours. If your home directory is not /home/runner but tlmgr is trying to use this directory, there must be something wrong in your TinyTeX installation (how did you install it?). Also check the output of tlmgr option sys_bin.

Second, when TinyTeX and pdfcrop are installed but $HOME/bin is not in your PATH variable, knitr should be able to find it. I just fixed this issue in knitr. You can install the development version via

remotes::install_github('yihui/knitr')

Thanks!

[dmkaplan2000]

I have no idea where /home/runner is coming from. It is certainly not my home directory and I have never heard mention of or created a directory with that name. Also, $HOME/bin is on my path. What was missing for some reason was the link to $HOME/.TinyTeX/bin/x86_64-linux/pdfcrop in $HOME/bin. I added that by hand and then restarted RStudio and now it can find pdfcrop, but something clearly went very wrong at some point. Perhaps RStudio uses /home/runner as a temporary place to run things??? A mystery. In any case, with the manually created symlink, pdfcrop now works so I guess the problem is solved...

[dmkaplan2000]

Ahh, I now see the sense of your comment - I was indeed running rstudio from a directory cloned from github. Perhaps that somehow messed things up. But I don't knowingly use Github Action runners. And I installed tinytex using the standard tinytex::install_tinytex(). If the problem creeps up again I will just reinstall from outside of the git repo.

[yihui]

I feel there might be something wrong on our side, but it should be very unlikely. If you installed TinyTeX via tinytex::install_tinytex(), it should adjust the sys_bin option of TeX Live to your actual HOME directory:

tinytex/R/install.R

Line 508 in 54eb1fd

tlmgr(c('option', 'sys_bin', bin_dir))

The /home/runner directory is from the Github Action runner that we use to build TinyTeX. It's hardcoded in TinyTeX, but as I said, when you install it, the installation script should adjust this hardcoded path to your own ~/bin. You can check the output of

tlmgr option sys_bin
tlmgr option sys_bin ~/bin
tlmgr option sys_bin

[dmkaplan2000]

$ tlmgr option sys_bin
Destination for symlinks for binaries (sys_bin): /home/runner/bin
$ tlmgr option sys_bin ~/bin
tlmgr: setting option sys_bin to /home/dmk/bin.
tlmgr: updating /home/dmk/.TinyTeX/tlpkg/texlive.tlpdb
$ tlmgr option sys_bin
Destination for symlinks for binaries (sys_bin): /home/dmk/bin

Does this permanently fix the issue?

[yihui]

When you (re)install TinyTeX next time, the option may be restored.

In your case, I don't understand why the command tlmgr option didn't work at

tinytex/R/install.R

Line 508 in 54eb1fd

tlmgr(c('option', 'sys_bin', bin_dir))

tinytex:::os_index must be 2 in your system, right?

[dmkaplan2000]

Yes, tinytex:::os_index is 2 on my system. I haven't reinstalled TinyTeX, but I could do that if you wanted me to test.

[yihui]

Yes, it will be nice if you could test reinstalling TinyTeX. Or simply test this:

tinytex::tlmgr(c('option', 'sys_bin', '~/bin'))

# check if it worked
tinytex::tlmgr(c('option', 'sys_bin'))

tinytex::tlmgr_path()

[dmkaplan2000]

I tried the code you sent (before reinstalling) and it gave:

> tinytex::tlmgr(c('option', 'sys_bin', '~/bin'))
tlmgr option sys_bin ~/bin
tlmgr: setting option sys_bin to /home/dmk/bin.
tlmgr: updating /home/dmk/.TinyTeX/tlpkg/texlive.tlpdb
> 
> # check if it worked
> tinytex::tlmgr(c('option', 'sys_bin'))
tlmgr option sys_bin
Destination for symlinks for binaries (sys_bin): /home/dmk/bin
> 
> tinytex::tlmgr_path()
> 

[dmkaplan2000]

I also tried uninstall and then install and it seems to be working:

> tinytex::uninstall_tinytex()
tlmgr: no auxiliary texmf trees defined, so nothing removed
tlmgr: action conf returned an error; continuing.
tlmgr: An error has occurred. See above messages. Exiting.
> tinytex::install_tinytex()
trying URL 'https://yihui.org/tinytex/TinyTeX-1.tar.gz'
Content type 'application/octet-stream' length 92431591 bytes (88.1 MB)
==================================================
downloaded 88.1 MB

tlmgr option sys_bin ~/bin
tlmgr: setting option sys_bin to /home/dmk/bin.
tlmgr: updating /home/dmk/.TinyTeX/tlpkg/texlive.tlpdb
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.
> tinytex::tlmgr(c('option', 'sys_bin'))
tlmgr option sys_bin
Destination for symlinks for binaries (sys_bin): /home/dmk/bin
> tinytex::tlmgr_path()
> 
> tinytex::tlmgr_install("pdfcrop")
tlmgr install pdfcrop
tlmgr: package repository https://mirror.ctan.org/systems/texlive/tlnet (verified)
[1/2, ??:??/??:??] install: pdfcrop.x86_64-linux [1k]
[2/2, 00:01/00:31] install: pdfcrop [11k]
running mktexlsr ...
done running mktexlsr.
tlmgr: package log updated: /home/dmk/.TinyTeX/texmf-var/web2c/tlmgr.log
tlmgr: command log updated: /home/dmk/.TinyTeX/texmf-var/web2c/tlmgr-commands.log

It is a mystery why it didn't work before...

[yihui]

Indeed it is a mystery...