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Install pdfcrop not working on Ubuntu 22 #435
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It seems there are at least two issues here. First, I wonder if Second, when TinyTeX and remotes::install_github('yihui/knitr') Thanks! |
I have no idea where |
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 |
I feel there might be something wrong on our side, but it should be very unlikely. If you installed TinyTeX via Line 508 in 54eb1fd
The tlmgr option sys_bin
tlmgr option sys_bin ~/bin
tlmgr option sys_bin |
Does this permanently fix the issue? |
When you (re)install TinyTeX next time, the option may be restored. In your case, I don't understand why the command Line 508 in 54eb1fd
|
Yes, |
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() |
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()
> |
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... |
Indeed it is a mystery... |
Kyle F Butts (2): Add support for `# %%` for chunk demarcation in `knitr::spin` (#2307) make spin() recognize `#|` comments as code chunks (#2320) Lee Mendelowitz (1): Fix the error when kable()'s caption value is of length > 1 (#2312) Max Schmit (1): add ALTER as sql statment, that is not returning anything (#2330) Yihui Xie (53): start the next version fix #2304: shouldn't have used `return(meta)` since `meta` is not the `citation()` but `packageDescription()` fix rstudio/rmarkdown#2526 by reverting bebf117 since the `cairo_pdf` device has been explicitly supported in chunk_device(); now all possible `pdf()` arguments are supported, including `family` Disallow unbalanced chunk delimiters (#2306) close #1679: obtain the caption from the chunk option `tab.cap` for `kable()` also try the chunk option tbl.cap when tab.cap is NULL (quarto-dev/quarto-cli#7555) tweak R Markdown v1 vignettes move mailing list link and use https in ref card move css and js to jsdelivr for html_vignette use jsdelivr for the Rhtml template rewrite the docco classic style using JS instead of R standardize the docco linear format new version of funmediation is on CRAN now support the ... argument in chunk hooks optimize PNG images in package vignettes via optipng and pngquant if they are installed use R Markdown v1 for the knitr-intro vignette, too delete some files that are no longer needed in inst/examples and also ignore some files fix #2308: don't trim trailing spaces escaped by `\` support in-body chunk options for ojs and mermaid (quarto-dev/quarto-cli#7799) amend 3dcfac4780accc3791855b298a556297f62dc73d to fix quarto-dev/quarto-cli#5994: add YAML options to code for dot/mermaid/ojs chunks so that the full chunk content can be returned to Quarto add trailing slashes to URLs use the `assert(fact, {})` syntax for all tests revert c9473ad: map the chunk option `tbl-cap` to `tab.cap` leave tbl.cap alone; don't convert it to tab.cap, since Quarto has its own special handling of `tbl-cap` Create FUNDING.yml use xfun::decimal_dot() to ensure dot as the decimal separator fix rstudio/rmarkdown#2525: ensure the dot is used as the decimal separator even when options(OutDec) is not `.` or `LC_NUMERIC` is inappropriate factor out code to xfun::csv_options() and xfun::divide_chunk() get_option_comment() has been moved to xfun roxygenize bump xfun version xfun 0.42 is on CRAN now revert 87d094a6c593c31a3667821865e91b4a530018ec per request from CRAN maintainers, since _R_CHECK_VIGNETTES_SKIP_RUN_MAYBE_=true has been made the default fix rstudio/tinytex#435: adjust PATH temporarily for pdf_crop() to be able to find the command `pdfcrop` from TinyTeX RStudio IDE still calls parse_params(): https://github.com/rstudio/rstudio/blob/9a6196233d8eae5aa365b73eaafba04f7714190c/src/cpp/session/modules/SessionRmdNotebook.R#L666 a follow-up on #2331: use xfun::fenced_block() from yihui/xfun@22a97ce xfun 0.43 is on CRAN now not sure what's wrong with pak `knitr::imgur_upload()` is now simply a wrapper function of `xfun::upload_imgur()` (#2325) too many ways to do the same thing... drop support for `#-` in spin() make spin() work again with input that can't be parsed as R code use xfun::check_old_package() markdown no longer sets this option internally, so no need to empty it now better detection of Rmd v2 input in knit2html(), so it no longer warns against documents that use markdown:: or litedown:: output formats make regex a little stricter so it won't match rmarkdown:: the loo issue has been fixed (#2306) roxygen2 requires _PACKAGE now rename class names 'block' to 'knitr_block', and 'inline' to 'knitr_inline' since I need to export the print() methods and the names 'block' and 'inline' are too general preserve trailing \n in source code by doubling it, because later we will remove trailing \n in fenced_block() a temporary workaround for davidgohel/flextable#621 StructFDR has been updated on CRAN but unfortunately the maintainer didn't seem to have seen my email about #2306 I can't use knitr_block/knitr_inline as class names since it would break the lightparser package; let me just get rid of these S3 methods, which are unnecessarily advanced---just use normal functions instead (i.e., use inherits() to do the dispatch by myself) CRAN release v1.46 knokknok (1): fix #2318: faster processing of dependencies in dep_auto() (#2321)
I am trying to install
pdfcrop
usingtinytex
0.37 in R 4.3.2 on Ubuntu 22.04.3 LTS. I get the following when I runtinytex::tlmgr_install("pdfcrop")
:It seems it is trying to create a directory called
/home/runner
. If I create that directory myself outside of R and then reruntinytex::tlmgr_install("pdfcrop")
, I get:Looking in
/home/runner/bin
I see thatpdfcrop
is indeed present, but this directory does not seem to be on the path, sohas_utility
cannot find it.Cryptically, if
has_utility
fails to findpdfcrop
, thenknitr::plot_crop
just returns the input filename with no message, which had me stumped for a bit.By filing an issue to this repo, I promise that
xfun::session_info('tinytex')
. I have upgraded all my packages to their latest versions (e.g., R, RStudio, and R packages), and also tried the development version:remotes::install_github('rstudio/tinytex')
.I understand that my issue may be closed if I don't fulfill my promises.
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