Recent Upgrade causes knit not to work.

jabunch · May 18, 2021, 5:04pm

I recently upgraded R to 4.0.5 and Rstudio to Version 1.4.1106.
When I run *.rmd files that executed fine previously they work fine when I execute them within Rstudio chunk by chunk. However, when I try to knit them to an html file I get the following error:

output file: VISSIMTravelTimer2.knit.md

Error: 'set_envvar' is not an exported object from 'namespace:xfun'
Execution halted.

I have tried to delete the rdata file. and also set any write statements to use the full rather than relative paths.
Nothing seems to work, and the knit fails for all projects that I have previously stored.

What can I do to fix this?
Also, where is the above output *.md file stored.

JAB

cderv · May 18, 2021, 5:40pm

Did you try updating the package version ? It seems updating R and RStudio have created a mismatch between version and your knitr or rmarkdown version needs some newer xfun

Can you update xfun, knitr and rmarkdown and see how it goes ? it should fix this.

Keeps me updated.

nicola0 · June 1, 2021, 9:31am

Hi, I'm having the same issue - recently updated R and RStudio to versions 4.1.0 and 1.4.1106 respectively, and updated all packages (including xfun, knitr and rmarkdown). I can't knit .rmd files to pdf or html anymore. I am getting this error message

sh: rmarkdown::render: command not found
Warning message:
In system(paste0("rmarkdown::render '", input, "'")) :
error in running command

Please do you have any advice how to fix this?

Thanks

cderv · June 1, 2021, 9:42am

This is a weird issue that is happening recently. See

github.com/rstudio/rmarkdown

render not found

opened 07:54AM - 21 Dec 20 UTC

closed 01:31PM - 12 Oct 21 UTC

data-al

bug RStudio IDE

After installing the latest `rmarkdown` package i have this issue trying to knit… the default or any other .rmd : ``` [1] 127 Warning message: In system(paste0("rmarkdown::render '", input, "'")) : 'rmarkdown::render' not found ``` No document is produced. I'm guessing it's some kind of problem with finding the function of the package ? Any guidance is appreciated > xfun::session_info('rmarkdown') R version 4.0.2 (2020-06-22) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18363), RStudio 1.4.1074 Locale: LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C LC_TIME=English_United Kingdom.1252 Package version: base64enc_0.1.3 digest_0.6.27 evaluate_0.14 glue_1.4.2 graphics_4.0.2 grDevices_4.0.2 highr_0.8 htmltools_0.5.0 jsonlite_1.7.1 knitr_1.30 magrittr_1.5 markdown_1.1 methods_4.0.2 mime_0.9 rlang_0.4.8 rmarkdown_2.6 stats_4.0.2 stringi_1.5.3 stringr_1.4.0 tinytex_0.27 tools_4.0.2 utils_4.0.2 xfun_0.19 yaml_2.2.1 Warning messages: 1: In get(Info[i, 1], envir = env) : internal error -3 in R_decompress1 2: In get(Info[i, 1], envir = env) : internal error -3 in R_decompress1 3: In get(Info[i, 1], envir = env) : internal error -3 in R_decompress1 4: In get(Info[i, 1], envir = env) : internal error -3 in R_decompress1 5: In get(Info[i, 1], envir = env) : internal error -3 in R_decompress1 6: In get(Info[i, 1], envir = env) : internal error -3 in R_decompress1 --- By filing an issue to this repo, I promise that - [x] I have fully read the issue guide at https://yihui.org/issue/. - [x] I have provided the necessary information about my issue. - If I'm asking a question, I have already asked it on Stack Overflow or RStudio Community, waited for at least 24 hours, and included a link to my question there. - If I'm filing a bug report, I have included a minimal, self-contained, and reproducible example, and have also included `xfun::session_info('rmarkdown')`. 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/rmarkdown')`. - If I have posted the same issue elsewhere, I have also mentioned it in this issue. - [x] I have learned the Github Markdown syntax, and formatted my issue correctly. I understand that my issue may be closed if I don't fulfill my promises.

We don't really know how to reproduce and what triggers it.

Last hint on this was something related to a .libPaths() were packages are stored. Is your library local or shared on a network ?

Please report in the issue above with useful info you have so that we can try fix this definitely.

Thanks!

nicola0 · June 1, 2021, 9:52am

Thank you. I have my R packages in a local library. I copied all my packages across from the past R library folder, and updated them all to their most recent versions. I'll look at the thread you have linked, hopefully it might have a solution!

cderv · June 1, 2021, 10:09am

We don't have obvious solution yet. The error you get is throw by RStudio IDE and it only happens if rmarkdown package was not found by RStudio IDE (meaning rmarkdown::render() is not seen as a valid R function )

Do you think of something that would cause RStudio IDE to not found your library ?
Can you do library(rmarkdown) with success in the console ? What is your lib path .libPaths() ?

nicola0 · June 1, 2021, 10:12am

Actually I just tried that, and although I can see rmarkdown in the library, I get this error

library(rmarkdown)
Error: package or namespace load failed for ‘rmarkdown’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/digest/libs/digest.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.1/Resources/library/digest/libs/digest.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/digest/libs/digest.so
Reason: image not found

nicola0 · June 1, 2021, 10:16am

PS > .libPaths()
[1] "/Library/Frameworks/R.framework/Versions/4.1/Resources/library"

cderv · June 1, 2021, 10:28am

So that is why you get the error I believe, because rmarkdown is not correctly installed.

Can you reinstall digest, then rmarkdown ?

install.packages("digest")
install.packages("rmarkdown")

Thanks

nicola0 · June 1, 2021, 10:38am

digest is corrupt?

Error: package or namespace load failed for ‘rmarkdown’ in get(Info[i, 1], envir = env):
lazy-load database '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/digest/R/digest.rdb' is corrupt
In addition: Warning message:
In get(Info[i, 1], envir = env) : internal error -3 in R_decompress1

cderv · June 1, 2021, 10:39am

Yes it seems. Did you reinstall it ? Did that went well ?

nicola0 · June 1, 2021, 10:43am

Yes, I installed them both, and that seemed fine, but library(digest) or library(markdown) gives that error about digest being corrupt...

cderv · June 1, 2021, 10:49am

digest installation is not going well. You should close everything R related. Then open R console and re try installing digest. Only this one. Then look at the installation messages to see if everything is fine. Then try library(digest) to see if it is loaded.

It is required by rmarkdown to work so you need to have this package installed.

I am not on Mac, so I don't know if there is anything to watch out specifically for this package

nicola0 · June 1, 2021, 11:21am

OK - some things are starting to work now - I had also to install htmltools, magrittr and jsonlite and then rmarkdown again to get the default .rmd in Rstudio to knit to a pdf and html document.

Also, not specifically an rmarkdown issue, but it looks as though I'll need to install various dependencies for other packages to work too.

Thanks for your help !

cderv · June 1, 2021, 12:20pm

It is possible that you library got corrupted. This happened to me in the past.
You need to reinstall everything, or try to identify the faulty packages (using a for loop to load package and catch error for example) and reinstall those.

You issue helped me understand more what happens so thanks!

nicola0 · June 1, 2021, 12:29pm

I've been working through reinstallations which has been a lengthy process - the only way it seemed to work was to quit R between every installation to get packages to reinstall correctly. Everything I need is working now though so thanks again

cderv · June 1, 2021, 12:38pm

You may be interested in using pak

This is a great R package for packages quick and safe package installation.

Install from here and use pak::pak()

install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")

One of the feature is to install in its own process, detect already loaded packages and more.

nkrishel · June 14, 2021, 8:32pm

I had this same issue with the default .rmd file in RStudio failing to knit after updating the rmarkdown package. Following the above advice to reinstall both digest and rmarkdown solved the issue for me. Thanks!

startz · June 17, 2021, 11:25pm

I have a similar issue--running on Windows 10. I have removed and reinstalled both digest and rmarkdown to no avail. When I hit knit I get told "Rendering R Markdown requires an updated version of the rmarkdown package." (I currently have version 2.8. I am running RStudio 1.4.1717 and R 4.0.5.)

The install fails with

Error in namespaceExport(ns, exports) : 
  undefined exports: Rcmd, Rscript, Rscript_call, as_strict_list, base64_decode, base64_encode, base64_uri, bg_process, broken_packages, bump_version, cache_rds, check_old_package, check_package_name, compare_Rcheck, del_empty_dir, dir_create, dir_exists, do_once, download_file, embed_dir, embed_file, embed_files, exit_call, file_exists, file_ext, file_string, format_bytes, from_root, github_releases, grep_sub, gsub_dir, gsub_ext, gsub_file, gsub_files, in_dir, install_dir, install_github, is_CRAN_incoming, is_R_CMD_check, is_abs_path, is_ascii, is_linux, is_macos, is_rel_path, is_sub_path, is_unix, is_web_path, is_windows, json_vector, loadable, magic_path, mark_dirs, msg_cat, n2w, native_encode, news2md, normalize_path, numbers_to_words, optipng, parse_only, pkg_attach, pkg_attach2, pkg_available, pkg_load, pkg_load2, proc_kill, process_file, proj_root, prose_index, protect_math, raw_string, read_bin, read_utf8, relative_path, rename_seq, retry, rev_check, root_rules, rstudio
Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace -> namespaceExport
Execution halted
ERROR: lazy loading failed for package 'rmarkdown'
* removing 'C:/Users/Dick/Documents/R/win-library/4.0/rmarkdown'
Warning in install.packages :
  installation of package ‘rmarkdown’ had non-zero exit status

cderv · June 18, 2021, 4:38am

Hi @startz

Can you check you have the package xfun installed ?

You need this package in its last version. It should have been installed with Rmarkdown but it seems it is not correctly are functions are not correctly found.

Just try to reinstall xfun then rmarkdown