render not found #1990
Comments
Can you be more precise about what you are doing ? What I did :
This will render the file correctly without any error. I let you restart RStudio and R, and try again. Thank you. |
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In case it is helpful to anyone: I got this error today after an R version 4.0.4 update. I solved it by updating
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This error is still puzzling to me. I am not sure to see how tinytex R package relates to [1] 127
Warning message:
In system(paste0("rmarkdown::render '", input, "'")) :
'rmarkdown::render' not foundIs this with a pdf file ? That would indeed require tinytex, but the error is not very informative. I would like to improve that. If you can share anything to help us reproduce and / or identify the cause that would help. Thank you |
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It is indeed puzzling. After updating R to the latest version (4.0.4), trying to knit a markdown doc (even the default Rmd, without added code) to pdf would throw that error (I know it says warning, but it will not knit). I closed and opened Rstudio again and the same thing. I updated the As an aside, I did initially try knitting to html as well, which didn't work either at first. It now does work. I am assuming updating |
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Thanks for sharing. Let's see if other encounter the same thing. |
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I am having the same issue. I've updated R and all the packages. Restarted R. But still I get this error message |
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@JosephLazarus Can you share your R version and R Studio version ? We need more information to be able to reproduce and fix this issue. I'll reopen in the meantime. thanks! |
cderv
added
bug
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I quickly search for the code |
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Yes I did exactly the same thing but did not found any hit. I am really curious where this comes from. 🤔 |
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Oh in fact I recall where I saw that! and it is the only hint I have: RStudio IDE does this paste thing in here: However, this should only be activated (the pasting) if So there is a state where rmarkdown is not available when this code is run and this cause this error I believe. I'll try to reproduce this state maybe. What do you think ? |
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Yeah I can't reproduce - if you don't have rmarkdown installed, clicking the knit button will asked you to install it. And after that no error. Maybe this is tied to a specific rstudio version and this has been fixed ? I tried daily and preview. |
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@data-al @dylangomes @JosephLazarus which version of RStudio are you using ? which OS are you on ? Considering the above hint, it could be link a RStudio IDE and maybe the last version solve this. Can you share with us the information ? and maybe update to last released version of RStudio IDE ? |
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Hello, I encountered the same issue with the same error message few times already. Today I tried If it helps in any way:
Thank you |
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@souckmi sorry you also hit this issue. Which is your RStudio version please ? |
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My RStudio version is 1.4.1103. Unfortunately I cannot say more than what was already said here. It seems to happen quite random, but if it occurs again I will try my best to give more information about what preceded. |
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Can you upgrade to last release bug fix version which is 1.4.1106 ? This last version was released shortly after first 1.4 release as a bugfix version. It is possible that this comes from RStudio and it has been fixed already. Thank you! |
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Sure! I will let you know if I encounter it sometime anyway after that. |
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I also encountered this issue today. It was solved after following @dylangomes suggestion to re-install tinytex. Thanks for the information. |
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Thanks for sharing @fytsai. |
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This is such a funny mystery to us. I can't imagine why the tinytex package could be relevant. If we can ever figure it out, it might become an inspiration for me to write a mystery book someday :) |
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I was able to get it out of this error by reinstalling the htmltools and jsonlite packages. |
This now gets even weirder for us. It is really a funny mystery... how those package could be link to that ? Our best guess was something related to RStudio version. 🤔 we have still no clue to where this comes from unfortunately. |
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I had a similar issue but by changing the file name was able to knit to pdf again. |
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What was your filename in the first place ? Any information you think could be useful will help us. And sorry you encountered this. |
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So the original file name was "Yahoo-Tumblr Case Study", and when I changed it to "Yahoo-Tumblr Case Study Final Version" I could suddenly knit to pdf again with out the render error. After doing a bit more work the error showed up again so I saved it as Version 2 and it was able to knit once again. Prior to the error occurring I had tried import a bunch of packages like imager, shiny to find the best way to display an image. When I tried to load Bioconductor using the code below I got a spinning wheel and I think that was when I first wasn't able to knit to pdf. if (!requireNamespace("BiocManager", quietly = TRUE)) Before I got to the render error I first had to deal with another error. My installed packages like ggplot and xts returned "Error: package ‘ggplot2’ could not be loaded" so I tried to reinstall them, and then reinstalled R and Rstudio which solved the problem. Then when I tried to knit to pdf I ran into the render issue. So in a hail mary I changed the file name and everything worked, and I liked R and Rstudio again. Hope this is helpful. |
🤯 I would have used this function a lot - This is really useful! So many things hidden. Too bad it is not working on Windows (forking not available) - I may try to fix it. |
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I encountered the same issue as well and this is funny because it occurs after I tried to debug under the guide of Yihui's website... |
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Hahaha the reinstall of RStudio really worked! Just remember to reinstall both the RStudio and the LaTex again. |
HughParsonage (1):
Include PACKAGE arg to avoid unresolved namespace (#53)
Liming (1):
fix #54: iterate through the rules correctly in proj_root() (#55)
Yihui Xie (8):
start the next version
improve, document, and export the broken_packages() function (rstudio/rmarkdown#1990 (comment))
roxygenize and bump version
don't use parallel, to make it work on Windows
add a news item
add a news item
add a global option to keep the intermediate .md file after converting it to .html
CRAN release v0.24
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Hello, I have this issue, I will try to give as much detail to help.
R history : install.packages('flexdashboard')
install.packages('shiny')
install.packages("remotes")
remotes::install_github("rstudio/bslib")
library(ggplot2)
renderPlot({
ggplot(mpg, aes(displ, hwy)) +
geom_point() + geom_smooth()
})
?renderPlot
??renderPlot
library(shiny)
renderPlot({
plot(pressure, col = thematic::thematic_get_option("accent"))
})
library(flexdashboard)
install.packages('flexdashboard')
library(flexdashboard)
library(flexdashboard)
install.packages('markdown')
library(flexdashboard)
install.packages("rlang")
install.packages("rlang")
install.packages("rlang")
install.packages("rlang")
install.packages("rlang")
library(flexdashboard)
install.packages("rlang")
install.packages("rlang")
install.packages("rlang")
install.packages("rlang")
install.packages("rlang")
install.packages("rlang")
install.packages("rlang")
install.packages("rlang")
library(flexdashboard)
library(rlang)
sessionInfo()
remove.packages(rlang)
remove.packages('rlang')
install.packages('rlang')
install.packages("rlang")
library(flexdashboard)
library(rlang)
sessionInfo()
remove.packages("rlang")
library(flexdashboard)
install.packages('rlang 0.4.11.9000')
install.packages('markdown')
install.packages('rlang')
install.packages("rlang")
install.packages("rmarkdown")
knitr::opts_chunk$set(echo = TRUE)
summary(cars)
plot(pressure)
install.packages('knitr')
install.packages("knitr")
install.packages("knitr")
install.packages("knitr")
install.packages("knitr")
install.packages("knitr")
install.packages("knitr")
install.packages("knitr")
install.packages('xfun')
install.packages("xfun")
install.packages("xfun")`Terminal > sh: rmarkdown::render: command not found
Warning message:
In system(paste0("rmarkdown::render '", input, "'")) :
error in running command`> library(flexdashboard)
Error: package or namespace load failed for ‘flexdashboard’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
namespace ‘rlang’ 0.4.11 is already loaded, but >= 0.4.11.9000 is required`
> install.packages('markdown')
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/markdown_1.1.tgz'
Content type 'application/x-gzip' length 198809 bytes (194 KB)
==================================================
downloaded 194 KB
> The downloaded binary packages are in
/var/folders/1g/ylfgpc813936cj34f1zs1h1h0000gn/T//RtmpdUw2cP/downloaded_packages
> install.packages('rlang')
Error in install.packages : Updating loaded packages
Restarting R session...
> install.packages("rlang")
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/rlang_0.4.11.tgz'
Content type 'application/x-gzip' length 1328785 bytes (1.3 MB)
==================================================
downloaded 1.3 MB
The downloaded binary packages are in
/var/folders/1g/ylfgpc813936cj34f1zs1h1h0000gn/T//Rtmp10BDdY/downloaded_packages
> install.packages("rmarkdown")
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/rmarkdown_2.9.tgz'
Content type 'application/x-gzip' length 3635877 bytes (3.5 MB)
==================================================
downloaded 3.5 MB
The downloaded binary packages are in
/var/folders/1g/ylfgpc813936cj34f1zs1h1h0000gn/T//Rtmp10BDdY/downloaded_packages
> knitr::opts_chunk$set(echo = TRUE)
> summary(cars)`
## the cars data loads inside the Rmd file but knit keeps giving errors. The message box goes into a loop of asking to restart the session, only clicking No does it try to install the package
> `install.packages("knitr")
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/knitr_1.33.tgz'
Content type 'application/x-gzip' length 1410317 bytes (1.3 MB)
==================================================
downloaded 1.3 MB
The downloaded binary packages are in
/var/folders/1g/ylfgpc813936cj34f1zs1h1h0000gn/T//Rtmpix9XqG/downloaded_packages
> install.packages('xfun')
Error in install.packages : Updating loaded packages
Restarting R session...
> install.packages("xfun")
Error in install.packages : Updating loaded packages
> install.packages("xfun")
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/xfun_0.24.tgz'
Content type 'application/x-gzip' length 340207 bytes (332 KB)
==================================================
downloaded 332 KB
> The downloaded binary packages are in
/var/folders/1g/ylfgpc813936cj34f1zs1h1h0000gn/T//Rtmp3M0ZRX/downloaded_packages`
## and one more time installing/updating rmarkdown
> `install.packages('rmarkdown')
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/rmarkdown_2.9.tgz'
Content type 'application/x-gzip' length 3635877 bytes (3.5 MB)
==================================================
downloaded 3.5 MB
> The downloaded binary packages are in
/var/folders/1g/ylfgpc813936cj34f1zs1h1h0000gn/T//Rtmp3M0ZRX/downloaded_packagesHope this helps find the error. I just wanted to try out a flexdashboard with the bslib theme. I uninstalled, reinstalled rlang just in case that was missed. |
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Please next time, format your issue correctly so that it is correctly readable (https://docs.github.com/en/github/writing-on-github/getting-started-with-writing-and-formatting-on-github/basic-writing-and-formatting-syntax). For this time, I edited your post. The issue is due to a corrupted packages library. In your case it could have been rlang but maybe other. Please reinstall rmarkdown correctly. You can install the last version of xfun and use If |
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The same happened to me now as well I get this message: I have the latest version of RStudio (Version 1.4.1717), reinstalled all the packages etc. The only thing that eventually worked was to reinstall RStudio entirely. |
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There is now a fix pushed in RStudio IDE codebase. If everything is ok, it should be available soon in the next daily build of Rstudio. |
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@cderv Thanks, |
# CHANGES IN xfun VERSION 0.25 - Fixed a bug in `broken_packages()` (thanks, @PythonCoderUnicorn, rstudio/rmarkdown#1990). - Added a `files` argument to `optipng()` so that users can specify the list of PNG files instead of running `optipng` on a whole directory. # CHANGES IN xfun VERSION 0.24 - Exported the internal function `broken_packages()` to reinstall broken R packages. - Fixed the bug in `proj_root()` #54 (thanks, @clarkliming).
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Hello, After reading the other comments, when I tried
I obeyed the message and reinstalled Each time, I reinstalled more packages, and now it works I have had many of this kind of errors today in R script files, probably because after switching from R 3.something to R 4.1.1, I copied my entire old package library into the new one, and updated. Updating seems not to be enough for R 4.1.1. It might be the cause for the Could that help? |
Yes I also think this is the case ! Your story complete the one above and confirm this. As I mentioned in #1990 (comment), it should be fixed in last RStudio version. But we did not had confirmation yet. And as Yihui mentioned in #1990 (comment), there is a function For the context, the issue you have while upgrading R is because Packages needs to be rebuild when a Major version of R changes (even when a minor version it could be a good idea). Thanks for sharing ! That is helpful for us and others ! |
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I am an infrequent Markdown user and I have just stumbled across the same issue. I am running R 4.1.1 and RStudio 2021.09.0 build 351 (which I uninstalled and reinstalled). I have updated ALL packages. I ran xfun::broken_packages() and it complained only that the package translations could not be updated. When I Knit a markdown document from the RStudio command line I get a rendered html document. When I execute knitr::knit(markdown_file.Rmd), it knits the file into markdown_file.md. However, when I execute markdown::render(markdown_file.md) I get: Error: 'render' is not an exported object from 'namespace:markdown'. |
I don't think this is related to this issue. The error you see is saying that the markdown R package (https://github.com/rstudio/markdown) has not Please try the correction call |
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I'll close this issue because the new release of RStudio IDE contains a fix for this. Please install newer version of RStudio if you stumble accross this. Version above 20201.09.0+351. |
I also had the issue (RStudio Server Version 1.4.1717) and tried loading rmarkdown: > library(rmarkdown)
Error: package or namespace load failed for ‘rmarkdown’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
namespace ‘xfun’ 0.24 is being loaded, but >= 0.27 is requiredUpdating xfun |
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I am getting the same issue. It all started when I tried to install |
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rmarkdown uses some packages that depends on fastmap > pak::pkg_deps_explain("rmarkdown", "fastmap")
v Updated metadata database: 3.97 MB in 5 files.
v Updating metadata database ... done
rmarkdown -> htmltools -> fastmap
rmarkdown -> jquerylib -> htmltools -> fastmapSo if there was an issue with fastmap installation, then those packages wouldn't load, and rmarkdown etiher. Anyway, I don't think this was related to this issue here. Glad you found the fix ! |
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Can confirm that I too had this error which was fixed after I installed Details about my setup: |
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I also met this issue. It happened when I'm trying to run |
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Hi all, sorry to revive this from August. I had the same issue today using R 4.1.0 and RStudio 1.4.1717 (I'm on a managed software catalog so cannot update). Neither installing
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Thanks for sharing this - I did not know this could be a side effect of this minimum requirement issue. |
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This old thread has been automatically locked. If you think you have found something related to this, please open a new issue by following the issue guide (https://yihui.org/issue/), and link to this old issue if necessary. |
and others
After installing the latest
rmarkdownpackage i have this issue trying to knit the default or any other .rmd :No document is produced. I'm guessing it's some kind of problem with finding the function of the package ? Any guidance is appreciated
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
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').I understand that my issue may be closed if I don't fulfill my promises.
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