Every time I run into an error while knitting a script that stops execution, RStudio behaves in a weird way: In the R markdown tab it reads in red that the execution is stopped but in the R markdown tab I see the continuing progress circle still moving, suggesting that knitting is still ongoing. Also on the right hand I see that "stop" sign but clicking on it also does not stop executing. I can still write text in the script but I can no longer execute the script and can also not kick off a new knitting attempt.
The only way of going back to normal is top close Rstudio and re-start it. That means, everytime I run into any kind of error while knitting I have to restart Rstudio. This does not occur on my private PC with the same scripts.
I have installed a new version of Rstudio (the new 1.4 Preview) and I have re-installed R Markdown. Do you have any tips?
edit:
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)
Matrix products: default
Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding
locale:
[1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=German_Germany.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
other attached packages:
[1] rmarkdown_2.5
loaded via a namespace (and not attached):
[1] rstudioapi_0.13 knitr_1.30 magrittr_2.0.1 tidyselect_1.1.0
[5] R6_2.5.0 rlang_0.4.9 dplyr_1.0.2 tools_4.0.3
[9] xfun_0.19 pacman_0.5.1 htmltools_0.5.0 ellipsis_0.3.1
[13] yaml_2.2.1 digest_0.6.27 tibble_3.0.4 lifecycle_0.2.0
[17] crayon_1.3.4 purrr_0.3.4 tidyr_1.1.2 vctrs_0.3.5
[21] clisymbols_1.2.0 glue_1.4.2 evaluate_0.14 compiler_4.0.3
[25] pillar_1.4.7 generics_0.1.0 pkgconfig_2.0.3 tidylog_1.0.2
Related
I have ggplot2 3.4.0 installed on Ubuntu 22.04, but for some reasons I would like to use older version ggplot2 3.3.6.
library(ggplot2, lib.loc="~/R/ggplot336/")
I worked fine when I started with a clean script file. However, when I use an existing script file like:
library(ggplot2, lib.loc="~/R/ggplot336/")
ggimage::geom_image()
I got the following error massage:
Error in value[3L] :
Package ‘ggplot2’ version 3.4.0 cannot be unloaded:
Error in unloadNamespace(package) : namespace ‘ggplot2’ is imported by ‘ggfun’, ‘ggplotify’, ‘ggimage’ so cannot be unloaded
Edit
Fresh start Rstudio
Open my R script file with following 3 lines:
sessionInfo()
library(ggplot2, lib.loc="~/R/ggplot336/")
ggimage::geom_image()
When I run the first line, sessionInfo() before doing anything else. We can see ggplot2_3.4.0 there. Could this be a Rstudio feature or an issue?
R version 4.2.2 Patched (2022-11-10 r83330)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C LC_TIME=en_AU.UTF-8
[4] LC_COLLATE=en_AU.UTF-8 LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 highr_0.9 pillar_1.8.1 compiler_4.2.2
[5] R.utils_2.12.2 R.methodsS3_1.8.2 yulab.utils_0.0.5 tools_4.2.2
[9] digest_0.6.30 evaluate_0.18 jsonlite_1.8.3 lifecycle_1.0.3
[13] tibble_3.1.8 gtable_0.3.1 ggimage_0.3.1 R.cache_0.16.0
[17] pkgconfig_2.0.3 rlang_1.0.6 reprex_2.0.2 DBI_1.1.3
[21] cli_3.4.1 ggplotify_0.1.0 rstudioapi_0.14 magick_2.7.3
[25] yaml_2.3.6 xfun_0.35 fastmap_1.1.0 knitr_1.41
[29] withr_2.5.0 dplyr_1.0.10 styler_1.8.1 generics_0.1.3
[33] vctrs_0.5.1 fs_1.5.2 gridGraphics_0.5-1 grid_4.2.2
[37] tidyselect_1.2.0 glue_1.6.2 R6_2.5.1 processx_3.8.0
[41] fansi_1.0.3 rmarkdown_2.18 clipr_0.8.0 callr_3.7.3
[45] ggplot2_3.4.0 purrr_0.3.5 magrittr_2.0.3 ps_1.7.2
[49] htmltools_0.5.3 scales_1.2.1 assertthat_0.2.1 colorspace_2.0-3
[53] utf8_1.2.2 munsell_0.5.0 ggfun_0.0.9 R.oo_1.25.0
It looks like R studio is loading in all of the previous libraries from a previous session. Maybe something leftover in .RData or .Rhistory. A fresh start of R should have far few loaded libraries.
Here is my fresh start:
sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.6.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/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_4.2.2 tools_4.2.2
In Rstudio's preference you should see this screen:
I would try unchecking all of the boxes and then quit and restart Rstudio to see if that clears up the problem.
After some experiments, I kind of worked out the problem. Since this has consumed so much time of my time, I thought this could be helpful to others.
The problem is :: (double colon) with packages using ggplot2, such as ggimage in my example. It appears that RStudio automatically load some dependent packages when a script file is open. One way to fix this problem for my work now is to remove ::, but use library() then function (geom_image) instead.
This fixed my problem but I still don't understand why RStudio behaves this way.
If :: (double colon) is necessary, comment lines containing ::, then after loading older version of ggplot2, uncomment those lines. A little awkward, but it works for me.
My website used to work fine in my previous laptop, which used R 3.6.3. In my new laptop when I run blogdown::serve_site() I get the error Error in !server$daemon : invalid argument type. I tried doing what was suggested here but didn't help.
Here is the session info:
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.2.3
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 bookdown_0.22 digest_0.6.27 later_1.2.0 R6_2.5.0
[6] jsonlite_1.7.2 magrittr_2.0.1 evaluate_0.14 blogdown_1.3.2 rlang_0.4.11
[11] rstudioapi_0.13 promises_1.2.0.1 rmarkdown_2.9 tools_4.1.0 servr_0.22
[16] httpuv_1.6.1 xfun_0.24 yaml_2.2.1 compiler_4.1.0 htmltools_0.5.1.1
[21] knitr_1.33
This is the website link and you can find the Github repo here.
You should remove the quotes on interactive(). It should be
servr.daemon = interactive()
instead of
servr.daemon = "interactive()"
Actually servr.daemon = interactive() is the default, so you don't really need to set it explicitly (i.e., you can remove this setting).
This issue shook me. Lets a minimal reproducible example:
On RStudio, create a New Project... Choose Shiny Web App. Check that sample app runs well.
Create inside the standard R folder, to put all your *.R scripts.
Create a dummy script inside the R folder that fails, but you do not want run yet. For example
str(do_not_exist) ## foo.R
4.Run the App again. Now, the App fails
> runApp()
Error in str(do_not_exist) : objeto 'do_not_exist' no encontrado
Why Shiny runs undesirable scripts? They are OUT of the root directory.
I am not finding ways to save scripts that are not functions within the project.
This is my R Session
> sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=Spanish_Argentina.1252 LC_CTYPE=Spanish_Argentina.1252
[3] LC_MONETARY=Spanish_Argentina.1252 LC_NUMERIC=C
[5] LC_TIME=Spanish_Argentina.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] tidyr_1.1.3 dplyr_1.0.5 openxlsx_4.2.3.9000 shiny_1.6.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 magrittr_2.0.1 tidyselect_1.1.0 xtable_1.8-4
[5] R6_2.5.0 rlang_0.4.10 fastmap_1.1.0 fansi_0.4.2
[9] tools_4.0.5 utf8_1.2.1 DBI_1.1.1 withr_2.4.2
[13] htmltools_0.5.1.1 ellipsis_0.3.1 assertthat_0.2.1 digest_0.6.27
[17] tibble_3.1.1 lifecycle_1.0.0 crayon_1.4.1 zip_2.1.1
[21] purrr_0.3.4 later_1.1.0.1 vctrs_0.3.7 promises_1.2.0.1
[25] glue_1.4.2 mime_0.10 stringi_1.5.3 compiler_4.0.5
[29] pillar_1.6.0 generics_0.1.0 httpuv_1.5.5 pkgconfig_2.0.3
See here. One option is options(shiny.autoload.r = FALSE).
I have successfully used save_kable() from kableExtra to export latex tables into *.png before. However, after updating R to the version 4.0.2, save_kable always ends with R fatal error (no specific error message is shown, the session is just aborted). I installed a clean version o R 3.6.3 and everything works fine again.
Next, I re-installed MikTEX, but this does not seem to be the problem because R Markdown can knit a .pdf file without an issue (in the 4.0.2 version). Also, using save_kable with "html" options works fine and exports the table into .png. The problem seems to be specific for latex.
Looking at sessionInfo(), the only difference is that R 3.6.3 automatically loads the 'magick' package, while R 4.0.2 does not. However, loading the magick package manually in the latter R version does not solve the problem. Then, of course, the sessions differ in the "compiler" package versions. Maybe this is the source of the problem?
Any help would be much appreciated. The problem can be reproduced with minimal code such as
kable(mtcars, "latex") %>% save_kable("test.png")
Here is the sessionInfo
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)
Matrix products: default
Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] magick_2.4.0 kableExtra_1.1.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 rstudioapi_0.11 knitr_1.29 xml2_1.3.2 magrittr_1.5
[6] hms_0.5.3 rvest_0.3.5 munsell_0.5.0 viridisLite_0.3.0 colorspace_1.4-1
[11] R6_2.4.1 rlang_0.4.7 stringr_1.4.0 httr_1.4.1 tools_4.0.2
[16] webshot_0.5.2 xfun_0.15 htmltools_0.5.0 ellipsis_0.3.1 digest_0.6.25
[21] tibble_3.0.3 lifecycle_0.2.0 crayon_1.3.4 readr_1.3.1 vctrs_0.3.2
[26] glue_1.4.1 evaluate_0.14 rmarkdown_2.3 stringi_1.4.6 compiler_4.0.2
[31] pillar_1.4.6 scales_1.1.1 pkgconfig_2.0.3
This seems to be a windows specific problem. I actually just asked a recent question here
kableExtra HTML styling in Rmarkdown and kable_save()
Some of the things I have seen mentioned as potential fixes are listed there such as updating ghostscript, not using tinytext, updating some latex packages including 'standalone', and editing the policy.xls document in ImageMagick ImageMagick security policy 'PDF' blocking conversion.
None of these worked for me and I get the same crashing issues the second I try to kable_save a latex format into png. However, some other Windows users have found success with the steps above so maybe try that out and see how it goes.
I'm trying to deploy on a private server an app that allows me to edit an RHandsontable object. For privacy reasons I cannot be showing a demonstration here.
I have successfully tested my app locally, but when I deploy it on my server the RHandsontable doesn't display, and the app "screen goes gray" after I start interacting there, so it doesn't allow any further interactions there.
This is how it looks on my Windows 10 browser. You can even see a 2 rhandsontables (that are empty because it has no selection whatsoever), that can be edited. The "Guardar" button is currently a dummy.
This is how it looks on AWS Ubuntu 18.04 Shiny Server. No rhandsontable loads (though the button loads). Same script, just different directories. I verified that the data loaded into both shiny apps were the same. You can also appreciate that the dummy button "Guardar" still appears.
I tried the same rendering equivalent data.tables from both the shiny and DT packages, leading to the same results as shown above.
Also, when I check my server logs at /var/log/shiny-server/ no issue arises (eg.: missing packages, broken code, etc). Last log goes as follows:
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Attaching package: ‘DT’
The following objects are masked from ‘package:shiny’:
dataTableOutput, renderDataTable
Listening on http://127.0.0.1:41757
This suggests me that I have a compatibility / interaction issue that arises in Shiny Server or in Ubuntu that doesn't arise in my PC.
I have seen different sources in Stack Overflow and in jrowen's GitHub page without any success, and I'd like to know if I'm missing anything.
There's a minor difference between R version between both machines (my Ubuntu VM is fresh, so some packages are updated). This could also cause a problem, but I'm not positive this could be the reason.
I also installed JRE on both instances (I also thought this could be caused due to a Java issue that I haven't fixed properly). Running java -version on my VM yields
openjdk version "10.0.2" 2018-07-17
OpenJDK Runtime Environment (build 10.0.2+13-Ubuntu-1ubuntu0.18.04.4)
OpenJDK 64-Bit Server VM (build 10.0.2+13-Ubuntu-1ubuntu0.18.04.4, mixed mode)
My personal computer is a Windows 10 Machine. Details:
R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252
[3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C
[5] LC_TIME=Spanish_Spain.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] readxl_1.1.0 lubridate_1.7.4 mailR_0.4.1 forcats_0.3.0
[5] stringr_1.3.1 purrr_0.2.5 readr_1.1.1 tidyr_0.8.1
[9] tibble_2.0.1 ggplot2_3.0.0.9000 tidyverse_1.2.1 DBI_1.0.0
[13] RODBC_1.3-15 DT_0.4 rhandsontable_0.3.7 Cairo_1.5-9
[17] openxlsx_4.1.0 knitr_1.20 dplyr_0.8.0.1 shiny_1.1.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.0 lattice_0.20-35 assertthat_0.2.0 digest_0.6.15 mime_0.5
[6] R6_2.2.2 cellranger_1.1.0 plyr_1.8.4 backports_1.1.2 evaluate_0.10.1
[11] httr_1.3.1 highr_0.7 pillar_1.3.1 rlang_0.3.1 lazyeval_0.2.1
[16] rstudioapi_0.7 R.oo_1.22.0 R.utils_2.8.0 rmarkdown_1.11 htmlwidgets_1.2
[21] munsell_0.5.0 broom_0.5.0 compiler_3.5.0 httpuv_1.4.4.1 modelr_0.1.2
[26] pkgconfig_2.0.2 htmltools_0.3.6 tidyselect_0.2.5 crayon_1.3.4 withr_2.1.2
[31] later_0.7.3 R.methodsS3_1.7.1 grid_3.5.0 nlme_3.1-137 jsonlite_1.5
[36] xtable_1.8-2 gtable_0.2.0 magrittr_1.5 scales_0.5.0 zip_1.0.0
[41] cli_1.0.1 stringi_1.1.7 promises_1.0.1 xml2_1.2.0 tools_3.5.0
[46] glue_1.3.0 hms_0.4.2 rsconnect_0.8.12 yaml_2.1.19 colorspace_1.3-2
[51] rvest_0.3.2 rJava_0.9-10 haven_1.1.2
The Ubuntu 18.04 machine goes as follows:
R version 3.5.3 (2019-03-11)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] readxl_1.3.1 DT_0.5 rhandsontable_0.3.7
[4] knitr_1.22 shiny_1.2.0 dplyr_0.8.0.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 magrittr_1.5 tidyselect_0.2.5 xtable_1.8-3
[5] R6_2.4.0 rlang_0.3.3 tools_3.5.3 xfun_0.5
[9] htmltools_0.3.6 assertthat_0.2.1 digest_0.6.18 tibble_2.1.1
[13] crayon_1.3.4 purrr_0.3.2 later_0.8.0 htmlwidgets_1.3
[17] promises_1.0.1 glue_1.3.1 mime_0.6 cellranger_1.1.0
[21] compiler_3.5.3 pillar_1.3.1 jsonlite_1.6 httpuv_1.5.0
[25] pkgconfig_2.0.2
In advance, thanks very much for your help. Please clarify at comments if you need any extra information (that I can provide).
Edit: I checked as well outputting data.tables instead of rhandsontables both locally and on Ubuntu and failed as well rendering only on my Ubuntu VM.
For anyone interested in my problem, it was actually related to a firewall issue, not to a server-side or compatibility issue.
When I accessed my application from a network that wasn't my organization's (i.e. my cell phone's shared internet or home network) I had no problem at all.