r-spatial
Cannot save R Notebook after calling mapview()
After calling mapview() from an R notebook in RStudio, the R notebook is unable to save, returning an error saying: Error creating notebook: 'mode' for the clipboard must be 'r' or 'w'.
I only get this error after calling mapview().
I have tested with R.4.0.0 and R3.6.2 and get the error with both. I have been able to use mapview() with R notebooks in the past and find it very helpful. Has anyone else had this issue or have ideas of how to troubleshoot? I appreciate any information anyone might be able to provide, even if it is that you cannot reproduce the problem, or that I should direct my questions elsewhere.
Thanks!
Minimal example .Rmd file:
---
title: "R Notebook"
output: html_notebook
---
```{r}
library(mapview)
# Dummy data
x <- c(-112, -111, -110)
y <- c(40, 41, 42)
mapview(x, y)
```
Session info:
R version 4.0.0 (2020-04-24)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices
[4] utils datasets methods
[7] base
other attached packages:
[1] mapview_2.7.8
loaded via a namespace (and not attached):
[1] Rcpp_1.0.4.6
[2] RColorBrewer_1.1-2
[3] compiler_4.0.0
[4] base64enc_0.1-3
[5] class_7.3-17
[6] tools_4.0.0
[7] uuid_0.1-4
[8] digest_0.6.25
[9] jsonlite_1.6.1
[10] satellite_1.0.2
[11] lifecycle_0.2.0
[12] lattice_0.20-41
[13] viridisLite_0.3.0
[14] png_0.1-7
[15] rlang_0.4.6
[16] DBI_1.1.0
[17] crosstalk_1.1.0.1
[18] yaml_2.2.1
[19] xfun_0.14
[20] e1071_1.7-3
[21] raster_3.1-5
[22] systemfonts_0.2.3
[23] gdtools_0.2.2
[24] htmlwidgets_1.5.1
[25] stats4_4.0.0
[26] classInt_0.4-3
[27] leaflet_2.0.3
[28] grid_4.0.0
[29] webshot_0.5.2
[30] svglite_1.2.3
[31] sf_0.9-3
[32] R6_2.4.1
[33] sp_1.4-2
[34] leafpop_0.0.5
[35] magrittr_1.5
[36] scales_1.1.1
[37] codetools_0.2-16
[38] htmltools_0.4.0
[39] units_0.6-6
[40] mime_0.9
[41] colorspace_1.4-1
[42] brew_1.0-6
[43] KernSmooth_2.23-17
[44] munsell_0.5.0
[45] leafem_0.1.1
[46] markdown_1.1
For now I can only say that I don't have the issue with R 3.6.1
master > devtools::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────
setting value
version R version 3.6.1 (2019-07-05)
os Pop!_OS 18.04 LTS
system x86_64, linux-gnu
ui RStudio
language en_GB:en
collate en_GB.UTF-8
ctype en_GB.UTF-8
tz Europe/Berlin
date 2020-06-10
─ Packages ───────────────────────────────────────────────────────────────────────────
package * version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.1)
backports 1.1.6 2020-04-05 [1] CRAN (R 3.6.1)
base64enc 0.1-3 2015-07-28 [1] CRAN (R 3.6.1)
brew 1.0-6 2011-04-13 [1] CRAN (R 3.6.1)
callr 3.4.3 2020-03-28 [1] CRAN (R 3.6.1)
class 7.3-14 2015-08-30 [4] CRAN (R 3.5.0)
classInt 0.4-3 2020-04-07 [1] CRAN (R 3.6.1)
cli 2.0.2 2020-02-28 [1] CRAN (R 3.6.1)
clisymbols 1.2.0 2017-05-21 [1] CRAN (R 3.6.0)
codetools 0.2-15 2016-10-05 [4] CRAN (R 3.5.0)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.6.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.1)
crosstalk 1.1.0.1 2020-03-13 [1] CRAN (R 3.6.1)
DBI 1.1.0 2019-12-15 [1] CRAN (R 3.6.1)
desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.0)
devtools 2.1.0 2019-07-06 [1] CRAN (R 3.6.0)
digest 0.6.25 2020-02-23 [1] CRAN (R 3.6.1)
e1071 1.7-3 2019-11-26 [1] CRAN (R 3.6.1)
evaluate 0.14 2019-05-28 [2] CRAN (R 3.5.1)
fansi 0.4.1 2020-01-08 [1] CRAN (R 3.6.1)
fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.0)
gdtools 0.2.2 2020-04-03 [1] CRAN (R 3.6.1)
glue 1.4.0 2020-04-03 [1] CRAN (R 3.6.1)
htmltools 0.4.0 2019-10-04 [1] CRAN (R 3.6.0)
htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 3.6.0)
jsonlite 1.6.1 2020-02-02 [1] CRAN (R 3.6.1)
KernSmooth 2.23-15 2015-06-29 [4] CRAN (R 3.5.0)
knitr 1.28 2020-02-06 [1] CRAN (R 3.6.1)
lattice 0.20-35 2017-03-25 [4] CRAN (R 3.5.0)
leafem * 0.1.1 2020-06-10 [1] local
leaflet 2.0.3 2019-11-16 [1] CRAN (R 3.6.1)
leafpop 0.0.5 2020-05-22 [1] local
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 3.6.1)
magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.1)
mapview * 2.8.1 2020-06-10 [1] local
markdown 1.1 2019-08-07 [1] CRAN (R 3.6.0)
memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.0)
mime 0.9 2020-02-04 [1] CRAN (R 3.6.1)
munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.0)
packrat 0.5.0 2018-11-14 [1] CRAN (R 3.6.1)
pkgbuild 1.0.6 2019-10-09 [1] CRAN (R 3.6.1)
pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.0)
png 0.1-7 2013-12-03 [1] CRAN (R 3.6.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 3.6.1)
processx 3.4.2 2020-02-09 [1] CRAN (R 3.6.1)
prompt 1.0.0 2020-01-18 [1] Github (gaborcsardi/prompt@b332c42)
ps 1.3.2 2020-02-13 [1] CRAN (R 3.6.1)
R6 2.4.1 2019-11-12 [1] CRAN (R 3.6.1)
raster 3.0-12 2020-01-30 [1] CRAN (R 3.6.1)
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 3.6.0)
Rcpp 1.0.4.6 2020-04-09 [1] CRAN (R 3.6.1)
remotes 2.1.0 2019-06-24 [1] CRAN (R 3.6.0)
rlang 0.4.5 2020-03-01 [1] CRAN (R 3.6.1)
rmarkdown 1.13 2019-05-22 [1] CRAN (R 3.6.0)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.0)
rsconnect 0.8.16 2019-12-13 [1] CRAN (R 3.6.1)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 3.6.1)
satellite 1.0.2 2019-12-09 [1] CRAN (R 3.6.1)
scales 1.1.0 2019-11-18 [1] CRAN (R 3.6.1)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.0)
sf 0.9-3 2020-05-08 [1] Github (r-spatial/sf@83180aa)
sp 1.4-1 2020-02-28 [1] CRAN (R 3.6.1)
stringi 1.4.6 2020-02-17 [1] CRAN (R 3.6.1)
stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.1)
svglite 1.2.3 2020-02-07 [1] CRAN (R 3.6.1)
systemfonts 0.1.1 2019-07-01 [1] CRAN (R 3.6.0)
testthat 2.3.2 2020-03-02 [1] CRAN (R 3.6.1)
units 0.6-6 2020-03-16 [1] CRAN (R 3.6.1)
usethis 1.5.1 2019-07-04 [1] CRAN (R 3.6.0)
uuid 0.1-4 2020-02-26 [1] CRAN (R 3.6.1)
webshot 0.5.2 2019-11-22 [1] CRAN (R 3.6.1)
withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0)
xfun 0.12 2020-01-13 [1] CRAN (R 3.6.1)
yaml 2.2.1 2020-02-01 [1] CRAN (R 3.6.1)
[1] /home/timpanse/R/x86_64-pc-linux-gnu-library/3.6
[2] /usr/local/lib/R/site-library
[3] /usr/lib/R/site-library
[4] /usr/lib/R/library
Thank you for checking and for your reply. I have not been able to figure this out and have reverted to simply (or, rather, not-so-simply) using leaflet directly for my maps. I don't even know where such a problem would enter (like is it something in mapview, rmarkdown, rstudio). Since no one else seems to be reporting problems, there's also the possibility that there is something specific to my system causing the error. I can't be the only person who uses mapview in R Notebooks, right? For now, I'll keep my fingers crossed that the problem goes away in future updates to one of these packages, R, or RStudio itself. Thanks again!
Brief update: I also get the error if I simply add leafem::addMouseCoordinates() to an existing leaflet map. Without the addMouseCoordinates() line, the leaflet map works just fine with RStudio and I can save the result as an html notebook. With the addMouseCoordinates() line, I receive the same error when RStudio tries to save the notebook: Error creating notebook: 'mode' for the clipboard must be 'r' or 'w'.
The code below produces the error:
---
title: "R Notebook"
output: html_notebook
---
```{r}
library(leaflet)
leaflet() %>%
addTiles() %>%
addMarkers(lng=174.768, lat=-36.852, popup="The birthplace of R") %>%
leafem::addMouseCoordinates()
```
Could you please try:
---
title: "R Notebook"
output:
html_notebook:
self_contained: false
---
```{r}
tst = clipr::write_clip("bla bla")
cat(clipr::read_clip())
```
Does this work or produce a similar error?
That worked without any errors: the code ran and RStudio successfully saved the associated .nb.html file with the expected content.
Thanks!