mapshot broken without and with fgb

[rsbivand]

library(sf)
bp_file <- system.file("gpkg/b_pump.gpkg", package="sf")
b_pump_sf <- st_read(bp_file, quiet=TRUE)
library(mapview)
# GDAL version >= 3.1.0 | setting mapviewOptions(fgb = TRUE)
mapviewOptions(fgb = FALSE)
webmap1 <- mapview(b_pump_sf, map.type="OpenStreetMap")
webmap1
mapshot(webmap1, file="webmap1.png")
# File filef86516aae932_files/PopupTable-0.0.1/popup.css not found in resource path
# Error: pandoc document conversion failed with error 99

mapviewOptions(fgb = TRUE)
webmap1 <- mapview(b_pump_sf, map.type="OpenStreetMap"
mapshot(webmap1, file="webmap1.png")
# Could not determine mime type for `filef865709ec120_files/b_pump_sf-0.0.1/b_pump_sf_layer.fgb'
# Error: pandoc document conversion failed with error 63

mapview_2.9.0 sf_0.9-5

[tim-salabim]

Yeah, sorry, it should work again with mapviewOptions(fgb = FALSE) if you re-install from guthub (Note that the develop branch is obsolete now!). I messed up the css file lookup in the last CRAN release.

remotes::install_github("r-spatial/mapview")

As for mapviewOptions(fgb = TRUE) that is out of our hands. As long as pandoc doesn't know about the mime type for .fgb this will not work... I don't know how to get the file format recognised/included in pandoc

[rsbivand]

Thanks for a fast response! As pandoc is written in haskell, it looks hard to work out what to do as a PR, so maybe until then you'd need to convert internally to a format pandoc recognises. I guess the RStudio people could advise about how to get a MIME definition and the required haskell conversion functions submitted. Did you ask them?

[tim-salabim]

Not yet, I was thinking to ask @bjornharrtell first. I guess that the R community is not the only community to run into this issue...

[bjornharrtell]

I would say application/flatgeobuf should be safe to use.

It's a long road to get an official mimetype and requires an organization to apply, so it's a bit out of my hands as I'm not very interested in getting into the politics of that.

[tim-salabim]

Thanks @bjornharrtell for the input here. I have no experience with these kind of things, but from what you say it seems like we'd need to get ogc on board (as it's officially part of gdal). @rsbivand any thoughts?

[bjornharrtell]

Perhaps osgeo is easier to involve but ogc would be fun too (as long as it doesn't involve tons of administration). Any help with either would be very welcome. 🙂

[bjornharrtell]

I wouldn't bet on getting a proper mimetype any time soon. I find it strange that it would be a hard requirement for something as specific as geospatial software/formats. That would also mean you couldn't use that software with something internal/proprietary?

[tim-salabim]

Thanks! I'll leave this open as a reminder to not forget...

[OwenTheAnalyst]

Hello, Apologies - relatively new to R. I've worked through the steps above including fgb = FALSE and reinstalling from github, but I am still getting the same issue when trying to save an html file using mapshot.

The error message is:

`> mapshot(m51, url = "map1.html", file = ".html") Could not determine mime type for map1_files/tvp_lsoa3-Vehicle_Rate-0.0.1/tvp_lsoa3-Vehicle_Rate_layer.fgb' Error: pandoc document conversion failed with error 63

Is this the known issue still or something else going on?

[rsbivand]

@owenmiller95 use mapviewOptions(fgb = FALSE) - mime-types are not under the control of R packages. The option chooses not to use the FlatGeoBuf driver https://gdal.org/drivers/vector/flatgeobuf.html new in GDAL >= 3.1; hopefully a mime entry will be created sometime. FlatGeoBuf is a much faster format when it becomes usable, but for now use the option to turn its use off. The issue is known, see the earlier entries.

[beausoleilmo]

I'm not sure what was fixed, but it's still a problem:

library(mapview)
GDAL version >= 3.1.0 | setting mapviewOptions(fgb = TRUE)

But whenever I want to print this with the mapviewOptions(fgb = FALSE)

  mapviewOptions(fgb = FALSE)
  mapshot(x = map.out1, 
          remove_url = TRUE,
          vwidth = 840, 
          vheight = 500,
          file = file.path(normalizePath(dirname(f)),basename(f)),
          remove_controls = c("zoomControl", "layersControl", "homeButton"))

The error is still there...

Could not determine mime type for `file736f2dbc5366_files/layername-0.0.1/layername_layer.fgb'
Error: pandoc document conversion failed with error 63

Is there a fix or not? (I'm using mapview 2.9.0)

[tim-salabim]

The option needs to be set before creating the map - map.out1 in your case - not before calling mapshot.

[beausoleilmo]

Excellent catch! Thank you very much for the very fast reply 🥇

[donojazz]

I guess the .fgb and rmarkdown issue is still an open item. I built a dashboard about a year ago using mapview 2.7.8. It worked fine. I just updated the data an reran. Would not compile new dashboard. Spent two days screwing with mime, temp files and .fgb I files. Finally saw this post and reinstalled mapview 2.7.8. Worked fine.

[donojazz]

I tried .fgb = false trick. It did not work with 2.9 mapview. I am running r ver 4.0 on win 10. Also, I did update most recent pandoc. Best solution may be to use old mapview version.

[bjornharrtell]

Heads up that this is likely fixed in upstream dependency pandoc with https://github.com/jgm/pandoc/issues/7202 but unfortunately it's not released yet.

[donojazz]

Thanks for the update. Any timeframe for release?

[bjornharrtell]

@donojazz I have no idea, not involved/engaged in pandoc.

[donojazz]

Thanks

[tim-salabim]

@bjornharrtell thanks for linking the pandoc thread! @donojazz can you try the github version of mapview? This should be solved already...

[donojazz]

I tried to install that version during my quest and has issues installing the .dll file in windows. Decided to stop, delete 2.9 and backpedal to 2.8.

...\R\win-library\4.0\xfun\libs\x64\xfun.dll: Permission denied

Got tired of messing with it and just reverted back to old version. Then it worked.

[tim-salabim]

Ok, xfun.dll is not related to mapview but likely to one of its dependencies. I am hoping to release to cran soon.

[donojazz]

Looking forward to it.

[donojazz]

I finally figured out which level I needed to change for access to security permissions.
I installed using remotes::install_github("r-spatial/mapview") . Reran everything and it generated a flextable.
Here is attached packages: other attached packages: [1] knitr_1.33 maps_3.3.0 lubridate_1.7.10 sparklyr_1.6.2 fasttime_1.0-2 data.table_1.14.0 [7] RColorBrewer_1.1-2 plotly_4.9.3 ggmap_3.0.0 tidycensus_0.11.4 censusxy_1.0.1 mapview_2.9.9
[13] leafpop_0.0.6 leaflet_2.0.4.1 sf_0.9-8 rgdal_1.5-23 sp_1.4-5 forcats_0.5.1
[19] stringr_1.4.0 dplyr_1.0.6 purrr_0.3.4 readr_1.4.0 tidyr_1.1.3 tibble_3.1.1
[25] ggplot2_3.3.3 tidyverse_1.3.1

Looks like mapview 2.9.9 from github works. JD

[donojazz]

R version 4.0.2 (2020-06-22) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19042)

Pandoc v ‘2.13’

[jjyotikataria]

@bjornharrtell @tim-salabim @rsbivand @beausoleilmo @donojazz

Hi guys! Facing this issue all of a sudden. I have a couple of rmd files running one after the other and suddenly facing this issue in this fifth Rmd while knitting. Could you please help?

Falling back to 'combined_singleR.knit' Could not determine mime type for `/MG/SHARED/ANALYSIS/DEMUX/TEST_sc/2002332/sc_results/DMSO_LIB_GEX_hpca.annotation.rds' Error: pandoc document conversion failed with error 63

This is the required info.

version _ platform x86_64-pc-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 4 minor 0.5 year 2021 month 03 day 31 svn rev 80133 language R version.string R version 4.0.5 (2021-03-31) nickname Shake and Throw

rmarkdown::pandoc_version() [1] ‘2.7.2’ packageVersion("markdown") [1] ‘1.1’ packageVersion("rmarkdown") [1] ‘2.9’

[tim-salabim]

Seems like you want to include (read/write) some R specific data set (.rds) for which there does not seem to be a mime type definition for pandoc. Not convinced this is related to .fgb files...

[jjyotikataria]

@tim-salabim Yes, its an rds but my previous rmarkdown commands are working and the last one when I am using, I am getting this mime issue. Any way to surpass this?

[tim-salabim]

probably try another file format. Can you save the data as e.g. csv?