Possible conflict sf and tmap

[donojazz]

I love tmap and have been using it constantly for the 30 Day Map Challenge. It has been working great until yesterday on code that ran great 2 days ago, I now get:

Error: Shape contains invalid polygons. Please fix it or set tmap_options(check.and.fix = TRUE) and rerun the plot

constantly. After playing with marmap and having it hose my R environmant, especially tidyverse. I had to delete my entire R environment along with libraries. I worked with Jenny Bryan and she helped with the tidyverse issue tidyverse/tidyverse#316 (comment) We agreed about the fresh start with R. But, now, I am getting errors with tmap. I am getting the same errors off your sample vignettes (tmap: version changes). Can you assist? Thanks. Jim

Here is my sys info.

sessionInfo()

R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] DT_0.26 mapview_2.11.0 tigris_1.6.1 spdplyr_0.4.0 readxl_1.4.1
[6] rgdal_1.6-2 sp_1.5-1 sf_1.0-9 tmaptools_3.1-1 tmap_3.3-3
[11] leaflet_2.1.1 forcats_0.5.2 stringr_1.4.1 dplyr_1.0.10 purrr_0.3.5
[16] readr_2.1.3 tidyr_1.2.1 tibble_3.1.8 ggplot2_3.4.0 tidyverse_1.3.2

loaded via a namespace (and not attached):
[1] googledrive_2.0.0 leafem_0.2.0 colorspace_2.0-3
[4] ellipsis_0.3.2 class_7.3-20 satellite_1.0.4
[7] base64enc_0.1-3 fs_1.5.2 dichromat_2.0-0.1
[10] rstudioapi_0.14 proxy_0.4-27 bit64_4.0.5
[13] fansi_1.0.3 lubridate_1.9.0 xml2_1.3.3
[16] codetools_0.2-18 cachem_1.0.6 knitr_1.40
[19] jsonlite_1.8.3 broom_1.0.1 dbplyr_2.2.1
[22] png_0.1-7 compiler_4.2.2 httr_1.4.4
[25] backports_1.4.1 assertthat_0.2.1 fastmap_1.1.0
[28] gargle_1.2.1 cli_3.4.1 leaflet.providers_1.9.0
[31] htmltools_0.5.3 tools_4.2.2 gtable_0.3.1
[34] glue_1.6.2 rappdirs_0.3.3 Rcpp_1.0.9
[37] jquerylib_0.1.4 cellranger_1.1.0 raster_3.6-3
[40] vctrs_0.5.0 leafsync_0.1.0 crosstalk_1.2.0
[43] lwgeom_0.2-9 xfun_0.34 rvest_1.0.3
[46] timechange_0.1.1 lifecycle_1.0.3 XML_3.99-0.12
[49] googlesheets4_1.0.1 terra_1.6-17 scales_1.2.1
[52] vroom_1.6.0 hms_1.1.2 parallel_4.2.2
[55] RColorBrewer_1.1-3 curl_4.3.3 yaml_2.3.6
[58] sass_0.4.2 stringi_1.7.8 maptools_1.1-5
[61] e1071_1.7-12 rlang_1.0.6 pkgconfig_2.0.3
[64] spbabel_0.5.5 evaluate_0.18 lattice_0.20-45
[67] htmlwidgets_1.5.4 bit_4.0.4 tidyselect_1.2.0
[70] magrittr_2.0.3 R6_2.5.1 generics_0.1.3
[73] DBI_1.1.3 pillar_1.8.1 haven_2.5.1
[76] foreign_0.8-83 withr_2.5.0 units_0.8-0
[79] stars_0.5-6 abind_1.4-5 modelr_0.1.10
[82] crayon_1.5.2 uuid_1.1-0 KernSmooth_2.23-20
[85] utf8_1.2.2 tzdb_0.3.0 rmarkdown_2.18
[88] grid_4.2.2 reprex_2.0.2 digest_0.6.30
[91] classInt_0.4-8 webshot_0.5.4 stats4_4.2.2
[94] munsell_0.5.0 viridisLite_0.4.1 bslib_0.4.1

Originally posted by @donojazz in #1649 (comment)

[donojazz]

Not sure if related to my tmap issue. I found something on sf and tested with their code demonstrations using their
sf::basic |   | simple feature test script Could newest versions of R and RStudio be creating sf issues that affect tmap? BTW, plot seems to work fine on those polygon objects.

http://127.0.0.1:31629/doc/html/Search?package=sf&agrep=0&types.demo=1&pattern=

Test:
(p1 = st_point(c(1,2)))

Return:
POINT (1 2)

Test:
hole1 = matrix(c(1,1,1,2,2,2,2,1,1,1),ncol=2, byrow=TRUE)
hole2 = matrix(c(5,5,5,6,6,6,6,5,5,5),ncol=2, byrow=TRUE)
pts = list(outer, hole1, hole2)
(pl1 = st_polygon(pts))

Retturn:
Error in FUN(X[[i]], ...) : is.numeric(x) is not TRUE

Test:
pts3 = lapply(pts, function(x) cbind(x, 0))
(pl2 = st_polygon(pts3))

Return
Error in FUN(X[[i]], ...) : is.numeric(x) is not TRUE
sf::basic simple feature test script

[mtennekes]

Could you share some reproducible code @donojazz ?

Have you tried to apply st_make_validon your sf object, and feed the returned object to tmap?

[donojazz]

Here it is, I tried adding in this code but it didn't help : tmap_options(check.and.fix = TRUE)

Not sure why the problems. Initial problem was tidyverse will not load. Once I deleted old versions, and files, then reloaded R and RStudio and libraries tidyverse worked but my older (2 day old) containing tmap would not. The sample below was from your tmap documentation.

I will try your suggestion. Thanks.

library(tigris)
#> To enable caching of data, set `options(tigris_use_cache = TRUE)`
#> in your R script or .Rprofile.
library(sf)
#> Linking to GEOS 3.9.3, GDAL 3.5.2, PROJ 8.2.1; sf_use_s2() is TRUE
library(dplyr)
#> 
#> 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
library(tmap)
data(World, metro)
tmap_mode("view")
#> tmap mode set to interactive viewing
tm_basemap(leaflet::providers$CartoDB.PositronNoLabels, group = "CartoDB basemap") +
  tm_shape(World) +
  tm_polygons("HPI", group = "Countries") +
  tm_tiles(leaflet::providers$CartoDB.PositronOnlyLabels, group = "CartoDB labels") +
  tm_shape(metro) +
  tm_dots(col = "red", group = "Metropolitan areas")
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> old-style crs object detected; please recreate object with a recent sf::st_crs()
#> Error: Shape contains invalid polygons. Please fix it or set tmap_options(check.and.fix = TRUE) and rerun the plot

^{Created on 2022-11-18 with reprex v2.0.2}

[edzer]

Works fine for me, with

> sessionInfo()
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/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] tmap_3.3-3   dplyr_1.0.9  sf_1.0-10    tigris_1.6.1

loaded via a namespace (and not attached):
 [1] terra_1.6-40            tidyselect_1.2.0        lattice_0.20-45        
 [4] leaflet.providers_1.9.0 vctrs_0.5.1             generics_0.1.3         
 [7] htmltools_0.5.3         stars_0.6-0             viridisLite_0.4.1      
[10] yaml_2.3.5              s2_1.1.0                base64enc_0.1-3        
[13] utf8_1.2.2              XML_3.99-0.10           rlang_1.0.6            
[16] e1071_1.7-12            pillar_1.8.1            foreign_0.8-82         
[19] glue_1.6.2              DBI_1.1.3               rappdirs_0.3.3         
[22] sp_1.5-0                RColorBrewer_1.1-3      wk_0.7.0               
[25] uuid_1.1-0              lifecycle_1.0.3         stringr_1.4.0          
[28] raster_3.6-3            htmlwidgets_1.5.4       codetools_0.2-18       
[31] leafsync_0.1.0          fastmap_1.1.0           maptools_1.1-4         
[34] crosstalk_1.2.0         parallel_4.2.2          class_7.3-20           
[37] fansi_1.0.3             leafem_0.2.0            Rcpp_1.0.9             
[40] KernSmooth_2.23-20      classInt_0.4-8          lwgeom_0.2-10          
[43] jsonlite_1.8.3          leaflet_2.1.1           abind_1.4-5            
[46] png_0.1-7               digest_0.6.30           stringi_1.7.8          
[49] tmaptools_3.1-1         grid_4.2.2              rgdal_1.5-32           
[52] cli_3.4.0.9000          tools_4.2.2             magrittr_2.0.3         
[55] proxy_0.4-27            tibble_3.1.8            dichromat_2.0-0.1      
[58] pkgconfig_2.0.3         assertthat_0.2.1        httr_1.4.4             
[61] R6_2.5.1                units_0.8-0             compiler_4.2.2         

[donojazz]

Any ideas where I should start digging? Think it may be a windows thing causing it. Jenny said to remove all the extraneous vctrs files. I got rid of 7 and only one left is the one I installed on 11/17.

[donojazz]

I kept searching around for ideas and someone here suggested I make sure geos is installed. I tryied installing from R Studio and it failed. Then I installed directly from console directly. These files finally loaded:

package ‘libgeos’ successfully unpacked and MD5 sums checked
package ‘wk’ successfully unpacked and MD5 sums checked
package ‘geos’ successfully unpacked and MD5 sums checked

Part of the error message was:
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘wk’

Bottom line: tmap runs that reprex code I sent. I think the problem is fixed. Thanks.

Jim