vulnerability to PROJ6/GDAL3

[rsbivand]

Running revdeps from sp (sp (my github fork) with development rgdal from R-Forge):

> packageVersion("sp")
[1] ‘1.3.4’
> packageVersion("rgdal")
[1] ‘1.5.3’
> rgdal::rgdal_extSoftVersion()
          GDAL GDAL_with_GEOS           PROJ             sp 
       "3.0.2"         "TRUE"        "6.2.1"        "1.3-2" 

a test fails:

> library(testthat)
> library(spdplyr)
Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: sp
> 
> test_check("spdplyr")
── 1. Failure: group by and summarize is quiet (@test-adv-dplyr.R#14)  ─────────
`g[1:20, ] %>% summarize(alon = mean(LON), mxlat = max(LAT), mxarea = max(AREA))` produced warnings.

── 2. Failure: group by and summarize is quiet (@test-adv-dplyr.R#15)  ─────────
``%>%`(...)` produced warnings.

── 3. Failure: group by and summarize is quiet (@test-adv-dplyr.R#16)  ─────────
`g[1:10, ] %>% summarise(alon = mean(LON))` produced warnings.

══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 43 | SKIPPED: 4 | WARNINGS: 6 | FAILED: 3 ]
1. Failure: group by and summarize is quiet (@test-adv-dplyr.R#14) 
2. Failure: group by and summarize is quiet (@test-adv-dplyr.R#15) 
3. Failure: group by and summarize is quiet (@test-adv-dplyr.R#16) 

Error: testthat unit tests failed
Execution halted

See:

http://rgdal.r-forge.r-project.org/articles/PROJ6_GDAL3.html
r-spatial/sf#1231
r-spatial/sf#1187
r-spatial/sf#1146
r-spatial/discuss#28

for background. See:

r-spatial/discuss#28 (comment)

for a way of testing fixes in a docker container contributed by Jakub Nowosad.

[rsbivand]

Seeing more errors with sf 0.9-0, sp 1.4-1, rgdal 1.5-6, and dplyr, rlang and vctrs from github:

* checking examples ... ERROR
Running examples in ‘spdplyr-Ex.R’ failed
The error most likely occurred in:

> ### Name: dplyr-Spatial
> ### Title: Dplyr verbs for Spatial
> ### Aliases: dplyr-Spatial mutate.Spatial mutate_.Spatial
> ###   summarise_.Spatial summarise.Spatial group_by_.Spatial
> ###   group_by.Spatial filter_.Spatial filter.Spatial arrange_.Spatial
> ###   arrange.Spatial slice_.Spatial slice.Spatial select_.Spatial
> ###   select.Spatial rename_.Spatial rename.Spatial distinct_.Spatial
> ###   distinct.Spatial left_join.Spatial inner_join.Spatial
> 
> ### ** Examples
> 
> library(sp)
> library(maptools)
Checking rgeos availability: TRUE
> data(wrld_simpl)
> library(spdplyr) 
> library(raster)  

Attaching package: ‘raster’

The following object is masked from ‘package:dplyr’:

    select

> wrld_simpl %>% mutate(NAME = "allthesame", REGION = row_number())
class       : SpatialPolygonsDataFrame 
features    : 246 
extent      : -180, 180, -90, 83.57027  (xmin, xmax, ymin, ymax)
coord. ref. :  +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +towgs84=0,0,0 
variables   : 11
# A tibble: 246 x 11
   FIPS  ISO2  ISO3     UN NAME      AREA POP2005 REGION SUBREGION     LON   LAT
   <fct> <fct> <fct> <int> <chr>    <int>   <dbl>  <int>     <int>   <dbl> <dbl>
 1 AC    AG    ATG      28 allthe…     44  8.30e4      1        29  -61.8   17.1
 2 AG    DZ    DZA      12 allthe… 238174  3.29e7      2        15    2.63  28.2
 3 AJ    AZ    AZE      31 allthe…   8260  8.35e6      3       145   47.4   40.4
 4 AL    AL    ALB       8 allthe…   2740  3.15e6      4        39   20.1   41.1
 5 AM    AM    ARM      51 allthe…   2820  3.02e6      5       145   44.6   40.5
 6 AO    AO    AGO      24 allthe… 124670  1.61e7      6        17   17.5  -12.3
 7 AQ    AS    ASM      16 allthe…     20  6.41e4      7        61 -171.   -14.3
 8 AR    AR    ARG      32 allthe… 273669  3.87e7      8         5  -65.2  -35.4
 9 AS    AU    AUS      36 allthe… 768230  2.03e7      9        53  136.   -25.0
10 BA    BH    BHR      48 allthe…     71  7.25e5     10       145   50.6   26.0
# … with 236 more rows
> wrld_simpl %>% transmute(alpha = paste0(FIPS, NAME))
Error in UseMethod("transmute") : 
  no applicable method for 'transmute' applied to an object of class "c('SpatialPolygonsDataFrame', 'SpatialPolygons', 'Spatial', 'SpatialVector')"
Calls: %>% ... _fseq -> freduce -> withVisible -> <Anonymous> -> transmute
Execution halted

* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   16. dplyr::group_vars(x)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 35 | SKIPPED: 3 | WARNINGS: 7 | FAILED: 8 ]
  1. Failure: group by and summarize is quiet (@test-adv-dplyr.R#14) 
  2. Failure: group by and summarize is quiet (@test-adv-dplyr.R#15) 
  3. Failure: group by and summarize is quiet (@test-adv-dplyr.R#16) 
  4. Error: mutate works for all geometric types (@test-basic-dplyr.R#58) 
  5. Error: mutate works (@test-basic-dplyr.R#118) 
  6. Failure: joins work (@test-basic-dplyr.R#156) 
  7. Failure: joins work (@test-basic-dplyr.R#163) 
  8. Error: tibble requirements (@test-dplyr-0.6.0.R#5) 
  
  Error: testthat unit tests failed
  Execution halted

[mdsumner]

thanks, not a vulnerability to new gdal/proj rather leftover changes required by dplyr