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wk_crs_projjson(sf::st_crs(...)) test failure #212

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kyleam opened this issue Dec 14, 2023 · 3 comments · May be fixed by #214
Open

wk_crs_projjson(sf::st_crs(...)) test failure #212

kyleam opened this issue Dec 14, 2023 · 3 comments · May be fixed by #214

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@kyleam
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kyleam commented Dec 14, 2023

On an Ubuntu 20.04-based system, I've hit into a wk test failure:

Error (test-pkg-sf.R:31:3): wk_crs_projjson() works for sf crs objects
Error in `expect_match(wk_crs_projjson(sf::st_crs(4326)), "GeographicCRS")`: is.character(act$val) is not TRUE
Backtrace:
    ▆
 1. └─testthat::expect_match(wk_crs_projjson(sf::st_crs(4326)), "GeographicCRS") at test-pkg-sf.R:31:3
 2.   └─base::stopifnot(is.character(act$val))

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 1655 ]

I verified that I can trigger the same error with a Docker image based on rstudio/r-base:4.3.1-focal.

Dockerfile 
FROM rstudio/r-base:4.3.1-focal
ENV DEBIAN_FRONTEND=noninteractive
RUN apt-get update && \
    apt-get install -y --no-install-recommends eatmydata && \
    eatmydata apt-get install -y --no-install-recommends locales && \
    echo 'en_US.UTF-8 UTF-8' >>/etc/locale.gen && locale-gen && \
    eatmydata apt-get install -y --no-install-recommends \
      git \
      libgdal-dev \
      libgeos-dev \
      libproj-dev \
      libudunits2-dev \
      sqlite3 \
      && \
    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
ARG COMMIT=24be4ac61913cba6a51eb30f1c740aed01e0222c
RUN git clone https://github.com/paleolimbot/wk.git && \
    git -C wk checkout "$COMMIT"
ARG CRAN=https://packagemanager.posit.co/cran/__linux__/focal/2023-12-14
RUN printf 'options(repos = c("CRAN"= "%s"))\n' "$CRAN" >/opt/R/4.3.1/lib/R/etc/Rprofile.site
RUN Rscript -e 'install.packages("remotes")' && \
    Rscript -e 'remotes::install_deps("wk", dependencies = TRUE, upgrade = "always")' && \
    rm -rf /tmp/R*
CMD ["Rscript", "-e", "testthat::test_local('/wk')"]

Here's what I see if I execute the R relevant code from that assertion:

> sf::st_crs(4326)
Coordinate Reference System:
  User input: EPSG:4326
  wkt:
GEOGCRS["WGS 84",
    DATUM["World Geodetic System 1984",
        ELLIPSOID["WGS 84",6378137,298.257223563,
            LENGTHUNIT["metre",1]]],
    PRIMEM["Greenwich",0,
        ANGLEUNIT["degree",0.0174532925199433]],
    CS[ellipsoidal,2],
        AXIS["geodetic latitude (Lat)",north,
            ORDER[1],
            ANGLEUNIT["degree",0.0174532925199433]],
        AXIS["geodetic longitude (Lon)",east,
            ORDER[2],
            ANGLEUNIT["degree",0.0174532925199433]],
    USAGE[
        SCOPE["unknown"],
        AREA["World"],
        BBOX[-90,-180,90,180]],
    ID["EPSG",4326]]

> wk::wk_crs_projjson(sf::st_crs(4326))
<CHARSXP: NA>

System library versions:

# apt-cache policy libproj-dev libgdal-dev libgeos-dev
libproj-dev:
  Installed: 6.3.1-1
  Candidate: 6.3.1-1
  Version table:
 *** 6.3.1-1 500
        500 http://archive.ubuntu.com/ubuntu focal/universe amd64 Packages
        100 /var/lib/dpkg/status
libgdal-dev:
  Installed: 3.0.4+dfsg-1build3
  Candidate: 3.0.4+dfsg-1build3
  Version table:
 *** 3.0.4+dfsg-1build3 500
        500 http://archive.ubuntu.com/ubuntu focal/universe amd64 Packages
        100 /var/lib/dpkg/status
libgeos-dev:
  Installed: 3.8.0-1build1
  Candidate: 3.8.0-1build1
  Version table:
 *** 3.8.0-1build1 500
        500 http://archive.ubuntu.com/ubuntu focal/universe amd64 Packages
        100 /var/lib/dpkg/status

Any idea what might be triggering the failure?

Thanks in advance
@anthonynorth
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anthonynorth commented Dec 18, 2023 •
edited
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I think the problem here is GDAL < 3.1.0 and crs$ProjJson = NA. We can patch this with a 1-liner, but unsure if the fix belongs here of in sf though?

wk/R/pkg-sf.R

Line 141 in 030fcce

if (is.null(json)) { 

if (is.null(json) || is.na(json[1])) {

A CRS object from the 2004 Docker environment:

sf:::crs_parameters(sf::st_crs(4326))
#> $SemiMajor
#> 6378137 [m]
#> 
#> $SemiMinor
#> 6356752 [m]
#> 
#> $InvFlattening
#> [1] 298.2572
#> 
#> $IsGeographic
#> [1] TRUE
#> 
#> $units_gdal
#> [1] "degree"
#> 
#> $IsVertical
#> [1] FALSE
#> 
#> $WktPretty
#> [1] "GEOGCS[\"WGS 84\",\n    DATUM[\"WGS_1984\",\n        SPHEROID[\"WGS 84\",6378137,298.257223563]],\n    PRIMEM[\"Greenwich\",0],\n    UNIT[\"degree\",0.0174532925199433,\n        AUTHORITY[\"EPSG\",\"9122\"]],\n    AXIS[\"Latitude\",NORTH],\n    AXIS[\"Longitude\",EAST],\n    AUTHORITY[\"EPSG\",\"4326\"]]"
#> 
#> $Wkt
#> [1] "GEOGCS[\"WGS 84\",DATUM[\"WGS_1984\",SPHEROID[\"WGS 84\",6378137,298.257223563]],PRIMEM[\"Greenwich\",0],UNIT[\"degree\",0.0174532925199433,AUTHORITY[\"EPSG\",\"9122\"]],AXIS[\"Latitude\",NORTH],AXIS[\"Longitude\",EAST],AUTHORITY[\"EPSG\",\"4326\"]]"
#> 
#> $Name
#> [1] "WGS 84"
#> 
#> $proj4string
#> [1] "+proj=longlat +datum=WGS84 +no_defs"
#> 
#> $epsg
#> [1] 4326
#> 
#> $yx
#> [1] TRUE
#> 
#> $ProjJson
#> <CHARSXP: NA>
#> 
#> $WKT1_ESRI
#> [1] "GEOGCS[\"GCS_WGS_1984\",\n    DATUM[\"D_WGS_1984\",\n        SPHEROID[\"WGS_1984\",6378137.0,298.257223563]],\n    PRIMEM[\"Greenwich\",0.0],\n    UNIT[\"Degree\",0.0174532925199433]]"
#> 
#> $srid
#> [1] "EPSG:4326"
#> 
#> $axes
#>                 name orientation
#> 1  Geodetic latitude           1
#> 2 Geodetic longitude           3
#> 
#> attr(,"class")
#> [1] "crs_parameters"
attributes(sf::st_crs(4326))
#> $names
#> [1] "input" "wkt"  
#> 
#> $class
#> [1] "crs"
unclass(sf::st_crs(4326))
#> $input
#> [1] "EPSG:4326"
#> 
#> $wkt
#> [1] "GEOGCRS[\"WGS 84\",\n    DATUM[\"World Geodetic System 1984\",\n        ELLIPSOID[\"WGS 84\",6378137,298.257223563,\n            LENGTHUNIT[\"metre\",1]]],\n    PRIMEM[\"Greenwich\",0,\n        ANGLEUNIT[\"degree\",0.0174532925199433]],\n    CS[ellipsoidal,2],\n        AXIS[\"geodetic latitude (Lat)\",north,\n            ORDER[1],\n            ANGLEUNIT[\"degree\",0.0174532925199433]],\n        AXIS[\"geodetic longitude (Lon)\",east,\n            ORDER[2],\n            ANGLEUNIT[\"degree\",0.0174532925199433]],\n    USAGE[\n        SCOPE[\"unknown\"],\n        AREA[\"World\"],\n        BBOX[-90,-180,90,180]],\n    ID[\"EPSG\",4326]]"

Created on 2023-12-18 with reprex v2.0.2

@anthonynorth
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Seems sf ensuring ProjJson has a value is intended.
https://github.com/r-spatial/sf/blob/b29613b6939102eb728abebc499394f7ede631da/src/gdal.cpp#L287-L296

@anthonynorth anthonynorth linked a pull request Dec 18, 2023 that will close this issue
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@kyleam
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kyleam commented Dec 18, 2023

@anthonynorth Thanks for the details and for working on a fix!

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Patch wk_crs_projjson for GDAL < 3.1 anthonynorth/wk
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@anthonynorth @kyleam