[R-pkg-team] Bug#961211: r-cran-lwgeom: autopkgtest failures on s390x

Gianfranco Costamagna locutusofborg at debian.org
Thu May 21 13:30:21 BST 2020

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Source: r-cran-lwgeom
Version: 0.2-3-1
Severity: serious

Hello, looks like some changes in r-cran-lwgeom/proj/geom made the testsuite fail with the latest versions
of the programs in sid.
Looks like an endianess regression introduced in the last version fo lwgeom, can you please have a look?

I'm attaching a log taken from a test on zelenka.debian.org

thanks

Gianfranco
-------------- next part --------------
BEGIN TEST azimuth.R

R version 4.0.0 (2020-04-24) -- "Arbor Day"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: s390x-ibm-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> suppressPackageStartupMessages(library(sf))
> suppressPackageStartupMessages(library(lwgeom))
> p = st_sfc(st_point(c(7,52)), st_point(c(8,53)), crs = 4326)
> st_geod_azimuth(p)
Unknown WKB type (248)! Full WKB type number was (16777248).
Error in CPL_geodetic_azimuth(st_geometry(x), p$SemiMajor, p$InvFlattening) : 
  lwgeom error
Calls: st_geod_azimuth -> CPL_geodetic_azimuth
Execution halted
BEGIN TEST dist.R

R version 4.0.0 (2020-04-24) -- "Arbor Day"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: s390x-ibm-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> suppressPackageStartupMessages(library(sf))
> library(sp)
> suppressPackageStartupMessages(library(units))
> library(geosphere)
> 
> x = st_sfc(
+ st_point(c(0,0)),
+ st_point(c(1,0)),
+ st_point(c(2,0)),
+ st_point(c(3,0)),
+ crs = 4326
+ )
> 
> y = st_sfc(
+ st_point(c(0,10)),
+ st_point(c(1,0)),
+ st_point(c(2,0)),
+ st_point(c(3,0)),
+ st_point(c(4,0)),
+ crs = 4326
+ )
> 
> st_crs(y) = 4326
> st_crs(x) = 4326
> (d.sf = st_distance(x, y))
Error in CPL_geodetic_distance(st_geometry(x), st_geometry(y), p$SemiMajor,  : 
  Unknown WKB type (248)! Full WKB type number was (16777248).
Calls: st_distance -> <Anonymous> -> CPL_geodetic_distance
Execution halted
BEGIN TEST geod.R

R version 4.0.0 (2020-04-24) -- "Arbor Day"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: s390x-ibm-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> ### Name: lw_geodetic
> ### Title: geodetic length, area, and predicates
> ### Aliases: lw_geodetic st_geod_area lw_geodetic st_geod_length
> ###   lw_geodetic st_geod_segmentize lw_geodetic st_geod_covers
> 
> ### ** Examples
> 
> suppressPackageStartupMessages(library(sf))
> suppressPackageStartupMessages(library(lwgeom))
> suppressPackageStartupMessages(library(units))
> nc = st_read(system.file("gpkg/nc.gpkg", package="sf"), quiet = TRUE)
> st_geod_area(nc[1:3,])
Unknown WKB type (296)! Full WKB type number was (100663296).
Error in CPL_geodetic_area(st_geometry(x), p$SemiMajor, p$InvFlattening) : 
  lwgeom error
Calls: st_geod_area -> CPL_geodetic_area
Execution halted
BEGIN TEST perimeter.R

R version 4.0.0 (2020-04-24) -- "Arbor Day"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: s390x-ibm-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> suppressPackageStartupMessages(library(lwgeom))
> suppressPackageStartupMessages(library(sf))
> nc = st_read(system.file("gpkg/nc.gpkg", package="sf"), quiet = TRUE)
> nc = st_transform(nc, 3857)
> st_perimeter(nc)[1:5]
Unknown WKB type (328)! Full WKB type number was (100663328).
Error in CPL_perimeter(st_geometry(x), FALSE) : lwgeom error
Calls: st_perimeter -> CPL_perimeter
Execution halted
BEGIN TEST testthat.R

R version 4.0.0 (2020-04-24) -- "Arbor Day"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: s390x-ibm-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> suppressPackageStartupMessages(library(sf))
> suppressPackageStartupMessages(library(lwgeom))
> 
> test_check("lwgeom")
Unknown WKB type (248)! Full WKB type number was (16777248).
-- 1. Error: Prints Points (@test-as_text.R#6)  --------------------------------
lwgeom error
Backtrace:
 1. testthat::expect_equal(st_asewkt(pt, 1), "SRID=4326;POINT(1 2.3)")
 4. lwgeom::st_asewkt(pt, 1)
 5. lwgeom::st_astext(x, digits = digits, EWKT = TRUE)
 6. lwgeom:::CPL_sfc_to_wkt(st_geometry(x), as.integer(digits))

Unknown WKB type (648)! Full WKB type number was (50331648).
-- 2. Error: Prints Polygons and Lines (@test-as_text.R#17)  -------------------
lwgeom error
Backtrace:
 1. testthat::expect_equal(st_astext(pol), txt)
 4. lwgeom::st_astext(pol)
 5. lwgeom:::CPL_sfc_to_wkt(st_geometry(x), as.integer(digits))

Unknown WKB type (648)! Full WKB type number was (50331648).
-- 3. Error: st_is_polygon_cw works on all classes (@test-clockwise.R#10)  -----
lwgeom error
Backtrace:
 1. testthat::expect_equal(c(FALSE, TRUE), st_is_polygon_cw(polys))
 5. lwgeom:::st_is_polygon_cw.sf(polys)
 7. lwgeom:::st_is_polygon_cw.sfc(st_geometry(x))
 8. lwgeom:::CPL_is_polygon_cw(x)

Unknown WKB type (648)! Full WKB type number was (50331648).
-- 4. Error: st_force_polygon_cw works on all classes (@test-clockwise.R#17)  --
lwgeom error
Backtrace:
 1. lwgeom::st_force_polygon_cw(polys)
 2. lwgeom:::st_force_polygon_cw.sf(polys)
 5. lwgeom:::st_force_polygon_cw.sfc(st_geometry(x))
 7. lwgeom:::CPL_force_polygon_cw(x)

Unknown WKB type (680)! Full WKB type number was (50331680).
-- 5. Error: st_force_polygon_cw preserves crs (@test-clockwise.R#28)  ---------
lwgeom error
Backtrace:
  1. testthat::expect_equal(st_crs(st_force_polygon_cw(polys)), st_crs(polys))
  6. lwgeom:::st_force_polygon_cw.sf(polys)
  9. lwgeom:::st_force_polygon_cw.sfc(st_geometry(x))
 11. lwgeom:::CPL_force_polygon_cw(x)

Unknown WKB type (648)! Full WKB type number was (50331648).
-- 6. Error: st_force_polyfon_cw works with Single polygon, ccw exterior ring on
lwgeom error
Backtrace:
 1. testthat::expect_false(st_is_polygon_cw(obj))
 5. lwgeom:::st_is_polygon_cw.sfc(obj)
 6. lwgeom:::CPL_is_polygon_cw(x)

Unknown WKB type (648)! Full WKB type number was (50331648).
-- 7. Error: st_force_polyfon_cw works with Single polygon, cw exterior ring onl
lwgeom error
Backtrace:
 1. testthat::expect_true(st_is_polygon_cw(obj))
 5. lwgeom:::st_is_polygon_cw.sfc(obj)
 6. lwgeom:::CPL_is_polygon_cw(x)

Unknown WKB type (648)! Full WKB type number was (50331648).
-- 8. Error: st_force_polyfon_cw works with Single polygon, ccw exterior ring, c
lwgeom error
Backtrace:
 1. testthat::expect_false(st_is_polygon_cw(obj))
 5. lwgeom:::st_is_polygon_cw.sfc(obj)
 6. lwgeom:::CPL_is_polygon_cw(x)

Unknown WKB type (648)! Full WKB type number was (50331648).
-- 9. Error: st_force_polyfon_cw works with Single polygon, cw exterior ring, cc
lwgeom error
Backtrace:
 1. testthat::expect_true(st_is_polygon_cw(obj))
 5. lwgeom:::st_is_polygon_cw.sfc(obj)
 6. lwgeom:::CPL_is_polygon_cw(x)

Unknown WKB type (648)! Full WKB type number was (50331648).
-- 10. Error: st_force_polyfon_cw works with Single polygon, ccw exterior ring, 
lwgeom error
Backtrace:
 1. testthat::expect_false(st_is_polygon_cw(obj))
 5. lwgeom:::st_is_polygon_cw.sfc(obj)
 6. lwgeom:::CPL_is_polygon_cw(x)

Unknown WKB type (648)! Full WKB type number was (50331648).
-- 11. Error: st_force_polyfon_cw works with Single polygon, cw exterior ring, m
lwgeom error
Backtrace:
 1. testthat::expect_false(st_is_polygon_cw(obj))
 5. lwgeom:::st_is_polygon_cw.sfc(obj)
 6. lwgeom:::CPL_is_polygon_cw(x)

Unknown WKB type (296)! Full WKB type number was (100663296).
-- 12. Error: st_force_polyfon_cw works with MultiPolygon, ccw exterior rings on
lwgeom error
Backtrace:
 1. testthat::expect_false(st_is_polygon_cw(obj))
 5. lwgeom:::st_is_polygon_cw.sfc(obj)
 6. lwgeom:::CPL_is_polygon_cw(x)

Unknown WKB type (296)! Full WKB type number was (100663296).
-- 13. Error: st_force_polyfon_cw works with MultiPolygon, cw exterior rings onl
lwgeom error
Backtrace:
 1. testthat::expect_true(st_is_polygon_cw(obj))
 5. lwgeom:::st_is_polygon_cw.sfc(obj)
 6. lwgeom:::CPL_is_polygon_cw(x)

Unknown WKB type (296)! Full WKB type number was (100663296).
-- 14. Error: st_force_polyfon_cw works with MultiPolygon, mixed exterior rings 
lwgeom error
Backtrace:
 1. testthat::expect_false(st_is_polygon_cw(obj))
 5. lwgeom:::st_is_polygon_cw.sfc(obj)
 6. lwgeom:::CPL_is_polygon_cw(x)

Unknown WKB type (648)! Full WKB type number was (50331648).
-- 15. Error: st_make_valid works (@test_lwgeom.R#12)  -------------------------
lwgeom error
Backtrace:
 1. testthat::expect_true(st_is_valid(lwgeom_make_valid(x)))
 5. lwgeom::lwgeom_make_valid(x)
 7. lwgeom:::CPL_make_valid(x)

Unknown WKB type (864)! Full WKB type number was (67108864).
-- 16. Error: st_minimum_bounding_circle works (@test_lwgeom.R#41)  ------------
lwgeom error
Backtrace:
 1. base::plot(st_minimum_bounding_circle(x), axes = TRUE)
 3. lwgeom:::st_minimum_bounding_circle.sfg(x)
 5. lwgeom:::st_minimum_bounding_circle.sfc(st_geometry(x), nQuadSegs)
 7. lwgeom:::generate_circles(x, nQuadSegs)
 8. lwgeom:::CPL_minimum_bounding_circle(geom)

-- 17. Error: st_subdivide works (@test_lwgeom.R#52)  --------------------------
lwgeom error
Backtrace:
  1. testthat::expect_silent(st_subdivide(x, 10))
 10. lwgeom:::st_subdivide.sf(x, 10)
 13. lwgeom:::st_subdivide.sfc(st_geometry(x), max_vertices)
 15. lwgeom:::CPL_subdivide(x, max_vertices)

Unknown WKB type (328)! Full WKB type number was (100663328).
Unknown WKB type (296)! Full WKB type number was (100663296).
-- 18. Error: st_transform_proj finds sf's PROJ files (@test_lwgeom.R#94)  -----
lwgeom error
Backtrace:
 1. sf::st_bbox(st_transform_proj(nc, "+proj=longlat"))
 3. lwgeom:::st_transform_proj.sf(nc, "+proj=longlat")
 5. lwgeom:::st_transform_proj.sfc(st_geometry(x), crs, ...)
 6. lwgeom:::CPL_lwgeom_transform(x, crs)

Unknown WKB type (464)! Full WKB type number was (33554464).
-- 19. Error: st_linesubstring warns on 4326 (@test_lwgeom.R#105)  -------------
lwgeom error
Backtrace:
 1. testthat::expect_warning(...)
 7. lwgeom:::st_linesubstring.sfc(lines, 0.2, 0.8)
 9. lwgeom:::CPL_linesubstring(x, from, to, tolerance)

Unknown WKB type (464)! Full WKB type number was (33554464).
-- 20. Error: st_startpoint works (@test_lwgeom.R#115)  ------------------------
lwgeom error
Backtrace:
 1. lwgeom::st_startpoint(...)
 2. lwgeom:::CPL_startpoint(st_geometry(x))

== testthat results  ===========================================================
[ OK: 3 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 20 ]
1. Error: Prints Points (@test-as_text.R#6) 
2. Error: Prints Polygons and Lines (@test-as_text.R#17) 
3. Error: st_is_polygon_cw works on all classes (@test-clockwise.R#10) 
4. Error: st_force_polygon_cw works on all classes (@test-clockwise.R#17) 
5. Error: st_force_polygon_cw preserves crs (@test-clockwise.R#28) 
6. Error: st_force_polyfon_cw works with Single polygon, ccw exterior ring only (@test-clockwise.R#36) 
7. Error: st_force_polyfon_cw works with Single polygon, cw exterior ring only (@test-clockwise.R#43) 
8. Error: st_force_polyfon_cw works with Single polygon, ccw exterior ring, cw interior rings (@test-clockwise.R#50) 
9. Error: st_force_polyfon_cw works with Single polygon, cw exterior ring, ccw interior rings (@test-clockwise.R#57) 
1. ...

Error: testthat unit tests failed
Execution halted
BEGIN TEST twkb.R

R version 4.0.0 (2020-04-24) -- "Arbor Day"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: s390x-ibm-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> l = structure(list(as.raw(c(0x02, 0x00, 0x02, 0x02, 0x02, 0x08, 0x08))), class = "TWKB")
> suppressPackageStartupMessages(library(sf))
> suppressPackageStartupMessages(library(lwgeom))
> st_as_sfc(l)
type is 0
Error in CPL_sfc_from_twkb(x) : 
  reading this sf type is not supported, please file an issue
Calls: st_as_sfc -> st_as_sfc.TWKB -> st_sfc -> CPL_sfc_from_twkb
Execution halted

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