Missing or unexported object: ‘rgdal::OSRIsProjected’

[edzer]

current check:

* checking dependencies in R code ... NOTE
Missing or unexported object: ‘rgdal::OSRIsProjected’

[rsbivand]

Yes, and with R-devel a WARNING for the same. Time to release 1.4-4 to permit an rgdal release (telling CRAN team that the NOTE/WARNING will go away when rgdal is released)?

[edzer]

Done!

[rsbivand]

Any news on progress? No sign yet on: https://cran.r-project.org/web/checks/check_results_sp.html, which I'd prefer to see before moving on rgdal.

[edzer]

I'm sorry - yes, this came back:

Dear maintainer,

package sp_1.4-4.tar.gz has been auto-processed. The auto-check found problems when checking the first order strong reverse dependencies.
Please reply-all and explain: Is this expected or do you need to fix anything in your package? If expected, have all maintainers of affected packages been informed well in advance? Are there false positives in our results?

*** Changes to worse in reverse dependencies ***
Debian: <https://win-builder.r-project.org/incoming_pretest/sp_1.4-4_20201005_152003/reverseDependencies/summary.txt>

Log dir: <https://win-builder.r-project.org/incoming_pretest/sp_1.4-4_20201005_152003/>
The files will be removed after roughly 7 days.

Pretests:
Windows: <https://win-builder.r-project.org/incoming_pretest/sp_1.4-4_20201005_152003/Windows/00check.log>
Debian: <https://win-builder.r-project.org/incoming_pretest/sp_1.4-4_20201005_152003/Debian/00check.log>

Last published version on CRAN:

CRAN Web: <https://cran.r-project.org/package=sp>

Best regards,
CRAN teams' auto-check service

Package check result: WARN

Check: CRAN incoming feasibility, Result: Note_to_CRAN_maintainers
  Maintainer: ‘Edzer Pebesma <edzer.pebesma@uni-muenster.de>’

Check: dependencies in R code, Result: WARNING
  Missing or unexported object: ‘rgdal::OSRIsProjected’

Changes to worse in reverse depends:

Package: BIRDS
Check: examples
New result: ERROR
  Running examples in ‘BIRDS-Ex.R’ failed
  The error most likely occurred in:

  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: spatialVisits
  > ### Title: A function to make the exploreVisits Spatial
  > ### Aliases: spatialVisits
  > 
  > ### ** Examples
  > 
  > # create a visit-based data object from the original observation-based data
  > library(sp)
  > OB<-organizeBirds(bombusObsShort)
  Warning in proj4string(x) :
    CRS object has comment, which is lost in output
  Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO") :
    Discarded datum WGS_1984 in CRS definition,
   but +towgs84= values preserved
  > visitStats<-exploreVisits(OB)
  Analysing 765 visits...
  Error in .pointsToMatrix(p1) : 
    Points are projected. They should be in degrees (longitude/latitude)
  Calls: exploreVisits -> lapply -> FUN -> <Anonymous> -> .pointsToMatrix
  Execution halted

Package: GapAnalysis
Check: examples
New result: ERROR
  Running examples in ‘GapAnalysis-Ex.R’ failed
  The error most likely occurred in:

  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: ERSex
  > ### Title: Ecological representativeness score ex situ
  > ### Aliases: ERSex
  > 
  > ### ** Examples
  > 
  > ##Obtaining occurrences from example
  > data(CucurbitaData)
  > Cucurbita_splist <- unique(CucurbitaData$species)
  > ## Obtaining rasterList object. ##
  > data(CucurbitaRasters)
  > CucurbitaRasters <- raster::unstack(CucurbitaRasters)
  > ##Obtaining ecoregions shapefile
  > data(ecoregions)
  > #Running ERSex
  > ERSex_df <- ERSex(Species_list = Cucurbita_splist,
  +                     Occurrence_data = CucurbitaData,
  +                     Raster_list = CucurbitaRasters,
  +                     Buffer_distance = 50000,
  +                     Ecoregions_shp=ecoregions,
  +                     Gap_Map=FALSE)
  Error in .check_input(xy, dist_m, step_dg, crs, output) : 
    The spatial object `xy` is projected.  Expecting unprojected coordinates, i.e. longitude-latitude in decimal degrees.
  Calls: ERSex -> <Anonymous> -> .check_input
  Execution halted

Package: trip
Check: tests
New result: ERROR
    Running ‘spelling.R’ [0s/0s]
    Running ‘testthat.R’ [11s/11s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(trip)
    > 
    > test_check("trip")
    ── 1. Failure: speedfilter and sdafilter works (@test-algos.R#27)  ─────────────
    `speedfilter(tr, 20)` did not produce any warnings.

    ── 2. Failure: speedfilter and sdafilter works (@test-algos.R#29)  ─────────────
    `expect_equal(expect_output(speedfilter(tr)), tr)` did not produce any warnings.

    ── 3. Error: angle calculation works (@test-algos.R#39)  ───────────────────────
    no 'source' projection included, and does not look like longitude/latitude values
    Backtrace:
      1. testthat::expect_warning(trackAngle(tra))
      7. trip:::trackAngle.trip(tra)
      9. trip:::reproj.trip(x, .llproj())
     13. reproj:::reproj.matrix(xy, target = target, source = x@proj4string@projargs)

    Longitudes contain values greater than 180, 

     Data fully validated: returning object of class  trip 
    ══ testthat results  ═══════════════════════════════════════════════════════════
    [ OK: 117 | SKIPPED: 0 | WARNINGS: 12 | FAILED: 3 ]
    1. Failure: speedfilter and sdafilter works (@test-algos.R#27) 
    2. Failure: speedfilter and sdafilter works (@test-algos.R#29) 
    3. Error: angle calculation works (@test-algos.R#39) 

    Error: testthat unit tests failed
    Execution halted

[rsbivand]

BIRDS is failing because a BOUNDCRS is seen as projected - they are passing in very badly formed Proj4 strings including +towgs84=0,0,0,0,0,0,0. I also have https://github.com/Greensway/BIRDS/issues/17, to which they should respond. Their R/organizeBirds.R is hopeless.

trip is resolved https://github.com/Trackage/trip/issues/45 but not yet released.

GapAnalysis passes for me with rgdal devel, fails with CRAN rgdal, again a BOUNDCRS problem. Will pass when rgdal gets to CRAN.

These three responses should be enough for CRAN team, I hope.

[edzer]

sp 1.4-4 is now on CRAN!