Bug#1049438: marked as done (r-cran-rgdal: autopkgtest needs update for new version of r-cran-sp)

Wed, 29 Nov 2023 10:39:23 -0800 

Your message dated Wed, 29 Nov 2023 18:35:54 +0000
with message-id <e1r8ppe-0037ir...@fasolo.debian.org>
and subject line Bug#1055606: Removed package(s) from unstable
has caused the Debian Bug report #1049438,
regarding r-cran-rgdal: autopkgtest needs update for new version of r-cran-sp
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

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-- 
1049438: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1049438
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message --- 
Source: r-cran-rgdal
Version: 1.6-7+dfsg-1
Severity: serious
X-Debbugs-CC: r-cran...@packages.debian.org
Tags: sid trixie
User: debian...@lists.debian.org
Usertags: needs-update
Control: affects -1 src:r-cran-sp

Dear maintainer(s),
With a recent upload of r-cran-sp the autopkgtest of r-cran-rgdal fails in testing when that autopkgtest is run with the binary packages of r-cran-sp from unstable. It passes when run with only packages from testing. In tabular form: 

                       pass            fail
r-cran-sp              from testing    1:2.0-0+dfsg-1
r-cran-rgdal           from testing    1.6-7+dfsg-1
all others             from testing    from testing

I copied some of the output at the bottom of this report.
Currently this regression is blocking the migration of r-cran-sp to testing [1]. Of course, r-cran-sp shouldn't just break your autopkgtest (or even worse, your package), but your package needs to update to the new situation (or you have to help r-cran-sp maintainers to fix the issue in their package).
If this is a real problem in your package (and not only in your autopkgtest), the right binary package(s) from r-cran-sp should really add a versioned Breaks on the unfixed version of (one of your) package(s). Note: the Breaks is nice even if the issue is only in the autopkgtest as it helps the migration software to figure out the right versions to combine in the tests. 

More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation

Paul

[1] https://qa.debian.org/excuses.php?package=r-cran-sp

https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-cran-rgdal/36836475/log.gz

 44s BEGIN TEST test_enforce_xy.R
 44s  44s R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
 44s Copyright (C) 2023 The R Foundation for Statistical Computing
 44s Platform: x86_64-pc-linux-gnu (64-bit)
 44s  44s R is free software and comes with ABSOLUTELY NO WARRANTY.
 44s You are welcome to redistribute it under certain conditions.
 44s Type 'license()' or 'licence()' for distribution details.
 44s  44s R is a collaborative project with many contributors.
 44s Type 'contributors()' for more information and
 44s 'citation()' on how to cite R or R packages in publications.
 44s  44s Type 'demo()' for some demos, 'help()' for on-line help, or
 44s 'help.start()' for an HTML browser interface to help.
 44s Type 'q()' to quit R.
 44s  44s > suppressPackageStartupMessages(library(rgdal))
 44s > set_thin_PROJ6_warnings(TRUE)
 44s > if (new_proj_and_gdal()) {
 44s + get_enforce_xy()
 44s + x0 <- showSRID("EPSG:4326", multiline=TRUE, EPSG_to_init=FALSE)
 44s + cat(x0, "\n")
 44s + set_enforce_xy(FALSE)
 44s + x1 <- showSRID("EPSG:4326", multiline=TRUE, EPSG_to_init=FALSE)
 44s + cat(x1, "\n")
 44s + set_enforce_xy(TRUE)
 44s + x2 <- showSRID("EPSG:4326", multiline=TRUE, EPSG_to_init=FALSE)
 44s + cat(x2, "\n")
 44s + get_enforce_xy()
44s + y0 <- showSRID("EPSG:4326", multiline=TRUE, EPSG_to_init=FALSE, prefer_proj=TRUE) 
 44s + cat(y0, "\n")
44s + showSRID("EPSG:4326", format="PROJ", EPSG_to_init=FALSE, prefer_proj=TRUE) 
 44s + set_enforce_xy(FALSE)
44s + y1 <- showSRID("EPSG:4326", multiline=TRUE, EPSG_to_init=FALSE, prefer_proj=TRUE) 
 44s + cat(y1, "\n")
44s + showSRID("EPSG:4326", format="PROJ", EPSG_to_init=FALSE, prefer_proj=TRUE) 
 44s + set_enforce_xy(TRUE)
44s + y2 <- showSRID("EPSG:4326", multiline=TRUE, EPSG_to_init=FALSE, prefer_proj=TRUE) 
 44s + cat(y2, "\n")
44s + showSRID("EPSG:4326", format="PROJ", EPSG_to_init=FALSE, prefer_proj=TRUE) 
 44s + }
 44s GEOGCRS["WGS 84 (with axis order normalized for visualization)",
 44s     ENSEMBLE["World Geodetic System 1984 ensemble",
 44s         MEMBER["World Geodetic System 1984 (Transit)",
 44s             ID["EPSG",1166]],
 44s         MEMBER["World Geodetic System 1984 (G730)",
 44s             ID["EPSG",1152]],
 44s         MEMBER["World Geodetic System 1984 (G873)",
 44s             ID["EPSG",1153]],
 44s         MEMBER["World Geodetic System 1984 (G1150)",
 44s             ID["EPSG",1154]],
 44s         MEMBER["World Geodetic System 1984 (G1674)",
 44s             ID["EPSG",1155]],
 44s         MEMBER["World Geodetic System 1984 (G1762)",
 44s             ID["EPSG",1156]],
 44s         MEMBER["World Geodetic System 1984 (G2139)",
 44s             ID["EPSG",1309]],
 44s         ELLIPSOID["WGS 84",6378137,298.257223563,
 44s             LENGTHUNIT["metre",1],
 44s             ID["EPSG",7030]],
 44s         ENSEMBLEACCURACY[2.0],
 44s         ID["EPSG",6326]],
 44s     PRIMEM["Greenwich",0,
 44s         ANGLEUNIT["degree",0.0174532925199433],
 44s         ID["EPSG",8901]],
 44s     CS[ellipsoidal,2],
 44s         AXIS["geodetic longitude (Lon)",east,
 44s             ORDER[1],
 44s             ANGLEUNIT["degree",0.0174532925199433,
 44s                 ID["EPSG",9122]]],
 44s         AXIS["geodetic latitude (Lat)",north,
 44s             ORDER[2],
 44s             ANGLEUNIT["degree",0.0174532925199433,
 44s                 ID["EPSG",9122]]],
 44s     USAGE[
 44s         SCOPE["Horizontal component of 3D system."],
 44s         AREA["World."],
 44s         BBOX[-90,-180,90,180]],
44s REMARK["Axis order reversed compared to EPSG:4326"]] 44s GEOGCRS["WGS 84", 
 44s     ENSEMBLE["World Geodetic System 1984 ensemble",
 44s         MEMBER["World Geodetic System 1984 (Transit)"],
 44s         MEMBER["World Geodetic System 1984 (G730)"],
 44s         MEMBER["World Geodetic System 1984 (G873)"],
 44s         MEMBER["World Geodetic System 1984 (G1150)"],
 44s         MEMBER["World Geodetic System 1984 (G1674)"],
 44s         MEMBER["World Geodetic System 1984 (G1762)"],
 44s         MEMBER["World Geodetic System 1984 (G2139)"],
 44s         ELLIPSOID["WGS 84",6378137,298.257223563,
 44s             LENGTHUNIT["metre",1]],
 44s         ENSEMBLEACCURACY[2.0]],
 44s     PRIMEM["Greenwich",0,
 44s         ANGLEUNIT["degree",0.0174532925199433]],
 44s     CS[ellipsoidal,2],
 44s         AXIS["geodetic latitude (Lat)",north,
 44s             ORDER[1],
 44s             ANGLEUNIT["degree",0.0174532925199433]],
 44s         AXIS["geodetic longitude (Lon)",east,
 44s             ORDER[2],
 44s             ANGLEUNIT["degree",0.0174532925199433]],
 44s     USAGE[
 44s         SCOPE["Horizontal component of 3D system."],
 44s         AREA["World."],
 44s         BBOX[-90,-180,90,180]],
44s ID["EPSG",4326]] 44s GEOGCRS["WGS 84 (with axis order normalized for visualization)", 
 44s     ENSEMBLE["World Geodetic System 1984 ensemble",
 44s         MEMBER["World Geodetic System 1984 (Transit)",
 44s             ID["EPSG",1166]],
 44s         MEMBER["World Geodetic System 1984 (G730)",
 44s             ID["EPSG",1152]],
 44s         MEMBER["World Geodetic System 1984 (G873)",
 44s             ID["EPSG",1153]],
 44s         MEMBER["World Geodetic System 1984 (G1150)",
 44s             ID["EPSG",1154]],
 44s         MEMBER["World Geodetic System 1984 (G1674)",
 44s             ID["EPSG",1155]],
 44s         MEMBER["World Geodetic System 1984 (G1762)",
 44s             ID["EPSG",1156]],
 44s         MEMBER["World Geodetic System 1984 (G2139)",
 44s             ID["EPSG",1309]],
 44s         ELLIPSOID["WGS 84",6378137,298.257223563,
 44s             LENGTHUNIT["metre",1],
 44s             ID["EPSG",7030]],
 44s         ENSEMBLEACCURACY[2.0],
 44s         ID["EPSG",6326]],
 44s     PRIMEM["Greenwich",0,
 44s         ANGLEUNIT["degree",0.0174532925199433],
 44s         ID["EPSG",8901]],
 44s     CS[ellipsoidal,2],
 44s         AXIS["geodetic longitude (Lon)",east,
 44s             ORDER[1],
 44s             ANGLEUNIT["degree",0.0174532925199433,
 44s                 ID["EPSG",9122]]],
 44s         AXIS["geodetic latitude (Lat)",north,
 44s             ORDER[2],
 44s             ANGLEUNIT["degree",0.0174532925199433,
 44s                 ID["EPSG",9122]]],
 44s     USAGE[
 44s         SCOPE["Horizontal component of 3D system."],
 44s         AREA["World."],
 44s         BBOX[-90,-180,90,180]],
44s REMARK["Axis order reversed compared to EPSG:4326"]] 44s GEOGCRS["WGS 84 (with axis order normalized for visualization)", 
 44s     ENSEMBLE["World Geodetic System 1984 ensemble",
 44s         MEMBER["World Geodetic System 1984 (Transit)",
 44s             ID["EPSG",1166]],
 44s         MEMBER["World Geodetic System 1984 (G730)",
 44s             ID["EPSG",1152]],
 44s         MEMBER["World Geodetic System 1984 (G873)",
 44s             ID["EPSG",1153]],
 44s         MEMBER["World Geodetic System 1984 (G1150)",
 44s             ID["EPSG",1154]],
 44s         MEMBER["World Geodetic System 1984 (G1674)",
 44s             ID["EPSG",1155]],
 44s         MEMBER["World Geodetic System 1984 (G1762)",
 44s             ID["EPSG",1156]],
 44s         MEMBER["World Geodetic System 1984 (G2139)",
 44s             ID["EPSG",1309]],
 44s         ELLIPSOID["WGS 84",6378137,298.257223563,
 44s             LENGTHUNIT["metre",1],
 44s             ID["EPSG",7030]],
 44s         ENSEMBLEACCURACY[2.0],
 44s         ID["EPSG",6326]],
 44s     PRIMEM["Greenwich",0,
 44s         ANGLEUNIT["degree",0.0174532925199433],
 44s         ID["EPSG",8901]],
 44s     CS[ellipsoidal,2],
 44s         AXIS["geodetic longitude (Lon)",east,
 44s             ORDER[1],
 44s             ANGLEUNIT["degree",0.0174532925199433,
 44s                 ID["EPSG",9122]]],
 44s         AXIS["geodetic latitude (Lat)",north,
 44s             ORDER[2],
 44s             ANGLEUNIT["degree",0.0174532925199433,
 44s                 ID["EPSG",9122]]],
 44s     USAGE[
 44s         SCOPE["Horizontal component of 3D system."],
 44s         AREA["World."],
 44s         BBOX[-90,-180,90,180]],
44s REMARK["Axis order reversed compared to EPSG:4326"]] 44s GEOGCRS["WGS 84", 
 44s     ENSEMBLE["World Geodetic System 1984 ensemble",
 44s         MEMBER["World Geodetic System 1984 (Transit)"],
 44s         MEMBER["World Geodetic System 1984 (G730)"],
 44s         MEMBER["World Geodetic System 1984 (G873)"],
 44s         MEMBER["World Geodetic System 1984 (G1150)"],
 44s         MEMBER["World Geodetic System 1984 (G1674)"],
 44s         MEMBER["World Geodetic System 1984 (G1762)"],
 44s         MEMBER["World Geodetic System 1984 (G2139)"],
 44s         ELLIPSOID["WGS 84",6378137,298.257223563,
 44s             LENGTHUNIT["metre",1]],
 44s         ENSEMBLEACCURACY[2.0]],
 44s     PRIMEM["Greenwich",0,
 44s         ANGLEUNIT["degree",0.0174532925199433]],
 44s     CS[ellipsoidal,2],
 44s         AXIS["geodetic latitude (Lat)",north,
 44s             ORDER[1],
 44s             ANGLEUNIT["degree",0.0174532925199433]],
 44s         AXIS["geodetic longitude (Lon)",east,
 44s             ORDER[2],
 44s             ANGLEUNIT["degree",0.0174532925199433]],
 44s     USAGE[
 44s         SCOPE["Horizontal component of 3D system."],
 44s         AREA["World."],
 44s         BBOX[-90,-180,90,180]],
44s ID["EPSG",4326]] 44s GEOGCRS["WGS 84 (with axis order normalized for visualization)", 
 44s     ENSEMBLE["World Geodetic System 1984 ensemble",
 44s         MEMBER["World Geodetic System 1984 (Transit)",
 44s             ID["EPSG",1166]],
 44s         MEMBER["World Geodetic System 1984 (G730)",
 44s             ID["EPSG",1152]],
 44s         MEMBER["World Geodetic System 1984 (G873)",
 44s             ID["EPSG",1153]],
 44s         MEMBER["World Geodetic System 1984 (G1150)",
 44s             ID["EPSG",1154]],
 44s         MEMBER["World Geodetic System 1984 (G1674)",
 44s             ID["EPSG",1155]],
 44s         MEMBER["World Geodetic System 1984 (G1762)",
 44s             ID["EPSG",1156]],
 44s         MEMBER["World Geodetic System 1984 (G2139)",
 44s             ID["EPSG",1309]],
 44s         ELLIPSOID["WGS 84",6378137,298.257223563,
 44s             LENGTHUNIT["metre",1],
 44s             ID["EPSG",7030]],
 44s         ENSEMBLEACCURACY[2.0],
 44s         ID["EPSG",6326]],
 44s     PRIMEM["Greenwich",0,
 44s         ANGLEUNIT["degree",0.0174532925199433],
 44s         ID["EPSG",8901]],
 44s     CS[ellipsoidal,2],
 44s         AXIS["geodetic longitude (Lon)",east,
 44s             ORDER[1],
 44s             ANGLEUNIT["degree",0.0174532925199433,
 44s                 ID["EPSG",9122]]],
 44s         AXIS["geodetic latitude (Lat)",north,
 44s             ORDER[2],
 44s             ANGLEUNIT["degree",0.0174532925199433,
 44s                 ID["EPSG",9122]]],
 44s     USAGE[
 44s         SCOPE["Horizontal component of 3D system."],
 44s         AREA["World."],
 44s         BBOX[-90,-180,90,180]],
44s REMARK["Axis order reversed compared to EPSG:4326"]] 44s [1] "+proj=longlat +datum=WGS84 +no_defs +type=crs" 
 44s >  44s >  44s BEGIN TEST test_proj.R
 44s  44s R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
 44s Copyright (C) 2023 The R Foundation for Statistical Computing
 44s Platform: x86_64-pc-linux-gnu (64-bit)
 44s  44s R is free software and comes with ABSOLUTELY NO WARRANTY.
 44s You are welcome to redistribute it under certain conditions.
 44s Type 'license()' or 'licence()' for distribution details.
 44s  44s R is a collaborative project with many contributors.
 44s Type 'contributors()' for more information and
 44s 'citation()' on how to cite R or R packages in publications.
 44s  44s Type 'demo()' for some demos, 'help()' for on-line help, or
 44s 'help.start()' for an HTML browser interface to help.
 44s Type 'q()' to quit R.
 44s  44s > suppressPackageStartupMessages(library(rgdal))
 45s > set_thin_PROJ6_warnings(TRUE)
 45s > data(state)
 45s > xy <- cbind(state.center$x, state.center$y)
45s > res <- project(xy, "+proj=lcc +lat_1=48 +lat_2=33 +lon_0=-100 +ellps=GRS80") 
 45s Warning message:
45s PROJ support is provided by the sf and terra packages among others 45s > res1 <- project(res, "+proj=lcc +lat_1=48 +lat_2=33 +lon_0=-100 +ellps=GRS80", 
 45s +  inv=TRUE)
 45s Warning messages:
45s 1: PROJ support is provided by the sf and terra packages among others 45s 2: PROJ support is provided by the sf and terra packages among others 45s > stopifnot(isTRUE(all.equal(res1, xy))) 
 45s > states <- data.frame(state.x77, state.center)
 45s > states <- states[states$x > -121,]
 45s > coordinates(states) <- c("x", "y")
 45s > proj4string(states) <- CRS("+proj=longlat +ellps=clrk66")
 45s Warning message:
 45s In CRS("+proj=longlat +ellps=clrk66") :
 45s   sf required for evolution_status==2L
 45s > state.ll83 <- spTransform(states, CRS("+proj=longlat +ellps=GRS80"))
 45s Warning messages:
 45s 1: In CRS("+proj=longlat +ellps=GRS80") :
 45s   sf required for evolution_status==2L
 45s 2: In spTransform(xSP, CRSobj, ...) :
 45s   NULL source CRS comment, falling back to PROJ string
 45s 3: In spTransform(xSP, CRSobj, ...) :
 45s   NULL target CRS comment, falling back to PROJ string
 45s 4: In is.projected(p4str) : Package sf not available
45s > state.ll <- spTransform(state.ll83, CRS("+proj=longlat +ellps=clrk66")) 
 45s Warning messages:
 45s 1: In spTransform(xSP, CRSobj, ...) :
 45s   NULL source CRS comment, falling back to PROJ string
 45s 2: In spTransform(xSP, CRSobj, ...) :
 45s   NULL target CRS comment, falling back to PROJ string
 45s 3: In is.projected(p4str) : Package sf not available
45s > stopifnot(isTRUE(all.equal(coordinates(states), coordinates(state.ll)))) 
 45s > broke_proj <- FALSE
 45s > pv <- .Call("PROJ4VersionInfo", PACKAGE="rgdal")[[2]]
 45s > # https://github.com/OSGeo/PROJ/issues/1525
 45s > if (pv >= 600 && pv < 620) broke_proj <- TRUE
 45s > if (!broke_proj) {
 45s + (crds <- matrix(data=c(9.05, 48.52), ncol=2))
 45s + (a <- project(crds, paste("+proj=ob_tran +o_proj=longlat",
 45s +  "+o_lon_p=-162 +o_lat_p=39.25 +lon_0=180 +ellps=sphere +no_defs"),
 45s +  use_ob_tran=TRUE, verbose=TRUE))
45s + stopifnot(isTRUE(all.equal(a, matrix(c(-5.917698, -1.87195), ncol=2), tolerance=.Machine$double.eps ^ 0.25))) 
 45s + (a1 <- project(a, paste("+proj=ob_tran +o_proj=longlat",
 45s +  "+o_lon_p=-162 +o_lat_p=39.25 +lon_0=180 +ellps=sphere +no_defs"),
 45s +  inv=TRUE, use_ob_tran=TRUE, verbose=TRUE))
45s + stopifnot(isTRUE(all.equal(a1, crds, tolerance=.Machine$double.eps ^ 0.25))) 
 45s + spPoint <- SpatialPoints(coords=crds,
 45s +  proj4string=CRS("+proj=longlat +ellps=sphere +no_defs"))
 45s + a <- spTransform(spPoint, CRS(paste("+proj=ob_tran +o_proj=longlat",
 45s +  "+o_lon_p=-162 +o_lat_p=39.25 +lon_0=180 +ellps=sphere +no_defs")),
 45s +  use_ob_tran=TRUE)
45s + stopifnot(isTRUE(all.equal(unname(coordinates(a)), matrix(c(-5.917698, -1.87195), ncol=2), tolerance=.Machine$double.eps ^ 0.25))) 
 45s + a1 <- spTransform(a, CRS("+proj=longlat +ellps=sphere +no_defs"),
 45s +  use_ob_tran=TRUE)
45s + stopifnot(isTRUE(all.equal(unname(coordinates(a1)), unname(coordinates(spPoint)), tolerance=.Machine$double.eps ^ 0.25))) 
 45s + }
 45s +proj=pipeline +step +proj=unitconvert +xy_in=deg +xy_out=rad +step
 45s +inv +proj=ob_tran +o_proj=longlat +o_lon_p=-162 +o_lat_p=39.25
45s +lon_0=180 +ellps=sphere +step +proj=unitconvert +xy_in=rad +xy_out=deg 
 45s +proj=pipeline +step +proj=unitconvert +xy_in=deg +xy_out=rad +step
 45s +proj=ob_tran +o_proj=longlat +o_lon_p=-162 +o_lat_p=39.25 +lon_0=180
 45s +ellps=sphere +step +proj=unitconvert +xy_in=rad +xy_out=deg
45s > sp <- SpatialPoints(matrix(c(1, 1), nrow=1), proj4string=CRS("+init=epsg:4326")) 
 45s There were 12 warnings (use warnings() to see them)
 45s Warning message:
 45s In CRS("+init=epsg:4326") : sf required for evolution_status==2L
 45s > sp.tr <- spTransform(sp, CRS("+init=epsg:3857"))
45s Error in spTransform(sp, CRS("+init=epsg:3857")) : 45s source crs creation failed: Invalid PROJ string syntax 
 45s Calls: spTransform -> spTransform
 45s In addition: Warning messages:
 45s 1: In CRS("+init=epsg:3857") : sf required for evolution_status==2L
 45s 2: In spTransform(sp, CRS("+init=epsg:3857")) :
 45s   NULL source CRS comment, falling back to PROJ string
 45s 3: In spTransform(sp, CRS("+init=epsg:3857")) :
 45s   +init dropped in PROJ string
 45s 4: In spTransform(sp, CRS("+init=epsg:3857")) :
 45s   NULL target CRS comment, falling back to PROJ string
 45s 5: In spTransform(sp, CRS("+init=epsg:3857")) :
 45s   +init dropped in PROJ string
 45s 6: In is.projected(p4str) : Package sf not available
45s 7: PROJ support is provided by the sf and terra packages among others 45s Execution halted 
 45s autopkgtest [23:22:38]: test run-unit-test

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--- End Message ---
--- Begin Message --- 
Version: 1.6-7+dfsg-1+rm

Dear submitter,

as the package r-cran-rgdal has just been removed from the Debian archive
unstable we hereby close the associated bug reports.  We are sorry
that we couldn't deal with your issue properly.

For details on the removal, please see https://bugs.debian.org/1055606

The version of this package that was in Debian prior to this removal
can still be found using https://snapshot.debian.org/.

Please note that the changes have been done on the master archive and
will not propagate to any mirrors until the next dinstall run at the
earliest.

This message was generated automatically; if you believe that there is
a problem with it please contact the archive administrators by mailing
ftpmas...@ftp-master.debian.org.

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