- using R Under development (unstable) (2025-09-08 r88797)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
clang version 21.1.0
flang version 21.1.0
- running under: Fedora Linux 42 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- checking for file ‘gstat/DESCRIPTION’ ... OK
- this is package ‘gstat’ version ‘2.1-4’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘gstat’ can be installed ... [35s/80s] OK
See the install log for details.
- used C compiler: ‘clang version 21.1.0’
- checking installed package size ... OK
- checking package directory ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... OK
- checking whether the package can be loaded with stated dependencies ... OK
- checking whether the package can be unloaded cleanly ... OK
- checking whether the namespace can be loaded with stated dependencies ... OK
- checking whether the namespace can be unloaded cleanly ... [2s/11s] OK
- checking loading without being on the library search path ... OK
- checking whether startup messages can be suppressed ... OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [42s/123s] OK
- checking Rd files ... OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking line endings in shell scripts ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking compilation flags in Makevars ... OK
- checking for GNU extensions in Makefiles ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking use of PKG_*FLAGS in Makefiles ... OK
- checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compilation flags used ... OK
- checking compiled code ... OK
- checking sizes of PDF files under ‘inst/doc’ ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [23s/55s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [0m/90m] ERROR
Running ‘allier.R’
Comparing ‘allier.Rout’ to ‘allier.Rout.save’ ... OK
Running ‘blockkr.R’
Comparing ‘blockkr.Rout’ to ‘blockkr.Rout.save’ ... OK
Running ‘covtable.R’
Comparing ‘covtable.Rout’ to ‘covtable.Rout.save’ ... OK
Running ‘cv.R’ [3s/12s]
Comparing ‘cv.Rout’ to ‘cv.Rout.save’ ... OK
Running ‘cv3d.R’ [4s/11s]
Comparing ‘cv3d.Rout’ to ‘cv3d.Rout.save’ ... OK
Running ‘fit.R’
Comparing ‘fit.Rout’ to ‘fit.Rout.save’ ... OK
Running ‘krige0.R’ [5s/14s]
Comparing ‘krige0.Rout’ to ‘krige0.Rout.save’ ... OK
Running ‘line.R’ [3s/11s]
Comparing ‘line.Rout’ to ‘line.Rout.save’ ... OK
Running ‘merge.R’
Comparing ‘merge.Rout’ to ‘merge.Rout.save’ ... OK
Running ‘na.action.R’
Comparing ‘na.action.Rout’ to ‘na.action.Rout.save’ ... OK
Running ‘rings.R’ [3s/10s]
Comparing ‘rings.Rout’ to ‘rings.Rout.save’ ... OK
Running ‘sim.R’
Comparing ‘sim.Rout’ to ‘sim.Rout.save’ ... OK
Running ‘stars.R’ [41s/86s]
Comparing ‘stars.Rout’ to ‘stars.Rout.save’ ... OK
Running ‘variogram.R’
Comparing ‘variogram.Rout’ to ‘variogram.Rout.save’ ... OK
Running ‘vdist.R’
Comparing ‘vdist.Rout’ to ‘vdist.Rout.save’ ... OK
Running ‘windst.R’ [0m/87m]
Running the tests in ‘tests/windst.R’ failed.
Complete output:
> suppressPackageStartupMessages(library(sp))
> suppressPackageStartupMessages(library(spacetime))
> suppressPackageStartupMessages(library(gstat))
> suppressPackageStartupMessages(library(stars))
>
> data(wind)
> wind.loc$y = as.numeric(char2dms(as.character(wind.loc[["Latitude"]])))
> wind.loc$x = as.numeric(char2dms(as.character(wind.loc[["Longitude"]])))
> coordinates(wind.loc) = ~x+y
> proj4string(wind.loc) = "+proj=longlat +datum=WGS84 +ellps=WGS84"
>
> wind$time = ISOdate(wind$year+1900, wind$month, wind$day)
> wind$jday = as.numeric(format(wind$time, '%j'))
> stations = 4:15
> windsqrt = sqrt(0.5148 * wind[stations]) # knots -> m/s
> Jday = 1:366
> daymeans = colMeans(
+ sapply(split(windsqrt - colMeans(windsqrt), wind$jday), colMeans))
> meanwind = lowess(daymeans ~ Jday, f = 0.1)$y[wind$jday]
> velocities = apply(windsqrt, 2, function(x) { x - meanwind })
> # match order of columns in wind to Code in wind.loc;
> # convert to utm zone 29, to be able to do interpolation in
> # proper Euclidian (projected) space:
> pts = coordinates(wind.loc[match(names(wind[4:15]), wind.loc$Code),])
> pts = SpatialPoints(pts)
> if (require(sp, quietly = TRUE) && require(maps, quietly = TRUE)) {
+ proj4string(pts) = "+proj=longlat +datum=WGS84 +ellps=WGS84"
+ utm29 = "+proj=utm +zone=29 +datum=WGS84 +ellps=WGS84"
+ pts = as(st_transform(st_as_sfc(pts), utm29), "Spatial")
+ # note the t() in:
+ w = STFDF(pts, wind$time, data.frame(values = as.vector(t(velocities))))
+
+ library(mapdata)
+ mp = map("worldHires", xlim = c(-11,-5.4), ylim = c(51,55.5), plot=FALSE)
+ sf = st_transform(st_as_sf(mp, fill = FALSE), utm29)
+ m = as(sf, "Spatial")
+
+ # setup grid
+ grd = SpatialPixels(SpatialPoints(makegrid(m, n = 300)),
+ proj4string = m@proj4string)
+ # grd$t = rep(1, nrow(grd))
+ #coordinates(grd) = ~x1+x2
+ #gridded(grd)=TRUE
+
+ # select april 1961:
+ w = w[, "1961-04"]
+
+ covfn = function(x, y = x) {
+ du = spDists(coordinates(x), coordinates(y))
+ t1 = as.numeric(index(x)) # time in seconds
+ t2 = as.numeric(index(y)) # time in seconds
+ dt = abs(outer(t1, t2, "-"))
+ # separable, product covariance model:
+ 0.6 * exp(-du/750000) * exp(-dt / (1.5 * 3600 * 24))
+ }
+
+ n = 10
+ tgrd = seq(min(index(w)), max(index(w)), length=n)
+ pred = krige0(sqrt(values)~1, w, STF(grd, tgrd), covfn)
+ layout = list(list("sp.points", pts, first=F, cex=.5),
+ list("sp.lines", m, col='grey'))
+ wind.pr0 = STFDF(grd, tgrd, data.frame(var1.pred = pred))
+
+ v = vgmST("separable",
+ space = vgm(1, "Exp", 750000),
+ time = vgm(1, "Exp", 1.5 * 3600 * 24),
+ sill = 0.6)
+ wind.ST = krigeST(sqrt(values)~1, w, STF(grd, tgrd), v)
+
+ all.equal(wind.pr0, wind.ST)
+
+ # stars:
+ df = data.frame(a = rep(NA, 324*10))
+ s = STF(grd, tgrd)
+ newd = addAttrToGeom(s, df)
+ wind.sta = krigeST(sqrt(values)~1, st_as_stars(w), st_as_stars(newd), v)
+ # 1
+ plot(stars::st_as_stars(wind.ST), breaks = "equal", col = sf.colors())
+ # 2
+ stplot(wind.ST)
+ # 3
+ plot(wind.sta, breaks = "equal", col = sf.colors())
+ st_as_stars(wind.ST)[[1]][1:3,1:3,1]
+ (wind.sta)[[1]][1:3,1:3,1]
+ st_bbox(wind.sta)
+ bbox(wind.ST)
+ all.equal(wind.sta, stars::st_as_stars(wind.ST), check.attributes = FALSE)
+
+ # 4: roundtrip wind.sta->STFDF->stars
+ rt = stars::st_as_stars(as(wind.sta, "STFDF"))
+ plot(rt, breaks = "equal", col = sf.colors())
+ # 5:
+ stplot(as(wind.sta, "STFDF"))
+ st_bbox(rt)
+
+ # 6:
+ stplot(as(st_as_stars(wind.ST), "STFDF"))
+ }
OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [69s/342s] OK
- checking PDF version of manual ... [12s/46s] OK
- checking HTML version of manual ... [7s/42s] OK
- checking for non-standard things in the check directory ... OK
- checking for detritus in the temp directory ... OK
- DONE
Status: 1 ERROR