Running ‘crop.R’
  Comparing ‘crop.Rout’ to ‘crop.Rout.save’ ... OK
  Running ‘meta.R’
  Running ‘nc.R’
  Comparing ‘nc.Rout’ to ‘nc.Rout.save’ ...5c5
< Reading layer `nc.gpkg' from data source `/data/gannet/ripley/R/test-3.6/sf/gpkg/nc.gpkg' using driver `GPKG'
---
> Reading layer `nc.gpkg' from data source `/home/edzer/R/x86_64-pc-linux-gnu-library/3.4/sf/gpkg/nc.gpkg' using driver `GPKG'
  Running ‘raster.R’
  Comparing ‘raster.Rout’ to ‘raster.Rout.save’ ... OK
  Running ‘rectilinear.R’
  Comparing ‘rectilinear.Rout’ to ‘rectilinear.Rout.save’ ... OK
  Running ‘sf.R’
  Running ‘spacetime.R’
  Running ‘stars.R’
  Running ‘testthat.R’
  Running ‘tidy.R’
  Comparing ‘tidy.Rout’ to ‘tidy.Rout.save’ ... OK
  Running ‘transform.R’
  Running ‘write.R’
Running the tests in ‘tests/meta.R’ failed.
Complete output:
  > suppressPackageStartupMessages(library(stars))
  > tif = system.file("tif/L7_ETMs.tif", package = "stars")
  > x = read_stars_meta(tif)
  > geomatrix = system.file("tif/geomatrix.tif", package = "stars")
  > x = read_stars_meta(geomatrix)
  Error in if (properties$bands[2] == 0) { : 
    missing value where TRUE/FALSE needed
  Calls: read_stars_meta
  Execution halted
Running the tests in ‘tests/sf.R’ failed.
Complete output:
  > suppressPackageStartupMessages(library(stars))
  > library(sf)
  > #jp2 = system.file("jp2/B01.jp2", package = "stars")
  > #(x = read_stars(jp2, options = c("OVERVIEW_LEVEL=3")))
  > tif = system.file("tif/L7_ETMs.tif", package = "stars")
  > (x = read_stars(tif, options = c("OVERVIEW_LEVEL=3")))
  stars object with 3 dimensions and 1 attribute
  attribute(s):
    L7_ETMs.tif    
   Min.   : 12.00  
   1st Qu.: 58.00  
   Median : 71.00  
   Mean   : 69.24  
   3rd Qu.: 83.00  
   Max.   :137.00  
  dimension(s):
       from to  offset   delta                       refsys point values
  x       1 22  288776 452.114 +proj=utm +zone=25 +south... FALSE   NULL
  y       1 22 9120761    -456 +proj=utm +zone=25 +south... FALSE   NULL
  band    1  6      NA      NA                           NA    NA   NULL
  > # names(x) = "L7_ETM"
  > 
  > # library(abind)
  > # x = adrop(x)
  > image(x)
  > (sfc = st_as_sfc(x, as_points = FALSE))
  Error in x[[xy_names[1]]] : 
    attempt to select less than one element in get1index
  Calls: st_as_sfc ... st_as_sfc.stars -> st_as_sfc -> st_as_sfc.dimensions
  Execution halted
Running the tests in ‘tests/spacetime.R’ failed.
Complete output:
  > suppressPackageStartupMessages(library(stars))
  > library(spacetime)
  > set.seed(1331)
  > example(STFDF)
  
  STFDF> sp = cbind(x = c(0,0,1), y = c(0,1,1))
  
  STFDF> row.names(sp) = paste("point", 1:nrow(sp), sep="")
  
  STFDF> library(sp)
  
  STFDF> sp = SpatialPoints(sp)
  
  STFDF> time = as.POSIXct("2010-08-05")+3600*(10:13)
  
  STFDF> m = c(10,20,30) # means for each of the 3 point locations
  
  STFDF> mydata = rnorm(length(sp)*length(time),mean=rep(m, 4))
  
  STFDF> IDs = paste("ID",1:length(mydata))
  
  STFDF> mydata = data.frame(values = signif(mydata,3), ID=IDs)
  
  STFDF> stfdf = STFDF(sp, time, mydata)
  
  STFDF> stfdf
  An object of class "STFDF"
  Slot "data":
     values    ID
  1    9.38  ID 1
  2   21.10  ID 2
  3   29.80  ID 3
  4   11.50  ID 4
  5   19.80  ID 5
  6   31.20  ID 6
  7   10.40  ID 7
  8   20.50  ID 8
  9   29.80  ID 9
  10  10.30 ID 10
  11  21.40 ID 11
  12  29.40 ID 12
  
  Slot "sp":
  SpatialPoints:
         x y
  point1 0 0
  point2 0 1
  point3 1 1
  Coordinate Reference System (CRS) arguments: NA 
  
  Slot "time":
                      timeIndex
  2010-08-05 10:00:00         1
  2010-08-05 11:00:00         2
  2010-08-05 12:00:00         3
  2010-08-05 13:00:00         4
  
  Slot "endTime":
  [1] "2010-08-05 11:00:00 BST" "2010-08-05 12:00:00 BST"
  [3] "2010-08-05 13:00:00 BST" "2010-08-05 14:00:00 BST"
  
  
  STFDF> stfdf[1:2,]
  An object of class "STFDF"
  Slot "data":
    values    ID
  1   9.38  ID 1
  2  21.10  ID 2
  3  11.50  ID 4
  4  19.80  ID 5
  5  10.40  ID 7
  6  20.50  ID 8
  7  10.30 ID 10
  8  21.40 ID 11
  
  Slot "sp":
  SpatialPoints:
         x y
  point1 0 0
  point2 0 1
  Coordinate Reference System (CRS) arguments: NA 
  
  Slot "time":
                      timeIndex
  2010-08-05 10:00:00         1
  2010-08-05 11:00:00         2
  2010-08-05 12:00:00         3
  2010-08-05 13:00:00         4
  
  Slot "endTime":
  [1] "2010-08-05 11:00:00 BST" "2010-08-05 12:00:00 BST"
  [3] "2010-08-05 13:00:00 BST" "2010-08-05 14:00:00 BST"
  
  
  STFDF> stfdf[,1:2]
  An object of class "STFDF"
  Slot "data":
    values   ID
  1   9.38 ID 1
  2  21.10 ID 2
  3  29.80 ID 3
  4  11.50 ID 4
  5  19.80 ID 5
  6  31.20 ID 6
  
  Slot "sp":
  SpatialPoints:
         x y
  point1 0 0
  point2 0 1
  point3 1 1
  Coordinate Reference System (CRS) arguments: NA 
  
  Slot "time":
                      timeIndex
  2010-08-05 10:00:00         1
  2010-08-05 11:00:00         2
  
  Slot "endTime":
  [1] "2010-08-05 11:00:00 BST" "2010-08-05 12:00:00 BST"
  
  
  STFDF> stfdf[,,2]
  An object of class "STFDF"
  Slot "data":
        ID
  1   ID 1
  2   ID 2
  3   ID 3
  4   ID 4
  5   ID 5
  6   ID 6
  7   ID 7
  8   ID 8
  9   ID 9
  10 ID 10
  11 ID 11
  12 ID 12
  
  Slot "sp":
  SpatialPoints:
         x y
  point1 0 0
  point2 0 1
  point3 1 1
  Coordinate Reference System (CRS) arguments: NA 
  
  Slot "time":
                      timeIndex
  2010-08-05 10:00:00         1
  2010-08-05 11:00:00         2
  2010-08-05 12:00:00         3
  2010-08-05 13:00:00         4
  
  Slot "endTime":
  [1] "2010-08-05 11:00:00 BST" "2010-08-05 12:00:00 BST"
  [3] "2010-08-05 13:00:00 BST" "2010-08-05 14:00:00 BST"
  
  
  STFDF> stfdf[,,"values"]
  An object of class "STFDF"
  Slot "data":
     values
  1    9.38
  2   21.10
  3   29.80
  4   11.50
  5   19.80
  6   31.20
  7   10.40
  8   20.50
  9   29.80
  10  10.30
  11  21.40
  12  29.40
  
  Slot "sp":
  SpatialPoints:
         x y
  point1 0 0
  point2 0 1
  point3 1 1
  Coordinate Reference System (CRS) arguments: NA 
  
  Slot "time":
                      timeIndex
  2010-08-05 10:00:00         1
  2010-08-05 11:00:00         2
  2010-08-05 12:00:00         3
  2010-08-05 13:00:00         4
  
  Slot "endTime":
  [1] "2010-08-05 11:00:00 BST" "2010-08-05 12:00:00 BST"
  [3] "2010-08-05 13:00:00 BST" "2010-08-05 14:00:00 BST"
  
  
  STFDF> stfdf[1,]
                      values  ID      timeIndex
  2010-08-05 10:00:00 " 9.38" "ID 1"  "1"      
  2010-08-05 11:00:00 "11.50" "ID 4"  "2"      
  2010-08-05 12:00:00 "10.40" "ID 7"  "3"      
  2010-08-05 13:00:00 "10.30" "ID 10" "4"      
  
  STFDF> stfdf[,2]
    coordinates values   ID
  1      (0, 0)   11.5 ID 4
  2      (0, 1)   19.8 ID 5
  3      (1, 1)   31.2 ID 6
  
  STFDF> as(stfdf[,,1], "xts")
                      point1 point2 point3
  2010-08-05 10:00:00   9.38   21.1   29.8
  2010-08-05 11:00:00  11.50   19.8   31.2
  2010-08-05 12:00:00  10.40   20.5   29.8
  2010-08-05 13:00:00  10.30   21.4   29.4
  
  STFDF> as(stfdf[,,2], "xts")
                      point1  point2  point3 
  2010-08-05 10:00:00 "ID 1"  "ID 2"  "ID 3" 
  2010-08-05 11:00:00 "ID 4"  "ID 5"  "ID 6" 
  2010-08-05 12:00:00 "ID 7"  "ID 8"  "ID 9" 
  2010-08-05 13:00:00 "ID 10" "ID 11" "ID 12"
  
  STFDF> # examples for [[, [[<-, $ and $<- 
  STFDF> stfdf[[1]]
   [1]  9.38 21.10 29.80 11.50 19.80 31.20 10.40 20.50 29.80 10.30 21.40 29.40
  
  STFDF> stfdf[["values"]]
   [1]  9.38 21.10 29.80 11.50 19.80 31.20 10.40 20.50 29.80 10.30 21.40 29.40
  
  STFDF> stfdf[["newVal"]] <- rnorm(12)
  
  STFDF> stfdf$ID
   [1] ID 1  ID 2  ID 3  ID 4  ID 5  ID 6  ID 7  ID 8  ID 9  ID 10 ID 11 ID 12
  Levels: ID 1 ID 10 ID 11 ID 12 ID 2 ID 3 ID 4 ID 5 ID 6 ID 7 ID 8 ID 9
  
  STFDF> stfdf$ID = paste("OldIDs", 1:12, sep="")
  
  STFDF> stfdf$NewID = paste("NewIDs", 12:1, sep="")
  
  STFDF> stfdf
  An object of class "STFDF"
  Slot "data":
     values       ID     newVal    NewID
  1    9.38  OldIDs1 -0.3125824 NewIDs12
  2   21.10  OldIDs2 -1.0536246 NewIDs11
  3   29.80  OldIDs3 -0.7188880 NewIDs10
  4   11.50  OldIDs4 -1.0525404  NewIDs9
  5   19.80  OldIDs5 -0.8441413  NewIDs8
  6   31.20  OldIDs6  1.1420848  NewIDs7
  7   10.40  OldIDs7  1.9479070  NewIDs6
  8   20.50  OldIDs8 -0.4512836  NewIDs5
  9   29.80  OldIDs9  0.6695716  NewIDs4
  10  10.30 OldIDs10  0.1269003  NewIDs3
  11  21.40 OldIDs11 -0.7273297  NewIDs2
  12  29.40 OldIDs12 -0.8151803  NewIDs1
  
  Slot "sp":
  SpatialPoints:
         x y
  point1 0 0
  point2 0 1
  point3 1 1
  Coordinate Reference System (CRS) arguments: NA 
  
  Slot "time":
                      timeIndex
  2010-08-05 10:00:00         1
  2010-08-05 11:00:00         2
  2010-08-05 12:00:00         3
  2010-08-05 13:00:00         4
  
  Slot "endTime":
  [1] "2010-08-05 11:00:00 BST" "2010-08-05 12:00:00 BST"
  [3] "2010-08-05 13:00:00 BST" "2010-08-05 14:00:00 BST"
  
  
  STFDF> x = stfdf[stfdf[1:2,],] 
  
  STFDF> all.equal(x, stfdf[1:2,]) 
  [1] TRUE
  
  STFDF> all.equal(stfdf, stfdf[stfdf,]) # converts character to factor...
  [1] "Attributes: < Component \"data\": Component \"ID\": Modes: character, numeric >"                         
  [2] "Attributes: < Component \"data\": Component \"ID\": Attributes: < target is NULL, current is list > >"   
  [3] "Attributes: < Component \"data\": Component \"ID\": target is character, current is factor >"            
  [4] "Attributes: < Component \"data\": Component \"NewID\": Modes: character, numeric >"                      
  [5] "Attributes: < Component \"data\": Component \"NewID\": Attributes: < target is NULL, current is list > >"
  [6] "Attributes: < Component \"data\": Component \"NewID\": target is character, current is factor >"         
  > 
  > x = st_as_stars(stfdf)
  > xx = as(x, "STFDF")
  > 
  > library(sp)
  > pts = SpatialPoints(rbind(c(0,0), c(0,1), c(1,0), c(1,1)))
  > gridded(pts) = TRUE
  > 
  > library(xts)
  Loading required package: zoo
  
  Attaching package: 'zoo'
  
  The following objects are masked from 'package:base':
  
      as.Date, as.Date.numeric
  
  > tm = xts(1:10, as.Date("2010-01-01")+0:9)
  > stfdf = STFDF(pts, tm, data.frame(foo = seq_len(length(pts) * length(tm))))
  > x = st_as_stars(stfdf)
  > xx = as(x, "STFDF")
  Error in x[[xy_names[1]]] : 
    attempt to select less than one element in get1index
  Calls: as ... st_as_sfc.stars -> st_as_sfc -> st_as_sfc.dimensions
  Execution halted
Running the tests in ‘tests/stars.R’ failed.
Complete output:
  > suppressPackageStartupMessages(library(stars))
  > set.seed(13521) # runif
  > tif = system.file("tif/L7_ETMs.tif", package = "stars")
  > (x_ = read_stars(c(tif,tif))) # FIXME: not what you'd expect
  stars object with 3 dimensions and 2 attributes
  attribute(s):
    L7_ETMs.tif     L7_ETMs.tif.1   
   Min.   :  1.00   Min.   :  1.00  
   1st Qu.: 54.00   1st Qu.: 54.00  
   Median : 69.00   Median : 69.00  
   Mean   : 68.91   Mean   : 68.91  
   3rd Qu.: 86.00   3rd Qu.: 86.00  
   Max.   :255.00   Max.   :255.00  
  dimension(s):
       from  to  offset delta                       refsys point values
  x       1 349  288776  28.5 +proj=utm +zone=25 +south... FALSE   NULL
  y       1 352 9120761 -28.5 +proj=utm +zone=25 +south... FALSE   NULL
  band    1   6      NA    NA                           NA    NA   NULL
  > (x = read_stars(tif))
  stars object with 3 dimensions and 1 attribute
  attribute(s):
    L7_ETMs.tif    
   Min.   :  1.00  
   1st Qu.: 54.00  
   Median : 69.00  
   Mean   : 68.91  
   3rd Qu.: 86.00  
   Max.   :255.00  
  dimension(s):
       from  to  offset delta                       refsys point values
  x       1 349  288776  28.5 +proj=utm +zone=25 +south... FALSE   NULL
  y       1 352 9120761 -28.5 +proj=utm +zone=25 +south... FALSE   NULL
  band    1   6      NA    NA                           NA    NA   NULL
  > image(x)
  > gdal_crs(tif)
  $nbands
  [1] 6
  
  $crs
  Coordinate Reference System:
    No EPSG code
    proj4string: "+proj=utm +zone=25 +south +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs"
  
  $gt
  [1]  288776.3      28.5       0.0 9120760.8       0.0     -28.5
  
  $gt_inv
  [1] -1.013250e+04  3.508772e-02  0.000000e+00  3.200267e+05  0.000000e+00
  [6] -3.508772e-02
  
  > plot(x)
  > 
  > x + x
  stars object with 3 dimensions and 1 attribute
  attribute(s):
    L7_ETMs.tif   
   Min.   :  2.0  
   1st Qu.:108.0  
   Median :138.0  
   Mean   :137.8  
   3rd Qu.:172.0  
   Max.   :510.0  
  dimension(s):
       from  to  offset delta                       refsys point values
  x       1 349  288776  28.5 +proj=utm +zone=25 +south... FALSE   NULL
  y       1 352 9120761 -28.5 +proj=utm +zone=25 +south... FALSE   NULL
  band    1   6      NA    NA                           NA    NA   NULL
  > x * x
  stars object with 3 dimensions and 1 attribute
  attribute(s):
    L7_ETMs.tif   
   Min.   :    1  
   1st Qu.: 2916  
   Median : 4761  
   Mean   : 5512  
   3rd Qu.: 7396  
   Max.   :65025  
  dimension(s):
       from  to  offset delta                       refsys point values
  x       1 349  288776  28.5 +proj=utm +zone=25 +south... FALSE   NULL
  y       1 352 9120761 -28.5 +proj=utm +zone=25 +south... FALSE   NULL
  band    1   6      NA    NA                           NA    NA   NULL
  > x[,,,1:3]
  stars object with 3 dimensions and 1 attribute
  attribute(s):
    L7_ETMs.tif    
   Min.   : 21.00  
   1st Qu.: 58.00  
   Median : 70.00  
   Mean   : 70.36  
   3rd Qu.: 83.00  
   Max.   :255.00  
  dimension(s):
       from  to  offset delta                       refsys point values
  x       1 349  288776  28.5 +proj=utm +zone=25 +south... FALSE   NULL
  y       1 352 9120761 -28.5 +proj=utm +zone=25 +south... FALSE   NULL
  band    1   3      NA    NA                           NA    NA   NULL
  > x[,1:100,100:200,]
  stars object with 3 dimensions and 1 attribute
  attribute(s):
    L7_ETMs.tif    
   Min.   : 13.00  
   1st Qu.: 54.00  
   Median : 65.00  
   Mean   : 67.22  
   3rd Qu.: 77.00  
   Max.   :252.00  
  dimension(s):
       from  to  offset delta                       refsys point values
  x       1 100  288776  28.5 +proj=utm +zone=25 +south... FALSE   NULL
  y     100 200 9120761 -28.5 +proj=utm +zone=25 +south... FALSE   NULL
  band    1   6      NA    NA                           NA    NA   NULL
  > sqrt(x)
  stars object with 3 dimensions and 1 attribute
  attribute(s):
    L7_ETMs.tif    
   Min.   : 1.000  
   1st Qu.: 7.348  
   Median : 8.307  
   Mean   : 8.094  
   3rd Qu.: 9.274  
   Max.   :15.969  
  dimension(s):
       from  to  offset delta                       refsys point values
  x       1 349  288776  28.5 +proj=utm +zone=25 +south... FALSE   NULL
  y       1 352 9120761 -28.5 +proj=utm +zone=25 +south... FALSE   NULL
  band    1   6      NA    NA                           NA    NA   NULL
  > st_apply(x, 3, min)
  stars object with 1 dimensions and 1 attribute
  attribute(s):
    L7_ETMs.tif   
   Min.   : 1.00  
   1st Qu.: 3.00  
   Median :15.00  
   Mean   :18.50  
   3rd Qu.:29.25  
   Max.   :47.00  
  dimension(s):
       from to offset delta refsys point values
  band    1  6     NA    NA     NA    NA   NULL
  > st_apply(x, 1:2, max)
  stars object with 2 dimensions and 1 attribute
  attribute(s):
    L7_ETMs.tif    
   Min.   : 55.00  
   1st Qu.: 85.00  
   Median : 96.00  
   Mean   : 99.36  
   3rd Qu.:113.00  
   Max.   :255.00  
  dimension(s):
    from  to  offset delta                       refsys point values
  x    1 349  288776  28.5 +proj=utm +zone=25 +south... FALSE   NULL
  y    1 352 9120761 -28.5 +proj=utm +zone=25 +south... FALSE   NULL
  > st_apply(x, 1:2, range)
  stars object with 3 dimensions and 1 attribute
  attribute(s):
    L7_ETMs.tif    
   Min.   :  1.00  
   1st Qu.: 50.00  
   Median : 71.00  
   Mean   : 72.44  
   3rd Qu.: 96.00  
   Max.   :255.00  
  dimension(s):
        from  to  offset delta                       refsys point values
  x        1 349  288776  28.5 +proj=utm +zone=25 +south... FALSE   NULL
  y        1 352 9120761 -28.5 +proj=utm +zone=25 +south... FALSE   NULL
  range    1   2      NA    NA                           NA    NA   NULL
  > 
  > geomatrix = system.file("tif/geomatrix.tif", package = "stars")
  > x = read_stars(geomatrix)
  Error in if (properties$bands[2] == 0) { : 
    missing value where TRUE/FALSE needed
  Calls: read_stars
  Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > ## load dependencies
  > library(testthat)
  > 
  > ## test package
  > test_check("stars")
  Loading required package: stars
  Loading required package: abind
  Loading required package: sf
  Linking to GEOS 3.6.1, GDAL 2.2.4, PROJ 4.9.3
Running the tests in ‘tests/transform.R’ failed.
Complete output:
  > suppressPackageStartupMessages(library(stars))
  > geomatrix = system.file("tif/geomatrix.tif", package = "stars")
  > (x = read_stars(geomatrix))
  Error in if (properties$bands[2] == 0) { : 
    missing value where TRUE/FALSE needed
  Calls: read_stars
  Execution halted
Running the tests in ‘tests/write.R’ failed.
Complete output:
  > suppressPackageStartupMessages(library(stars))
  > 
  > tif = system.file("tif/L7_ETMs.tif", package = "stars")
  > (x = read_stars(tif))
  stars object with 3 dimensions and 1 attribute
  attribute(s):
    L7_ETMs.tif    
   Min.   :  1.00  
   1st Qu.: 54.00  
   Median : 69.00  
   Mean   : 68.91  
   3rd Qu.: 86.00  
   Max.   :255.00  
  dimension(s):
       from  to  offset delta                       refsys point values
  x       1 349  288776  28.5 +proj=utm +zone=25 +south... FALSE   NULL
  y       1 352 9120761 -28.5 +proj=utm +zone=25 +south... FALSE   NULL
  band    1   6      NA    NA                           NA    NA   NULL
  > 
  > st_write(x, tempfile(), driver = "GTiff")
  Error in CPL_write_gdal(mat, file, driver, options, type, dims, geotransform,  : 
    argument "geotransform" is missing, with no default
  Calls: st_write -> st_write.stars -> <Anonymous> -> CPL_write_gdal
  Execution halted