* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/MRG.Rcheck’
* using R Under development (unstable) (2025-12-20 r89211)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘MRG/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MRG’ version ‘0.3.21’
* 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 ‘MRG’ can be installed ... [23s/24s] 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 ... OK
* checking loading without being on the library search path ... 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 ... [33s/34s] 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [12s/13s] OK
* checking examples with --run-donttest ... [16m/16m] ERROR
Running examples in ‘MRG-Ex.R’ failed
The error most likely occurred in:

> ### Name: multiResGrid
> ### Title: Create multi-resolution grids based on confidentiality or
> ###   reliability restrictions
> ### Aliases: multiResGrid multiResGrid.MRG multiResGrid.sf
> ###   multiResGrid.list
> 
> ### ** Examples
> 
> ## No test: 
> library(sf)
Linking to GEOS 3.12.2, GDAL 3.8.5, PROJ 9.3.1; sf_use_s2() is TRUE
> if (!require(ggplot2)) print("Plotting of results will not work 
+                      without installation of ggplot2")
Loading required package: ggplot2
> if (!require(viridis)) print("Some of the plots will not work 
+                      without installation of viridis package")
Loading required package: viridis
Loading required package: viridisLite
> if (!require(patchwork)) print("Some of the plots will not work 
+                      without installation of patchwork")
Loading required package: patchwork
> 
> if (require(giscoR)) {
+   useBorder = TRUE 
+ } else {
+   useBorder = FALSE
+   print("You need to install giscoR for plotting borders and clipping the gridded maps")
+ }
Loading required package: giscoR
> # These are SYNTHETIC agricultural FSS data 
> data(ifs_dk) # Census data
> ifs_weight = ifs_dk %>% dplyr::filter(Sample == 1) # Extract weighted subsample
> 
> # Create spatial data
> ifg = fssgeo(ifs_dk, locAdj = "LL")
> fsg = fssgeo(ifs_weight, locAdj = "LL")
> 
> if (useBorder) {
+ # Read country borders, only used for plotting
+   borders = gisco_get_nuts(nuts_level = 0)
+   dkb = borders[borders$CNTR_CODE == "DK",] %>% st_transform(crs = 3035)
+ }
> 
> ress = c(1,5,10,20,40, 80, 160)*1000
> # Gridding Utilized agricultural area (UAA)
> ifl = gridData(ifg, "UAA",res = ress)
> # Gridding organic utilized agricultural area
> ifl2 = gridData(ifg, vars = "UAAXK0000_ORG", res = ress)
> 
> # Gridding UAA and organic UAA together
> ifl3 = gridData(ifg, vars = c("UAA", "UAAXK0000_ORG"), res = ress)
> 
> # Gridding the UAA from the survey - the survey weights are in the column EXT_MODULE
> fsl = gridData(fsg,  vars = c("UAA"), weights = "EXT_MODULE",  res = ress)
> 
> # Create a multi-resolution grid only with farm number as confidentiality rule, then plot results
> himg0 = multiResGrid(ifl, checkReliability = FALSE, suppresslim = 0)
[1] "ires 2 5000 #himg-cells: 2179 ; removed: 23704 ; added: 2107 ; confidential: 72"
[1] "ires 3 10000 #himg-cells: 1642 ; removed: 768 ; added: 231 ; confidential: 41"
[1] "ires 4 20000 #himg-cells: 1539 ; removed: 137 ; added: 34 ; confidential: 9"
[1] "ires 5 40000 #himg-cells: 1451 ; removed: 96 ; added: 8 ; confidential: 1"
[1] "ires 6 80000 #himg-cells: 1366 ; removed: 86 ; added: 1 ; confidential: 0"
[1] "ires 7 160000 #himg-cells: 1366 ; removed: 0 ; added: 0 ; confidential: 0"
> ggplot(himg0) + geom_sf(aes(fill = count))
> 
> # Create a multi-resolution grid of UAA, also based on the dominance rule (default)
> himg1 = multiResGrid(ifl, vars = "UAA", ifg = ifg)
[1] "ires 2 5000 #himg-cells: 2179 ; removed: 23704 ; added: 2107 ; confidential: 72"
[1] "ires 3 10000 #himg-cells: 1601 ; removed: 824 ; added: 246 ; confidential: 42"
[1] "ires 4 20000 #himg-cells: 1493 ; removed: 145 ; added: 37 ; confidential: 9"
[1] "ires 5 40000 #himg-cells: 1405 ; removed: 96 ; added: 8 ; confidential: 1"
[1] "ires 6 80000 #himg-cells: 1333 ; removed: 73 ; added: 1 ; confidential: 0"
[1] "ires 7 160000 #himg-cells: 1333 ; removed: 0 ; added: 0 ; confidential: 0"
>   p1 = ggplot(himg1) + geom_sf(aes(fill = UAA))
>   p1
> 
> # Create a multi-resolution grid of UAA, also based on the p-percent rule
> himg101 = multiResGrid(ifl, vars = "UAA", ifg = ifg, checkPpercent = TRUE)
[1] "ires 2 5000 #himg-cells: 2179 ; removed: 23704 ; added: 2107 ; confidential: 72"
[1] "ires 3 10000 #himg-cells: 1601 ; removed: 824 ; added: 246 ; confidential: 42"
[1] "ires 4 20000 #himg-cells: 1492 ; removed: 147 ; added: 38 ; confidential: 9"
[1] "ires 5 40000 #himg-cells: 1404 ; removed: 96 ; added: 8 ; confidential: 1"
[1] "ires 6 80000 #himg-cells: 1332 ; removed: 73 ; added: 1 ; confidential: 0"
[1] "ires 7 160000 #himg-cells: 1332 ; removed: 0 ; added: 0 ; confidential: 0"
>   p11 = ggplot(himg101) + geom_sf(aes(fill = UAA))
>   p11
> 
> # Create multi-resolution grid of organic UAA
> himg2 = multiResGrid(ifl2, vars = "UAAXK0000_ORG", ifg = ifg)
[1] "ires 2 5000 #himg-cells: 5513 ; removed: 19922 ; added: 1659 ; confidential: 7"
[1] "ires 3 10000 #himg-cells: 894 ; removed: 5180 ; added: 561 ; confidential: 23"
[1] "ires 4 20000 #himg-cells: 229 ; removed: 832 ; added: 167 ; confidential: 13"
[1] "ires 5 40000 #himg-cells: 148 ; removed: 110 ; added: 29 ; confidential: 4"
[1] "ires 6 80000 #himg-cells: 125 ; removed: 29 ; added: 6 ; confidential: 3"
[1] "ires 7 160000 #himg-cells: 114 ; removed: 13 ; added: 2 ; confidential: 2"
> himg21 = multiResGrid(ifl2, vars = "UAAXK0000_ORG", ifg = ifg, postProcess = FALSE)
[1] "ires 2 5000 #himg-cells: 5513 ; removed: 19922 ; added: 1659 ; confidential: 7"
[1] "ires 3 10000 #himg-cells: 894 ; removed: 5180 ; added: 561 ; confidential: 23"
[1] "ires 4 20000 #himg-cells: 229 ; removed: 832 ; added: 167 ; confidential: 13"
[1] "ires 5 40000 #himg-cells: 148 ; removed: 110 ; added: 29 ; confidential: 4"
[1] "ires 6 80000 #himg-cells: 125 ; removed: 29 ; added: 6 ; confidential: 3"
[1] "ires 7 160000 #himg-cells: 114 ; removed: 13 ; added: 2 ; confidential: 2"
> 
> ggplot(himg2) + geom_sf(aes(fill = UAAXK0000_ORG))
> 
> # Create joint multi-resolution grid of organic UAA and total UAA
> himg3 = multiResGrid(ifl3, vars = c("UAA", "UAAXK0000_ORG"), ifg = ifg, 
+                   checkReliability = FALSE, suppresslim = 0)
[1] "ires 2 5000 #himg-cells: 2179 ; removed: 23704 ; added: 2107 ; confidential: 72"
[1] "ires 3 10000 #himg-cells: 636 ; removed: 2126 ; added: 583 ; confidential: 48"
[1] "ires 4 20000 #himg-cells: 192 ; removed: 613 ; added: 169 ; confidential: 17"
[1] "ires 5 40000 #himg-cells: 121 ; removed: 103 ; added: 32 ; confidential: 5"
[1] "ires 6 80000 #himg-cells: 103 ; removed: 25 ; added: 7 ; confidential: 3"
[1] "ires 7 160000 #himg-cells: 94 ; removed: 11 ; added: 2 ; confidential: 2"
> # Create multi-resolution grid of organic UAA, based on the UAA grid
> # The large number of missing values indicates that this feature should
> # mainly be used for data that have similar or higher resolution as the
> # original data set.
> himg33 = multiResGrid(himg1, vars = c("UAAXK0000_ORG"), ifg = ifg, 
+                   checkReliability = FALSE, suppresslim = 0)
MRGinp is not an sf-object 
> p31 = ggplot(himg3) + geom_sf(aes(fill = UAA))
> p32 = ggplot(himg3) + geom_sf(aes(fill = UAAXK0000_ORG))
> p33 = ggplot(himg33) + geom_sf(aes(fill = UAAXK0000_ORG))
> if (require(patchwork)) p31 + p32 + p33
> 
> # Create multi-resolution grid of UAA, based on survey data,
> # with and without applying reliability check
> # This is a relatively slow functionality
> # rounding is set to FALSE, to be better able to visualize the few records
> # (Not recommended for data to be published)
> himg4 = multiResGrid(fsl,  vars = c("UAA"), weights = "EXT_MODULE", ifg = fsg, 
+                       strat = "STRA_ID_CORE", checkReliability = FALSE, rounding = FALSE)
[1] "ires 2 5000 #himg-cells: 2034 ; removed: 8185 ; added: 1738 ; confidential: 272"
[1] "ires 3 10000 #himg-cells: 1190 ; removed: 1180 ; added: 336 ; confidential: 36"
[1] "ires 4 20000 #himg-cells: 1069 ; removed: 157 ; added: 36 ; confidential: 5"
[1] "ires 5 40000 #himg-cells: 1032 ; removed: 43 ; added: 6 ; confidential: 0"
[1] "ires 6 80000 #himg-cells: 1032 ; removed: 0 ; added: 0 ; confidential: 0"
[1] "ires 7 160000 #himg-cells: 1032 ; removed: 0 ; added: 0 ; confidential: 0"
> # The parameter reliabilitySplit = 15 will divide the data set in 15 groups for the 
> # reliabilityCheck.
> # A lower value would be recommended, but a high value speeds up the computation for this example
> himg5 = multiResGrid(fsl,  vars = c("UAA"), weights = "EXT_MODULE", ifg = fsg, 
+                       strat = "STRA_ID_CORE", checkReliability = TRUE, 
+                       reliabilitySplit = TRUE, rounding = FALSE, pseudoreg = "REGIONS")
Error in `[.data.table`(var_z_hi, , `:=`((paste0("var_", namY)), lapply(.SD[,  : 
  attempt access index 972/972 in VECTOR_ELT
Calls: multiResGrid ... mrg_varestim -> vardom -> variance_est -> [ -> [.data.table
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘multiResGrid.R’ [28s/28s]
 [28s/29s] ERROR
Running the tests in ‘tests/multiResGrid.R’ failed.
Complete output:
  > s1 = Sys.time()
  > library(MRG)
  > library(tidyr)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > # Neccessary to silence sf startup messages
  > suppressMessages(library(sf))
  > if (require(giscoR, quietly = TRUE)) {
  + # Read nuts borders, used for extracting smaller data set 
  +   borders = gisco_get_nuts(nuts_level = 2)
  +   dkb = borders[borders$CNTR_CODE == "DK",] %>% st_transform(crs = 3035)
  + } else {
  +   mrgpath = find.package("MRG")
  +   load(file.path(mrgpath, "ex/dkb.rda"))
  + }
  > #'
  > # These are SYNTHETIC agricultural FSS data 
  > data(ifs_dk) # Census data
  > ifs_weight = ifs_dk %>% dplyr::filter(Sample == 1) # Extract weighted subsample
  > 
  > # Create spatial data
  > ifg = fssgeo(ifs_dk, locAdj = "LL")
  > fsg = fssgeo(ifs_weight, locAdj = "LL")
  > 
  > ifg$dkb = st_join(ifg, dkb)$NUTS_ID
  > ifg = ifg[!is.na(ifg$dkb) & ifg$dkb == "DK01",]
  > fsg$dkb = st_join(fsg, dkb)$NUTS_ID
  > fsg = fsg[!is.na(fsg$dkb) & fsg$dkb == "DK01",]
  > 
  > ifg$ft = as.numeric(substr(ifg$FARMTYPE, 3, 4))^2
  > 
  > s2 = Sys.time()
  > #'
  > # Set the base resolutions, and create a hierarchical list with gridded data
  > ress = c(1,5,10,20,40)*1000
  > # Gridding Utilized agricultural area (UAA), organic UAA and ft together
  > ifl = gridData(ifg, c("UAA", "UAAXK0000_ORG", "ft"), res = ress)
  > 
  > # Gridding the UAA from the survey - the survey weights are in the column EXT_MODULE
  > fsl = gridData(fsg,  vars = c("UAA"), weights = "EXT_MODULE",  res = ress)
  > 
  > # Create a multi-resolution grid only with farm number as confidentiality rule, then plot results
  > himg0 = multiResGrid(ifl, checkReliability = FALSE, suppresslim = 0)
  [1] "ires 2 5000 #himg-cells: 117 ; removed: 1209 ; added: 108 ; confidential: 9"
  [1] "ires 3 10000 #himg-cells: 79 ; removed: 58 ; added: 20 ; confidential: 5"
  [1] "ires 4 20000 #himg-cells: 68 ; removed: 14 ; added: 3 ; confidential: 2"
  [1] "ires 5 40000 #himg-cells: 56 ; removed: 13 ; added: 1 ; confidential: 1"
  > 
  > # Create a multi-resolution grid of UAA, also based on the dominance rule (default)
  > himg1 = multiResGrid(ifl, vars = "UAA", ifg = ifg)
  [1] "ires 2 5000 #himg-cells: 117 ; removed: 1209 ; added: 108 ; confidential: 9"
  [1] "ires 3 10000 #himg-cells: 79 ; removed: 58 ; added: 20 ; confidential: 5"
  [1] "ires 4 20000 #himg-cells: 67 ; removed: 16 ; added: 4 ; confidential: 2"
  [1] "ires 5 40000 #himg-cells: 48 ; removed: 21 ; added: 2 ; confidential: 1"
  > 
  > # Create joint multi-resolution grid of organic UAA
  > himg2 = multiResGrid(ifl, vars = "UAAXK0000_ORG", ifg = ifg, 
  +                      checkReliability = FALSE, suppresslim = 0)
  [1] "ires 2 5000 #himg-cells: 298 ; removed: 1002 ; added: 82 ; confidential: 0"
  [1] "ires 3 10000 #himg-cells: 67 ; removed: 263 ; added: 32 ; confidential: 3"
  [1] "ires 4 20000 #himg-cells: 29 ; removed: 50 ; added: 12 ; confidential: 3"
  [1] "ires 5 40000 #himg-cells: 20 ; removed: 14 ; added: 5 ; confidential: 2"
  > 
  > # Create joint multi-resolution grid of organic UAA and total UAA
  > himg3 = multiResGrid(ifl, vars = c("UAA", "UAAXK0000_ORG"), ifg = ifg, 
  +                   checkReliability = FALSE, suppresslim = 0)
  [1] "ires 2 5000 #himg-cells: 117 ; removed: 1209 ; added: 108 ; confidential: 9"
  [1] "ires 3 10000 #himg-cells: 41 ; removed: 109 ; added: 33 ; confidential: 6"
  [1] "ires 4 20000 #himg-cells: 18 ; removed: 35 ; added: 12 ; confidential: 5"
  [1] "ires 5 40000 #himg-cells: 9 ; removed: 14 ; added: 5 ; confidential: 3"
  > 
  > 
  > # Create joint multi-resolution grid of organic UAA and total UAA, with suppression
  > himg4 = multiResGrid(ifl, vars = c("UAA", "UAAXK0000_ORG"), ifg = ifg, 
  +                      checkReliability = FALSE, suppresslim = 0.1)
  [1] "ires 2 5000 #himg-cells: 117 ; removed: 1209 ; added: 108 ; confidential: 9"
  [1] "ires 3 10000 #himg-cells: 41 ; removed: 109 ; added: 33 ; confidential: 6"
  [1] "ires 4 20000 #himg-cells: 18 ; removed: 35 ; added: 12 ; confidential: 5"
  [1] "ires 5 40000 #himg-cells: 16 ; removed: 4 ; added: 2 ; confidential: 7"
  > 
  > # Create joint multi-resolution grid of ft
  > himg5 = multiResGrid(ifl, vars = c("ft"), ifg = ifg, 
  +                      checkReliability = FALSE, suppresslim = 0.1)
  [1] "ires 2 5000 #himg-cells: 117 ; removed: 1209 ; added: 108 ; confidential: 9"
  [1] "ires 3 10000 #himg-cells: 90 ; removed: 43 ; added: 16 ; confidential: 9"
  [1] "ires 4 20000 #himg-cells: 85 ; removed: 7 ; added: 2 ; confidential: 6"
  > 
  > himg6 = multiResGrid(ifl, vars = c("UAA", "UAAXK0000_ORG", "ft"), ifg = ifg, 
  +                      checkReliability = FALSE, suppresslim = 0.1)
  [1] "ires 2 5000 #himg-cells: 117 ; removed: 1209 ; added: 108 ; confidential: 9"
  [1] "ires 3 10000 #himg-cells: 41 ; removed: 109 ; added: 33 ; confidential: 6"
  [1] "ires 4 20000 #himg-cells: 18 ; removed: 35 ; added: 12 ; confidential: 5"
  [1] "ires 5 40000 #himg-cells: 16 ; removed: 4 ; added: 2 ; confidential: 7"
  > 
  > himg7 = MRGmerge(himg1, himg2, himg3 = himg5)
  Warning messages:
  1: attribute variables are assumed to be spatially constant throughout all geometries 
  2: attribute variables are assumed to be spatially constant throughout all geometries 
  > 
  > s3 = Sys.time()
  > 
  > 
  > # Create multi-resolution grid of UAA and organic UAA, based on survey data,
  > # also applying reliability check
  > himg5 <-  multiResGrid(fsl, vars = c("UAA"), weights = "EXT_MODULE", ifg = fsg, 
  +                       strat = "STRA_ID_CORE", checkReliability = TRUE, reliabilitySplit = 5)
  Error in `[.data.table`(var_z_hi, , `:=`((paste0("var_", namY)), lapply(.SD[,  : 
    attempt access index 220/220 in VECTOR_ELT
  Calls: multiResGrid ... mrg_varestim -> vardom -> variance_est -> [ -> [.data.table
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 2 ERRORs
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/MRG.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 20:14.29, 1153.51 + 30.26