- using R Under development (unstable) (2025-03-09 r87914)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
Debian clang version 19.1.7 (1+b1)
Debian flang-new version 19.1.7 (1+b1)
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘spqdep/DESCRIPTION’ ... OK
- this is package ‘spqdep’ version ‘0.1.3.5’
- 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 serialization versions ... OK
- checking whether package ‘spqdep’ can be installed ... OK
See the install log for details.
- checking package directory ... OK
- checking for future file timestamps ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... NOTE
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘summary.spjctest.R’ ‘summary.spqtest.R’
- 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 ... [0s/0s] OK
- checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the package can be unloaded cleanly ... [0s/0s] OK
- checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
- checking loading without being on the library search path ... [0s/0s] 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 ... [16s/20s] OK
- checking Rd files ... [1s/1s] 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 ... [0s/0s] 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/14s] ERROR
Running examples in ‘spqdep-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Q.map.test
> ### Title: Compute the QE and QI tests of Equivalence and Independence
> ### between maps
> ### Aliases: Q.map.test
>
> ### ** Examples
>
>
> # Case 1:
> N <- 200
> cx <- runif(N)
> cy <- runif(N)
> x <- cbind(cx,cy)
> listw <- spdep::nb2listw(spdep::knn2nb(
+ spdep::knearneigh(cbind(cx,cy), k = 4)))
> p <- c(1/6, 3/6, 2/6)
> rho = 0.5
> QY1 <- dgp.spq(p = p, listw = listw, rho = rho)
> rho = 0.8
> QY2 <- dgp.spq(p = p, listw = listw, rho = rho)
> dt = data.frame(QY1,QY2)
> m = 3
> r = 1
> formula <- ~ QY1 + QY2
> control <- list(dtmaxknn = 10)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations", control = control)
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QE = 264.54, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QI = 63.928, df = 81, p-value = 0.9186
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> plot(qmap, ci=.6)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> plot(qmap[[1]]$mh)
> summary(qmap[[1]]$mh)
Characteristics of m-surrounding:
Number of m-surrounding (R): 90
Length of m-surrounding (m): 3
Number no-symbolized observations: 12
List of no-symbolized observations:
8 62 66 69 80 85 117 122 130 146 191 199
List of the degree overlaping:
There are 2 m-surrounding that have intersection with 0 m-surrounding
There are 12 m-surrounding that have intersection with 1 m-surrounding
There are 76 m-surrounding that have intersection with 2 m-surrounding
Mean degree of overlaping: 1.8222
>
> control <- list(dtmaxknn = 20)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="permutations", control = control)
Warning in Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r, :
The ratio between the number of symbolized observations and the number of symbols is lower than 5.
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: permutations
Ratio Symbolized observations/Num symbols = 3.44
data: QY1 and QY2
QE = 287.89, df = 26, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: permutations
Ratio Symbolized observations/Num symbols = 3.44
data: QY1 and QY2
QI = 238.55, df = 676, p-value = 1
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> plot(qmap[[1]]$mh)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations")
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9.9
data: QY1 and QY2
QE = 292, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9.9
data: QY1 and QY2
QI = 66.633, df = 81, p-value = 0.875
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
> control <- list(dtmaxknn = 10)
> qmap <- Q.map.test(formula = formula, data = dt, coor = x, m = m, r = r,
+ type ="combinations", control = control)
> print(qmap)
[[1]]
Q-Map test of Equivalence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QE = 264.54, df = 9, p-value < 2.2e-16
alternative hypothesis: two.sided
[[2]]
Q-Map test of Independence for qualitative data.
Symbols type: combinations
Ratio Symbolized observations/Num symbols = 9
data: QY1 and QY2
QI = 63.928, df = 81, p-value = 0.9186
alternative hypothesis: two.sided
attr(,"class")
[1] "qmap" "list"
> plot(qmap)
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
Warning: Use of `data$symb` is discouraged.
ℹ Use `symb` instead.
>
> # Case 2:
> data(provinces_spain)
> # sf::sf_use_s2(FALSE)
> m = 3
> r = 1
>
> provinces_spain$Mal2Fml <- factor(provinces_spain$Mal2Fml > 100)
> levels(provinces_spain$Mal2Fml) = c("men","woman")
> provinces_spain$Coast <- factor(provinces_spain$Coast)
> levels(provinces_spain$Coast) = c("no","yes")
> formula <- ~ Coast + Mal2Fml
> qmap <- Q.map.test(formula = formula, data = provinces_spain, m = m, r = r,
+ type ="combinations")
Error in UseMethod("units") :
no applicable method for 'units' applied to an object of class "NULL"
Calls: Q.map.test -> m.surround -> rbind -> rbind -> units
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [15s/19s] ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘user-guide.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/unnamed-chunk-5-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 30100 bytes
Input file size = 30214 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22188
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22188
Output IDAT size = 22188 bytes (7912 bytes decrease)
Output file size = 22266 bytes (7948 bytes = 26.31% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/plot mh-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 29819 bytes
Input file size = 29933 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27237
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27237
Output IDAT size = 27237 bytes (2582 bytes decrease)
Output file size = 27315 bytes (2618 bytes = 8.75% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/plot mh prune-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 28643 bytes
Input file size = 28757 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25872
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25872
Output IDAT size = 25872 bytes (2771 bytes decrease)
Output file size = 25950 bytes (2807 bytes = 9.76% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/unnamed-chunk-10-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 27669 bytes
Input file size = 27783 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20259
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20259
Output IDAT size = 20259 bytes (7410 bytes decrease)
Output file size = 20337 bytes (7446 bytes = 26.80% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/spqdep.Rcheck/vign_test/spqdep/vignettes/user-guide_files/figure-html/unnamed-chunk-10-2.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 21628 bytes
Input file size = 21730 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16151
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16151
Output IDAT size = 16151 bytes (5477 bytes decrease)
Output file size = 16229 bytes (5501 bytes = 25.32% decrease)
Quitting from lines 273-279 [unnamed-chunk-11] (user-guide.Rmd)
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
no applicable method for 'units' applied to an object of class "NULL"
--- failed re-building ‘user-guide.Rmd’
SUMMARY: processing the following file failed:
‘user-guide.Rmd’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [6s/8s] OK
- checking HTML version of manual ... [2s/4s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 2 ERRORs, 1 NOTE