* using log directory ‘/srv/hornik/tmp/CRAN/spqdep.Rcheck’ * using R Under development (unstable) (2023-12-18 r85702) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.6 (2) Debian flang-new version 17.0.6 (2) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘spqdep/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘spqdep’ version ‘0.1.3.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/6s] Note_to_CRAN_maintainers Maintainer: ‘Fernando Lopez ’ * 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 ‘spqdep’ can be installed ... [9s/9s] OK * checking package directory ... OK * checking for future file timestamps ... 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [2s/2s] OK * checking whether the package can be loaded with stated dependencies ... [2s/2s] OK * checking whether the package can be unloaded cleanly ... [2s/2s] OK * checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK * checking whether the namespace can be unloaded cleanly ... [2s/2s] OK * checking loading without being on the library search path ... [2s/2s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... NOTE Mismatches for apparent methods not registered: print: function(x, ...) print.qtest: function(Q) See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [14s/14s] OK * checking Rd files ... [0s/0s] NOTE checkRd: (-1) Q.test.Rd:80: Lost braces; missing escapes or markup? 80 | patterns of co-location are possible (the number of symbols is \eqn{n_{\sigma}}=8): {0,0,0}, {1,0,0}, | ^ checkRd: (-1) Q.test.Rd:80: Lost braces; missing escapes or markup? 80 | patterns of co-location are possible (the number of symbols is \eqn{n_{\sigma}}=8): {0,0,0}, {1,0,0}, | ^ checkRd: (-1) Q.test.Rd:81: Lost braces; missing escapes or markup? 81 | {0,1,0}, {0,0,1}, {1,1,0}, {1,0,1}, {0,1,1}, and {1,1,1}. Each unique co-locationtype | ^ checkRd: (-1) Q.test.Rd:81: Lost braces; missing escapes or markup? 81 | {0,1,0}, {0,0,1}, {1,1,0}, {1,0,1}, {0,1,1}, and {1,1,1}. Each unique co-locationtype | ^ checkRd: (-1) Q.test.Rd:81: Lost braces; missing escapes or markup? 81 | {0,1,0}, {0,0,1}, {1,1,0}, {1,0,1}, {0,1,1}, and {1,1,1}. Each unique co-locationtype | ^ checkRd: (-1) Q.test.Rd:81: Lost braces; missing escapes or markup? 81 | {0,1,0}, {0,0,1}, {1,1,0}, {1,0,1}, {0,1,1}, and {1,1,1}. Each unique co-locationtype | ^ checkRd: (-1) Q.test.Rd:81: Lost braces; missing escapes or markup? 81 | {0,1,0}, {0,0,1}, {1,1,0}, {1,0,1}, {0,1,1}, and {1,1,1}. Each unique co-locationtype | ^ checkRd: (-1) Q.test.Rd:81: Lost braces; missing escapes or markup? 81 | {0,1,0}, {0,0,1}, {1,1,0}, {1,0,1}, {0,1,1}, and {1,1,1}. Each unique co-locationtype | ^ checkRd: (-1) local.jc.test.Rd:54-55: Lost braces in \itemize; meant \describe ? checkRd: (-1) local.jc.test.Rd:56-58: Lost braces in \itemize; meant \describe ? checkRd: (-1) local.jc.test.Rd:59-62: Lost braces in \itemize; meant \describe ? checkRd: (-1) local.sp.runs.test.Rd:56-57: Lost braces in \itemize; meant \describe ? checkRd: (-1) local.sp.runs.test.Rd:58-60: Lost braces in \itemize; meant \describe ? checkRd: (-1) local.sp.runs.test.Rd:61-64: Lost braces in \itemize; meant \describe ? checkRd: (-1) m.surround.Rd:50-51: Lost braces in \itemize; meant \describe ? checkRd: (-1) m.surround.Rd:52-56: Lost braces in \itemize; meant \describe ? checkRd: (-1) m.surround.Rd:57-63: Lost braces in \itemize; meant \describe ? checkRd: (-1) m.surround.Rd:64-69: Lost braces in \itemize; meant \describe ? checkRd: (-1) sp.runs.test.Rd:62: Lost braces in \itemize; meant \describe ? checkRd: (-1) sp.runs.test.Rd:63-65: Lost braces in \itemize; meant \describe ? checkRd: (-1) sp.runs.test.Rd:66-68: Lost braces in \itemize; meant \describe ? * 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 ... [1s/1s] 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 ... [13s/13s] ERROR Running examples in ‘spqdep-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: m.surround > ### Title: A function to generate m-surroundings > ### Aliases: m.surround > > ### ** Examples > > > # Example 1: Obtain m-surroundings with degree of overlapping r > N <- 100 > cx <- runif(N) > cy <- runif(N) > x <- cbind(cx,cy) > m <- 3 > r <- 1 > msurr_points <- m.surround(x = x, m = m, r = r) > plot(msurr_points, type = 1) > plot(msurr_points, type = 2) Warning in mat2listw(W) : style is M (missing); style should be set to a valid value Warning in mat2listw(W) : no-neighbour observations found, set zero.policy to TRUE; this warning will soon become an error > summary(msurr_points) Characteristics of m-surrounding: Number of m-surrounding (R): 49 Length of m-surrounding (m): 3 Number no-symbolized observations: 1 List of no-symbolized observations: 31 List of the degree overlaping: There are 2 m-surrounding that have intersection with 1 m-surrounding There are 47 m-surrounding that have intersection with 2 m-surrounding Mean degree of overlaping: 1.9592 > msurr_points <- m.surround(x = x, m = m, r = r, + control = list(dtmaxpc = 0.1)) Threshold distance: 0.1223773 Number of m-surroundings excluded for exceeding the threshold distance: 15 Index of spatial observations excluded: 14 25 33 3 5 7 10 12 13 16 27 32 37 39 45 > plot(msurr_points, type = 1) > plot(msurr_points, type = 2) Warning in mat2listw(W) : style is M (missing); style should be set to a valid value Warning in mat2listw(W) : no-neighbour observations found, set zero.policy to TRUE; this warning will soon become an error > summary(msurr_points) Characteristics of m-surrounding: Number of m-surrounding (R): 34 Length of m-surrounding (m): 3 Number no-symbolized observations: 22 List of no-symbolized observations: 6 7 10 11 17 18 25 31 39 49 51 62 63 64 77 80 86 87 89 92 93 97 List of the degree overlaping: There are 1 m-surrounding that have intersection with 0 m-surrounding There are 18 m-surrounding that have intersection with 1 m-surrounding There are 15 m-surrounding that have intersection with 2 m-surrounding Mean degree of overlaping: 1.4118 > msurr_points <- m.surround(x = x, m = m, r = r, + control = list(dtmaxknn = 20)) > plot(msurr_points, type = 1) > plot(msurr_points, type = 2) Warning in mat2listw(W) : style is M (missing); style should be set to a valid value Warning in mat2listw(W) : no-neighbour observations found, set zero.policy to TRUE; this warning will soon become an error > summary(msurr_points) Characteristics of m-surrounding: Number of m-surrounding (R): 46 Length of m-surrounding (m): 3 Number no-symbolized observations: 5 List of no-symbolized observations: 31 51 77 80 97 List of the degree overlaping: There are 6 m-surrounding that have intersection with 1 m-surrounding There are 40 m-surrounding that have intersection with 2 m-surrounding Mean degree of overlaping: 1.8696 > > # Example 2: > > # Example 3: With isolated areas > data(provinces_spain) > sf::sf_use_s2(FALSE) > plot(sf::st_geometry(provinces_spain)) > m <- 3 > r <- 1 > msurr_points <- m.surround(x = provinces_spain, m = m, r = r, + distance = "Euclidean", + control = list(dtmaxknn = 8)) > plot(msurr_points, type = 1) Warning: st_centroid assumes attributes are constant over geometries Warning in st_centroid.sfc(st_geometry(x), of_largest_polygon = of_largest_polygon) : st_centroid does not give correct centroids for longitude/latitude data > plot(msurr_points, type = 2) Warning in mat2listw(W) : style is M (missing); style should be set to a valid value Warning in mat2listw(W) : no-neighbour observations found, set zero.policy to TRUE; this warning will soon become an error Warning: st_centroid assumes attributes are constant over geometries Warning in st_centroid.sfc(st_geometry(x), of_largest_polygon = of_largest_polygon) : st_centroid does not give correct centroids for longitude/latitude data > > # Example 4: Examples with multipolygons > fname <- system.file("shape/nc.shp", package="sf") > nc <- sf::st_read(fname) Reading layer `nc' from data source `/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/sf/shape/nc.shp' using driver `ESRI Shapefile' Simple feature collection with 100 features and 14 fields Geometry type: MULTIPOLYGON Dimension: XY Bounding box: xmin: -84.32385 ymin: 33.88199 xmax: -75.45698 ymax: 36.58965 Geodetic CRS: NAD27 > plot(sf::st_geometry(nc)) > m <- 3 > r <- 1 > msurr_polygonsf <- m.surround(x = nc, m = m, r = r, + distance = "Great Circle", + control=list(dtmaxpc = 0.20)) Error in loadNamespace(x) : there is no package called ‘lwgeom’ Calls: m.surround ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [65s/65s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 2 NOTEs