* using log directory ‘/srv/hornik/tmp/CRAN_pretest/cluster.Rcheck’ * using R Under development (unstable) (2025-10-03 r88899) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (3+b1) Debian flang-new version 19.1.7 (3+b1) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * checking for file ‘cluster/DESCRIPTION’ ... OK * this is package ‘cluster’ version ‘2.1.9’ * checking CRAN incoming feasibility ... [5s/7s] OK * 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 ‘cluster’ can be installed ... [5s/5s] OK * used C compiler: ‘Debian clang version 19.1.7 (3+b2)’ * checking package directory ... OK * checking for future file timestamps ... 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 ... [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 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 ... [5s/5s] OK * checking Rd files ... [0s/0s] 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 line endings in C/C++/Fortran sources/headers ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking examples ... [0s/0s] ERROR Running examples in ‘cluster-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: agnes > ### Title: Agglomerative Nesting (Hierarchical Clustering) > ### Aliases: agnes > ### Keywords: cluster > > ### ** Examples > > data(votes.repub) > agn1 <- agnes(votes.repub, metric = "manhattan", stand = TRUE) > agn1 Call: agnes(x = votes.repub, metric = "manhattan", stand = TRUE) Agglomerative coefficient: 0.7977555 Order of objects: [1] Alabama Georgia Arkansas Louisiana Mississippi [6] South Carolina Alaska Vermont Arizona Montana [11] Nevada Colorado Idaho Wyoming Utah [16] California Oregon Washington Minnesota Connecticut [21] New York New Jersey Illinois Ohio Indiana [26] Michigan Pennsylvania New Hampshire Wisconsin Delaware [31] Kentucky Maryland Missouri New Mexico West Virginia [36] Iowa South Dakota North Dakota Kansas Nebraska [41] Maine Massachusetts Rhode Island Florida North Carolina [46] Tennessee Virginia Oklahoma Hawaii Texas Height (summary): Min. 1st Qu. Median Mean 3rd Qu. Max. 8.382 12.804 18.528 23.118 28.411 87.455 Available components: [1] "order" "height" "ac" "merge" "diss" "call" [7] "method" "order.lab" "data" > plot(agn1) Fatal glibc error: malloc.c:4434 (_int_malloc): assertion failed: (unsigned long) (size) >= (unsigned long) (nb) Aborted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [28s/28s] ERROR Running ‘agnes-ex.R’ [1s/1s] Comparing ‘agnes-ex.Rout’ to ‘agnes-ex.Rout.save’ ... OK Running ‘clara-NAs.R’ [0s/0s] Comparing ‘clara-NAs.Rout’ to ‘clara-NAs.Rout.save’ ... OK Running ‘clara-ex.R’ [1s/1s] Comparing ‘clara-ex.Rout’ to ‘clara-ex.Rout.save’ ... OK Running ‘clara-gower.R’ [0s/0s] Running ‘clara.R’ [2s/2s] Comparing ‘clara.Rout’ to ‘clara.Rout.save’ ... OK Running ‘clusplot-out.R’ [0s/0s] Comparing ‘clusplot-out.Rout’ to ‘clusplot-out.Rout.save’ ... OK Running ‘daisy-ex.R’ [0s/0s] Comparing ‘daisy-ex.Rout’ to ‘daisy-ex.Rout.save’ ... OK Running ‘diana-boots.R’ [1s/1s] Running ‘diana-ex.R’ [0s/0s] Running ‘ellipsoid-ex.R’ [0s/0s] Comparing ‘ellipsoid-ex.Rout’ to ‘ellipsoid-ex.Rout.save’ ... OK Running ‘fanny-ex.R’ [0s/0s] Comparing ‘fanny-ex.Rout’ to ‘fanny-ex.Rout.save’ ... OK Running ‘mona.R’ [0s/0s] Comparing ‘mona.Rout’ to ‘mona.Rout.save’ ... OK Running ‘pam.R’ [20s/20s] Comparing ‘pam.Rout’ to ‘pam.Rout.save’ ... OK Running ‘silhouette-default.R’ [1s/1s] Comparing ‘silhouette-default.Rout’ to ‘silhouette-default.Rout.save’ ... OK Running ‘sweep-ex.R’ [0s/0s] Running the tests in ‘tests/diana-ex.R’ failed. Complete output: > library(cluster) > options(digits = 6) > data(votes.repub) > di.votes <- daisy(votes.repub) > > .p00 <- proc.time() > summary(diana(votes.repub, metric = "manhattan", stand = TRUE)) Merge: [,1] [,2] [1,] -7 -32 [2,] -13 -35 [3,] -12 -50 [4,] 1 -30 [5,] -26 -28 [6,] -5 -37 [7,] -22 -38 [8,] -21 -39 [9,] -16 -27 [10,] 4 2 [11,] -25 -48 [12,] -42 -46 [13,] -6 -14 [14,] -34 -41 [15,] -8 -20 [16,] 5 -31 [17,] 10 7 [18,] -17 -47 [19,] -3 -44 [20,] -33 12 [21,] 15 18 [22,] 17 -29 [23,] 22 -49 [24,] 21 11 [25,] 23 -15 [26,] -11 -19 [27,] 3 9 [28,] 8 -23 [29,] 19 16 [30,] 27 14 [31,] 6 25 [32,] -1 -10 [33,] 31 13 [34,] 29 -36 [35,] -2 -45 [36,] -9 -43 [37,] 24 20 [38,] 32 -4 [39,] -24 -40 [40,] 38 -18 [41,] 33 30 [42,] 34 37 [43,] 35 26 [44,] 41 28 [45,] 40 36 [46,] 42 44 [47,] 45 39 [48,] 43 46 [49,] 47 48 Order of objects: [1] Alabama Georgia Arkansas Louisiana Florida [6] Texas Mississippi South Carolina Alaska Vermont [11] Hawaii Maine Arizona Utah Montana [16] Nevada New Mexico Oklahoma Delaware Maryland [21] Kentucky Washington Missouri West Virginia North Carolina [26] Tennessee Virginia California Oregon Connecticut [31] New York New Jersey Illinois Ohio Michigan [36] Pennsylvania New Hampshire Wisconsin Iowa Colorado [41] Indiana Idaho Wyoming Kansas Nebraska [46] North Dakota South Dakota Massachusetts Rhode Island Minnesota Height: [1] 27.36345 33.96925 39.65826 48.53428 31.89965 72.59850 35.69152 [8] 167.58020 31.58222 43.84601 24.48796 85.55248 18.39339 25.67631 [15] 11.49397 17.45552 28.62550 42.54480 16.48510 20.04450 17.87516 [22] 21.98373 14.21808 33.61071 18.39733 14.75762 56.55675 11.70132 [29] 27.05887 8.38200 11.36820 13.25237 9.23004 17.83484 12.70819 [36] 20.66714 21.03997 23.66586 28.60541 15.31703 40.33905 10.46294 [43] 24.83525 12.80419 26.36292 16.25192 47.25773 12.79160 24.87206 Divisive coefficient: [1] 0.886918 1225 dissimilarities, summarized : Min. 1st Qu. Median Mean 3rd Qu. Max. 8.38 25.54 34.51 45.06 56.02 167.60 Metric : manhattan Number of objects : 50 Available components: [1] "order" "height" "dc" "merge" "diss" "call" [7] "order.lab" "data" > summary(diana(di.votes, keep.diss = FALSE)) Merge: [,1] [,2] [1,] -12 -50 [2,] -13 -32 [3,] -14 -35 [4,] -7 -29 [5,] -21 -39 [6,] -3 -28 [7,] -25 -48 [8,] -16 -27 [9,] -15 -41 [10,] 2 -30 [11,] 6 -26 [12,] -33 -42 [13,] 12 -46 [14,] 1 -44 [15,] 10 3 [16,] -22 -38 [17,] -11 -19 [18,] -5 -47 [19,] -17 -20 [20,] -2 -45 [21,] 14 -31 [22,] -37 -49 [23,] 9 8 [24,] 4 15 [25,] -8 19 [26,] -6 21 [27,] 5 -23 [28,] 24 16 [29,] 26 -36 [30,] 11 29 [31,] -1 -10 [32,] 28 22 [33,] 23 -34 [34,] 7 13 [35,] -4 -9 [36,] 20 17 [37,] -24 -40 [38,] 31 -43 [39,] 32 33 [40,] 25 34 [41,] 30 18 [42,] 35 -18 [43,] 38 42 [44,] 39 27 [45,] 41 40 [46,] 36 44 [47,] 43 37 [48,] 46 45 [49,] 47 48 Order of objects: [1] Alabama Georgia Texas Arkansas Florida [6] Louisiana Mississippi South Carolina Alaska Vermont [11] Hawaii Maine Connecticut New Hampshire Illinois [16] New York New Jersey Indiana Ohio Michigan [21] Pennsylvania Oregon Wisconsin Iowa South Dakota [26] Kansas Nebraska North Dakota Massachusetts Rhode Island [31] Minnesota Arizona Nevada Montana Colorado [36] Idaho Wyoming Utah New Mexico Oklahoma [41] California Washington Delaware Kentucky Maryland [46] Missouri West Virginia North Carolina Tennessee Virginia Height: [1] 48.2397 63.1862 72.9221 56.1363 72.9221 116.7048 63.0951 281.9508 [9] 33.8330 58.0384 32.7611 106.7448 20.5216 39.1728 19.8436 27.0243 [17] 31.4966 20.2258 47.1690 31.6595 49.2428 36.7667 64.4821 26.1547 [25] 37.4564 25.9221 50.7201 77.1184 22.6334 44.4594 178.4119 23.4206 [33] 27.8273 48.0483 43.7055 17.1992 31.1988 34.0510 48.0483 70.4868 [41] 33.2328 81.0764 43.3829 33.4744 66.7591 25.3953 54.7306 29.5099 [49] 30.1541 Divisive coefficient: [1] 0.878225 Available components: [1] "order" "height" "dc" "merge" "diss" "call" [7] "order.lab" > cat('Time elapsed: ', proc.time() - .p00,'\n') Time elapsed: 0.003 0.004 0.007 0 0 > > data(agriculture) > data(ruspini) > > .p0 <- proc.time() > dia.agr <- diana(agriculture) > drusp0 <- diana(ruspini, keep.diss=FALSE, keep.data=FALSE) > drusp1 <- diana(ruspini, metric = "manhattan") > cat('Time elapsed: ', proc.time() - .p0,'\n') Time elapsed: 0.001 0 0.002 0 0 > > summary(dia.agr) Merge: [,1] [,2] [1,] -1 -10 [2,] -2 -9 [3,] 1 -3 [4,] -6 -8 [5,] -5 -7 [6,] 3 -12 [7,] -4 -11 [8,] 6 4 [9,] 8 2 [10,] 7 5 [11,] 9 10 Order of objects: [1] B NL D UK F I DK L GR P E IRL Height: [1] 1.64924 2.43516 4.85077 6.72309 2.77308 8.05295 2.22036 24.03539 [9] 5.16236 12.56742 3.14006 Divisive coefficient: [1] 0.871106 66 dissimilarities, summarized : Min. 1st Qu. Median Mean 3rd Qu. Max. 1.65 4.36 7.99 9.59 13.25 24.04 Metric : euclidean Number of objects : 12 Available components: [1] "order" "height" "dc" "merge" "diss" "call" [7] "order.lab" "data" > summary(drusp0) Merge: [,1] [,2] [1,] -18 -19 [2,] -55 -56 [3,] -27 -28 [4,] -49 -51 [5,] -33 -34 [6,] -23 -24 [7,] -59 -60 [8,] -29 -30 [9,] -67 -69 [10,] -36 -39 [11,] -32 -35 [12,] -50 -54 [13,] -37 -38 [14,] -70 -71 [15,] -64 -68 [16,] -62 -66 [17,] -12 -13 [18,] -16 1 [19,] -9 -10 [20,] -42 -43 [21,] -15 -17 [22,] -47 -48 [23,] 12 -52 [24,] -21 -22 [25,] 9 14 [26,] 2 -57 [27,] -73 -74 [28,] 6 -25 [29,] -26 11 [30,] 4 -53 [31,] 3 8 [32,] -11 17 [33,] -6 -8 [34,] -2 -3 [35,] 10 -40 [36,] -14 21 [37,] -65 25 [38,] -4 33 [39,] 36 18 [40,] 29 5 [41,] 26 7 [42,] -1 34 [43,] 24 28 [44,] 16 -63 [45,] -46 22 [46,] -31 35 [47,] 27 -75 [48,] 37 -72 [49,] 43 31 [50,] 30 23 [51,] 13 20 [52,] 15 48 [53,] 32 -20 [54,] 41 -58 [55,] 42 -5 [56,] 40 46 [57,] -44 -45 [58,] 19 39 [59,] 38 -7 [60,] 51 -41 [61,] -61 44 [62,] 50 54 [63,] 52 47 [64,] 61 63 [65,] 49 56 [66,] 59 53 [67,] 55 58 [68,] 57 62 [69,] 65 60 [70,] 67 66 [71,] 68 45 [72,] 69 71 [73,] 70 64 [74,] 73 72 Order of objects: [1] 1 2 3 5 9 10 14 15 17 16 18 19 4 6 8 7 11 12 13 20 61 62 66 63 64 [26] 68 65 67 69 70 71 72 73 74 75 21 22 23 24 25 27 28 29 30 26 32 35 33 34 31 [51] 36 39 40 37 38 42 43 41 44 45 49 51 53 50 54 52 55 56 57 59 60 58 46 47 48 Height: [1] 10.04988 6.40312 16.12452 29.12044 4.12311 17.02939 8.48528 [8] 4.24264 9.21954 4.12311 1.41421 40.24922 8.94427 6.32456 [15] 19.02630 28.84441 6.32456 4.12311 14.14214 102.07840 21.40093 [22] 4.12311 10.81665 27.07397 3.60555 13.60147 8.54400 2.82843 [29] 5.09902 3.60555 12.80625 22.80351 5.65685 12.36932 154.49595 [36] 4.47214 10.77033 2.23607 5.83095 13.03840 2.00000 6.32456 [43] 2.82843 28.16026 6.08276 3.00000 9.43398 2.23607 16.27882 [50] 11.04536 3.00000 6.70820 36.61967 3.60555 13.34166 4.24264 [57] 20.02498 94.57801 17.02939 35.35534 2.23607 6.32456 13.15295 [64] 3.16228 4.47214 22.20360 2.00000 5.38516 9.84886 2.82843 [71] 15.29706 47.63402 11.00000 4.47214 Divisive coefficient: [1] 0.960566 Available components: [1] "order" "height" "dc" "merge" "diss" "call" [7] "order.lab" > summary(drusp1) Merge: [,1] [,2] [1,] -55 -56 [2,] -27 -28 [3,] -18 -19 [4,] -49 -51 [5,] -33 -34 [6,] -32 -35 [7,] -23 -24 [8,] -59 -60 [9,] -50 -54 [10,] -29 -30 [11,] -67 -69 [12,] -37 -38 [13,] 11 -71 [14,] -64 -68 [15,] -62 -66 [16,] -12 -13 [17,] -16 3 [18,] -9 -10 [19,] -47 -48 [20,] 9 -52 [21,] -42 -43 [22,] -39 -40 [23,] -21 -22 [24,] 13 -70 [25,] -15 -17 [26,] 1 -57 [27,] -26 6 [28,] 4 -53 [29,] 7 -25 [30,] 2 10 [31,] -11 16 [32,] -6 -8 [33,] -31 -36 [34,] -74 -75 [35,] -2 -3 [36,] -46 19 [37,] -65 24 [38,] -14 17 [39,] -4 32 [40,] 38 25 [41,] -1 35 [42,] 26 8 [43,] 27 5 [44,] 23 30 [45,] 28 20 [46,] 15 -63 [47,] 43 33 [48,] 44 29 [49,] 46 -73 [50,] 31 -20 [51,] 42 -58 [52,] -44 -45 [53,] 12 22 [54,] 37 -72 [55,] 14 54 [56,] 39 -7 [57,] 41 -5 [58,] 53 21 [59,] 18 40 [60,] 48 47 [61,] -61 49 [62,] 45 51 [63,] 58 -41 [64,] 55 34 [65,] 61 64 [66,] 57 59 [67,] 56 50 [68,] 52 62 [69,] 60 63 [70,] 66 67 [71,] 68 36 [72,] 69 71 [73,] 70 65 [74,] 73 72 Order of objects: [1] 1 2 3 5 9 10 14 16 18 19 15 17 4 6 8 7 11 12 13 20 61 62 66 63 73 [26] 64 68 65 67 69 71 70 72 74 75 21 22 27 28 29 30 23 24 25 26 32 35 33 34 31 [51] 36 37 38 39 40 42 43 41 44 45 49 51 53 50 54 52 55 56 57 59 60 58 46 47 48 Height: [1] 12 9 22 36 5 24 11 5 2 12 6 54 12 8 20 40 8 5 16 [20] 142 30 5 15 16 33 5 19 11 4 5 6 18 32 9 187 6 14 2 [39] 8 4 16 3 8 26 7 3 13 3 16 9 51 5 18 6 24 6 32 [58] 123 18 48 3 8 15 4 6 31 2 7 13 4 18 67 11 6 Divisive coefficient: [1] 0.958075 2775 dissimilarities, summarized : Min. 1st Qu. Median Mean 3rd Qu. Max. 2.0 52.5 97.0 91.0 128.0 187.0 Metric : manhattan Number of objects : 75 Available components: [1] "order" "height" "dc" "merge" "diss" "call" [7] "order.lab" "data" > str (drusp1) free(): invalid next size (normal) Aborted * checking PDF version of manual ... [5s/5s] OK * checking HTML version of manual ... [2s/2s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs