* using log directory ‘/srv/hornik/tmp/CRAN/lakhesis.Rcheck’ * using R Under development (unstable) (2024-05-30 r86652) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.5 (2) Debian flang-new version 18.1.5 (2) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘lakhesis/DESCRIPTION’ ... OK * this is package ‘lakhesis’ version ‘0.0.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [2s/3s] NOTE Maintainer: ‘Stephen A. Collins-Elliott ’ New submission Non-FOSS package license (`use_gpl3_license()`) Possibly misspelled words in DESCRIPTION: Deterimining (7:14) Lakhesis (7:263) Seriation (2:18) seriated (7:321) seriations (7:37, 7:181) * 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 ‘lakhesis’ can be installed ... [1s/1s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... WARNING Non-standard license specification: `use_gpl3_license()` Standardizable: FALSE * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. Non-standard file/directory found at top level: ‘README.Rmd’ * 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 ... [3s/3s] NOTE ca.procrustes.poly: no visible global function definition for ‘lm’ ca.procrustes.poly: no visible global function definition for ‘predict’ element.eval: no visible global function definition for ‘glm’ element.eval: no visible global function definition for ‘binomial’ element.eval: no visible global function definition for ‘pchisq’ lakhesize: no visible global function definition for ‘prcomp’ lakhesize: no visible global function definition for ‘lm’ lakhesize: no visible global function definition for ‘na.omit’ spearman.sq: no visible global function definition for ‘na.omit’ spearman.sq: no visible global function definition for ‘cor’ Undefined global functions or variables: binomial cor glm lm na.omit pchisq prcomp predict Consider adding importFrom("stats", "binomial", "cor", "glm", "lm", "na.omit", "pchisq", "prcomp", "predict") to your NAMESPACE file. * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... WARNING Missing link or links in Rd file 'im.csv.read.Rd': ‘[readr::locale]{locale}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 ... WARNING 'library' or 'require' call not declared from: ‘seriation’ * 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 examples ... [0s/0s] ERROR Running examples in ‘lakhesis-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: ca.procrustes > ### Title: Correspondence Analysis with Procrustes Fitting > ### Aliases: ca.procrustes > > ### ** Examples > > # Quattro Fontanili > data(quattofontanili) Warning in data(quattofontanili) : data set ‘quattofontanili’ not found > ca.procrustes(quattrofontanili) $ref Dim1 Dim2 R1 7.073063e-01 -0.70690725 R2 7.062424e-01 -0.70265583 R3 7.041163e-01 -0.69417855 R4 7.009311e-01 -0.68152640 R5 6.966917e-01 -0.66477547 R6 6.914044e-01 -0.64402650 R7 6.850771e-01 -0.61940428 R8 6.777194e-01 -0.59105689 R9 6.693424e-01 -0.55915482 R10 6.599586e-01 -0.52388992 R11 6.495821e-01 -0.48547429 R12 6.382287e-01 -0.44413896 R13 6.259152e-01 -0.40013252 R14 6.126604e-01 -0.35371964 R15 5.984840e-01 -0.30517945 R16 5.834075e-01 -0.25480387 R17 5.674535e-01 -0.20289587 R18 5.506459e-01 -0.14976763 R19 5.330101e-01 -0.09573868 R20 5.145727e-01 -0.04113394 R21 4.953613e-01 0.01371819 R22 4.754048e-01 0.06848781 R23 4.547332e-01 0.12284554 R24 4.333777e-01 0.17646446 R25 4.113703e-01 0.22902211 R26 3.887442e-01 0.28020238 R27 3.655334e-01 0.32969749 R28 3.417728e-01 0.37720976 R29 3.174982e-01 0.42245344 R30 2.927460e-01 0.46515644 R31 2.675534e-01 0.50506194 R32 2.419585e-01 0.54192993 R33 2.159996e-01 0.57553869 R34 1.897158e-01 0.60568609 R35 1.631467e-01 0.63219083 R36 1.363322e-01 0.65489350 R37 1.093127e-01 0.67365756 R38 8.212869e-02 0.68837016 R39 5.482118e-02 0.69894282 R40 2.743122e-02 0.70531197 R41 1.832803e-13 0.70743928 R42 -2.743122e-02 0.70531197 R43 -5.482118e-02 0.69894282 R44 -8.212869e-02 0.68837016 R45 -1.093127e-01 0.67365756 R46 -1.363322e-01 0.65489350 R47 -1.631467e-01 0.63219083 R48 -1.897158e-01 0.60568609 R49 -2.159996e-01 0.57553869 R50 -2.419585e-01 0.54192993 R51 -2.675534e-01 0.50506194 R52 -2.927460e-01 0.46515644 R53 -3.174982e-01 0.42245344 R54 -3.417728e-01 0.37720976 R55 -3.655334e-01 0.32969749 R56 -3.887442e-01 0.28020238 R57 -4.113703e-01 0.22902211 R58 -4.333777e-01 0.17646446 R59 -4.547332e-01 0.12284554 R60 -4.754048e-01 0.06848781 R61 -4.953613e-01 0.01371819 R62 -5.145727e-01 -0.04113394 R63 -5.330101e-01 -0.09573868 R64 -5.506459e-01 -0.14976763 R65 -5.674535e-01 -0.20289587 R66 -5.834075e-01 -0.25480387 R67 -5.984840e-01 -0.30517945 R68 -6.126604e-01 -0.35371964 R69 -6.259152e-01 -0.40013252 R70 -6.382287e-01 -0.44413896 R71 -6.495821e-01 -0.48547429 R72 -6.599586e-01 -0.52388992 R73 -6.693424e-01 -0.55915482 R74 -6.777194e-01 -0.59105689 R75 -6.850771e-01 -0.61940428 R76 -6.914044e-01 -0.64402650 R77 -6.966917e-01 -0.66477547 R78 -7.009311e-01 -0.68152640 R79 -7.041163e-01 -0.69417855 R80 -7.062424e-01 -0.70265583 R81 -7.073063e-01 -0.70690725 $x [,1] [,2] QF W15 0.649934655 -0.51963527 QF X15 0.657104639 -0.55734884 QF M22 0.690101892 -0.61577045 QF O21 0.622502957 -0.47071097 QF O16 0.622502957 -0.47071097 V la F 29/18 0.631922849 -0.48394989 V la F 33/1 0.544021465 -0.35317014 QF S7 0.712435434 -0.65574766 V la F 29/15 0.685054341 -0.60470744 V la F 29/2 0.598787664 -0.40887014 QF AAMA 0.543716031 -0.31041328 QF M7 0.578133288 -0.32297027 QF AAMB 0.585645023 -0.34923065 QF BBMB 0.517131323 -0.19321230 QF CC14B 0.507137439 -0.16719454 QF CC15 0.474023634 -0.08652763 QF CC12 0.333314601 0.14277145 V la F 29/5 0.456295858 -0.23809157 QF 18-19B 0.456295858 -0.23809157 QF BB16B 0.471010532 -0.19736391 V la F 29/20 0.403474244 -0.04945475 QF CC17A 0.412294825 0.04735244 QF EE14-15 0.355580015 0.17363988 QF AA12 0.424784619 0.07570335 QF CCDD19 0.234217482 0.18658300 QF EE16-17 0.378069310 0.16008791 QG DD17 0.308792029 0.16210719 QF BB18A 0.281423697 0.17011070 QF EE17-18B 0.220237147 0.31435582 QG FF18-19A 0.019376528 0.28477614 QF FF19B 0.077863717 0.23494917 QF II 15-16 0.204857509 0.05222894 QF FF14-15 -0.074146115 0.45242560 QF JJ17-18 -0.031126408 0.33353960 QF JJ18-19B -0.178407039 0.43761405 QF JJ14-15 -0.170634036 0.43279425 QF HH18 0.009525962 0.24493168 QF GGHH13 -0.134956369 0.44239949 QF GGHH19 -0.044235527 0.36189819 QF IIJJ19 -0.150693271 0.46560397 QF II13-14B -0.200202691 0.58297569 QF GG16-17 -0.175672269 0.57603179 QF II18-19 -0.138051692 0.45164932 QF JJ17 -0.046822745 0.08578561 QG KKLL16 0.026334821 0.22486532 QF KKLL17 -0.197097698 0.53166479 QF LL18 -0.144074782 0.52668872 QF KKLL18-19 -0.172175663 0.55174882 QF HH11-12 -0.154012746 0.50882095 QF II9-10 -0.149247322 0.54350161 QF LL12-13 -0.187367749 0.54387358 QF KK15 -0.204738504 0.55140537 QF MM14 -0.232909977 0.62195302 QF MM19-20 -0.200208481 0.53823682 QF MM10-11 -0.150713106 0.30107326 QF CCDD15-16 -0.270014925 0.37095261 QF ZAA17-18 -0.232688020 0.35934760 QF HH7-8 -0.270247759 0.47473029 QF JJ12-13 -0.113994362 0.46555632 QF Z15 -0.025671774 0.18514860 QF JJ8 -0.445554739 -0.01461350 XIII -0.250718085 0.26168566 XV -0.235892913 0.25873087 XVI -0.385462547 0.01574085 XIX -0.304879199 0.10903687 I -0.509043211 -0.30891391 XII -0.440351760 -0.12755938 IV -0.537382493 -0.39472525 VII -0.536395364 -0.40583681 XIV -0.642251923 -0.69766952 XVII -0.527825754 -0.31727329 XXIV -0.541031985 -0.35485124 XX -0.537030744 -0.39099969 VIII -0.509475882 -0.36221386 V -0.606723094 -0.58767912 X -0.536455174 -0.40303075 IX -0.584286813 -0.53693063 XI -0.620551208 -0.62620880 VI -0.598619514 -0.55038915 XXIII -0.656277020 -0.75452003 XVIII -0.637583893 -0.69048999 $y [,1] [,2] Type 1 0.679942347 -0.57434568 Type 2 0.688898886 -0.58058417 Type 3 0.728132601 -0.68033264 Type 4 0.743809698 -0.70934451 Type 5 0.631228570 -0.44586755 Type 6 0.623000863 -0.46834115 Type 7 0.755703041 -0.73153103 Type 8 0.726520575 -0.67488957 Type 9 0.726520575 -0.67488957 Type 10 0.632905947 -0.46226304 Type 11 0.497327799 -0.18113770 Type 12 0.565011447 -0.26867313 Type 13 0.602409520 -0.36762356 Type 14 0.298031730 -0.01720595 Type 15 0.532074976 -0.29970929 Type 16 0.615822968 -0.37720503 Type 17 0.443304002 0.01038537 Type 18 0.326591263 0.08471419 Type 19 0.444609624 0.01446243 Type 20 0.342371139 0.14303354 Type 21 0.394565672 0.09370417 Type 22 0.483296492 -0.26772727 Type 23 0.256447663 -0.03658899 Type 24 0.299981754 0.02482751 Type 25 0.281627395 0.22723712 Type 26 0.447220794 0.07916751 Type 27 0.363727503 0.15182997 Type 28 0.003328672 0.33683902 Type 29 0.314034054 0.25879212 Type 30 0.008869438 0.40972919 Type 31 0.296116474 0.18484091 Type 32 -0.026170355 0.45839644 Type 33 -0.110709601 0.41568187 Type 34 -0.153002170 0.40245067 Type 35 -0.110604721 0.26621994 Type 36 -0.128515809 0.43975015 Type 37 -0.205875231 0.46970706 Type 38 -0.147695801 0.50128554 Type 39 -0.146757672 0.50867204 Type 40 -0.093354326 0.28773450 Type 41 -0.227558529 0.30734690 Type 42 -0.178799729 0.42435024 Type 43 -0.199261269 0.62848114 Type 44 -0.175020206 0.60042325 Type 45 -0.133096684 0.37630901 Type 46 -0.075257628 0.29406604 Type 47 -0.200621086 0.56778802 Type 48 -0.186991622 0.60965735 Type 49 -0.251210566 0.35476074 Type 50 -0.215875671 0.34680065 Type 51 -0.191409013 0.60481017 Type 52 -0.241705415 0.56446206 Type 53 -0.321357299 0.33690054 Type 54 -0.247970223 0.60391639 Type 55 -0.265941335 0.60780392 Type 56 -0.228166781 0.49750825 Type 57 -0.426386884 -0.08146577 Type 58 -0.406055927 -0.21848027 Type 59 -0.468913454 -0.30109634 Type 60 -0.535249386 -0.37039881 Type 61 -0.494512560 -0.28859566 Type 62 -0.522350521 -0.34783749 Type 63 -0.491011005 -0.26278491 Type 64 -0.548327600 -0.42562817 Type 65 -0.543645177 -0.39314924 Type 66 -0.562579646 -0.45979673 Type 67 -0.614340221 -0.61362076 Type 68 -0.607568061 -0.59906599 Type 69 -0.587522037 -0.54201027 Type 70 -0.643638596 -0.69798328 Type 71 -0.553610778 -0.36625872 Type 72 -0.587280981 -0.51463394 Type 73 -0.610423734 -0.62203549 Type 74 -0.640939426 -0.69102521 Type 75 -0.599985015 -0.57124055 Type 76 -0.622437846 -0.63675796 Type 77 -0.618762136 -0.60235609 Type 78 -0.618762136 -0.60235609 Type 79 -0.677169098 -0.82725577 Type 80 -0.658211977 -0.75671708 Type 81 -0.658211977 -0.75671708 Type C 0.451259538 -0.24191675 $x.dat index match dist 1 QF W15 10 1.185810e-04 2 QF X15 9 1.530236e-04 3 QF M22 7 3.845333e-05 4 QF O21 11 9.512376e-04 5 QF O16 11 9.512376e-04 6 V la F 29/18 11 3.141743e-04 7 V la F 33/1 14 4.711603e-03 8 QF S7 5 3.293669e-04 9 V la F 29/15 7 2.159976e-04 10 V la F 29/2 13 8.122518e-04 11 QF AAMA 15 3.026926e-03 12 QF M7 15 7.306658e-04 13 QF AAMB 14 7.499808e-04 14 QF BBMB 17 2.626088e-03 15 QF CC14B 18 2.196684e-03 16 QF CC15 19 3.564252e-03 17 QF CC12 24 1.114784e-02 18 V la F 29/5 17 1.359475e-02 19 QF 18-19B 17 1.359475e-02 20 QF BB16B 18 8.607199e-03 21 V la F 29/20 20 1.241210e-02 22 QF CC17A 22 4.429567e-03 23 QF EE14-15 24 6.060456e-03 24 QF AA12 22 2.614462e-03 25 QF CCDD19 26 3.264311e-02 26 QF EE16-17 24 3.327208e-03 27 QG DD17 25 1.499991e-02 28 QF BB18A 25 2.035668e-02 29 QF EE17-18B 28 1.872154e-02 30 QG FF18-19A 30 1.072679e-01 31 QF FF19B 28 8.988609e-02 32 QF II 15-16 23 6.742457e-02 33 QF FF14-15 49 3.527924e-02 34 QF JJ17-18 51 8.531765e-02 35 QF JJ18-19B 51 1.249630e-02 36 QF JJ14-15 51 1.461599e-02 37 QF HH18 29 1.263609e-01 38 QF GGHH13 50 2.135576e-02 39 QF GGHH19 51 7.036675e-02 40 QF IIJJ19 50 1.415499e-02 41 QF II13-14B 49 3.048514e-04 42 QF GG16-17 48 1.076600e-03 43 QF II18-19 50 1.894721e-02 44 QF JJ17 57 1.534116e-01 45 QG KKLL16 28 1.227100e-01 46 QF KKLL17 50 2.117863e-03 47 QF LL18 49 7.559499e-03 48 QF KKLL18-19 49 2.486496e-03 49 QF HH11-12 49 8.293627e-03 50 QF II9-10 49 5.482241e-03 51 QF LL12-13 49 1.822462e-03 52 QF KK15 49 7.092295e-04 53 QF MM14 48 2.130346e-03 54 QF MM19-20 49 1.640789e-03 55 QF MM10-11 54 4.230058e-02 56 QF CCDD15-16 53 4.906994e-03 57 QF ZAA17-18 53 1.117511e-02 58 QF HH7-8 52 5.978277e-04 59 QF JJ12-13 50 2.220774e-02 60 QF Z15 55 1.364003e-01 61 QF JJ8 61 3.283374e-03 62 XIII 55 1.780817e-02 63 XV 55 2.184292e-02 64 XVI 60 1.087184e-02 65 XIX 58 2.105834e-02 66 I 67 8.013605e-03 67 XII 63 9.598134e-03 68 IV 68 7.348222e-03 69 VII 69 8.046348e-03 70 XIV 78 3.703849e-03 71 XVII 67 5.138852e-03 72 XXIV 68 5.131908e-03 73 XX 68 7.109645e-03 74 VIII 68 1.071919e-02 75 V 73 4.734809e-03 76 X 69 8.011504e-03 77 IX 72 5.896275e-03 78 XI 75 4.209891e-03 79 VI 72 4.464690e-03 80 XXIII 81 4.870960e-03 81 XVIII 78 4.093217e-03 $y.dat index match dist 1 Type 1 8 2.842061e-04 2 Type 2 8 2.346586e-04 3 Type 3 4 7.413456e-04 4 Type 4 1 1.338441e-03 5 Type 5 12 5.198946e-05 6 Type 6 12 8.176325e-04 7 Type 7 1 2.948579e-03 8 Type 8 4 6.988677e-04 9 Type 9 4 6.988677e-04 10 Type 10 12 3.568138e-04 11 Type 11 18 3.826902e-03 12 Type 12 16 5.307708e-04 13 Type 13 14 2.983993e-04 14 Type 14 22 3.880461e-02 15 Type 15 15 4.440084e-03 16 Type 16 14 5.615654e-04 17 Type 17 21 2.721065e-03 18 Type 18 23 1.787436e-02 19 Type 19 21 2.576282e-03 20 Type 20 24 9.399818e-03 21 Type 21 23 4.469351e-03 22 Type 22 16 1.018923e-02 23 Type 23 22 5.898334e-02 24 Type 24 22 3.267945e-02 25 Type 25 26 1.427934e-02 26 Type 26 22 9.083916e-04 27 Type 27 24 5.458006e-03 28 Type 28 31 9.811368e-02 29 Type 29 26 6.040010e-03 30 Type 30 33 7.039569e-02 31 Type 31 25 1.523543e-02 32 Type 32 48 4.844137e-02 33 Type 33 51 3.258878e-02 34 Type 34 52 2.346034e-02 35 Type 35 54 6.575743e-02 36 Type 36 50 2.330995e-02 37 Type 37 51 5.054168e-03 38 Type 38 49 1.017894e-02 39 Type 39 49 9.265593e-03 40 Type 40 53 6.838965e-02 41 Type 41 54 1.792573e-02 42 Type 42 51 1.439160e-02 43 Type 43 48 6.107292e-04 44 Type 44 48 2.436592e-04 45 Type 45 52 3.338176e-02 46 Type 46 53 7.516380e-02 47 Type 47 49 2.965717e-04 48 Type 48 48 2.319226e-05 49 Type 49 54 8.705482e-03 50 Type 50 53 1.605048e-02 51 Type 51 48 3.634084e-06 52 Type 52 50 5.077612e-04 53 Type 53 55 2.003414e-03 54 Type 54 49 1.827415e-03 55 Type 55 49 3.535222e-03 56 Type 56 51 1.608367e-03 57 Type 57 62 9.403392e-03 58 Type 58 64 2.562769e-02 59 Type 59 66 1.525188e-02 60 Type 60 68 6.270658e-03 61 Type 61 66 9.044193e-03 62 Type 62 67 7.616019e-03 63 Type 63 66 8.600807e-03 64 Type 64 69 6.669871e-03 65 Type 65 68 6.317793e-03 66 Type 66 70 5.967941e-03 67 Type 67 74 4.526050e-03 68 Type 68 74 4.985357e-03 69 Type 69 72 5.575399e-03 70 Type 70 78 3.553262e-03 71 Type 71 68 3.644085e-03 72 Type 72 71 4.731719e-03 73 Type 73 74 5.488381e-03 74 Type 74 78 3.689231e-03 75 Type 75 73 4.956507e-03 76 Type 76 75 4.224825e-03 77 Type 77 74 3.603632e-03 78 Type 78 74 3.603632e-03 79 Type 79 81 1.539201e-02 80 Type 80 81 4.891268e-03 81 Type 81 81 4.891268e-03 82 Type C 17 1.502365e-02 > > # Münsingen-Rain > library(seriation) Error in library(seriation) : there is no package called ‘seriation’ Execution halted * checking PDF version of manual ... [4s/4s] WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! LaTeX Error: Unicode character β (U+03B2) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character β (U+03B2) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. * checking PDF version of manual without index ... ERROR * checking HTML version of manual ... [0s/1s] OK * checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘lakhesis-manual.tex’ * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs, 4 WARNINGs, 4 NOTEs