* using log directory ‘/Users/ripley/R/packages/tests-devel/fishboot.Rcheck’ * using R Under development (unstable) (2026-09-18 r90566) * using platform: aarch64-apple-darwin27.0.0 * R was compiled by Apple clang version 21.0.0 (clang-2100.3.34.2) GNU Fortran (GCC) 14.2.0 * running under: macOS Golden Gate 27.0 * using session charset: UTF-8 * current time: 2026-09-28 15:32:16 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘fishboot/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘fishboot’ version ‘1.0.3’ * 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 ‘fishboot’ can be installed ... OK * checking installed package size ... OK * checking package 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 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 ... OK * checking Rd files ... OK * checking Rd metadata ... 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 examples ... ERROR Running examples in ‘fishboot-Ex.R’ failed The error most likely occurred in: > ### Name: grotag_boot > ### Title: Bootstrapped tag-and-recapture growth analysis > ### Aliases: grotag_boot > > ### ** Examples > > # Load example DB from fishmethods package > data(bonito, package = "fishmethods") > > # Run the example cited on ?grotag > fishmethods::grotag(L1 = bonito$L1, + L2 = bonito$L2, + T1 = bonito$T1, + T2 = bonito$T2, + alpha = 35, beta = 55, + design = list(nu = 1, m = 1,p = 1, sea = 1), + stvalue = list(sigma = 0.9, nu = 0.4, m = -1, p = 0.2, u = 0.4, w = 0.4), + upper = list(sigma = 5, nu = 1, m = 2, p = 0.5, u = 1, w = 1), + lower = list(sigma = 0, nu = 0, m = -2, p = 0.0, u = 0, w = 0), + control = list(maxit = 1e4)) $table Estimate SE Parameters NA NA Mean growth rates ga 11.000 0.7900 Mean growth rates gb 7.480 0.8900 Seasonal variation u 0.660 0.1280 w 0.653 0.0230 Growth variability nu 0.353 0.0570 Measurement error s 0.757 0.0720 m -0.725 0.1100 Outliers p 0.000 0.1061 NA NA -Log likelihood 205.300 NA AIC 426.700 NA $VBparms Estimate Parameters NA Linf 97.5127614 K 0.1935559 $correlation [,1] [,2] [,3] [,4] [,5] [,6] [1,] 1.000000000 0.35141643 0.005506919 -0.36432732 -0.604872233 -0.07619574 [2,] 0.351416427 1.00000000 0.028361780 -0.25786403 -0.385218777 -0.01109765 [3,] 0.005506919 0.02836178 1.000000000 -0.34337785 0.009501885 -0.17215205 [4,] -0.364327318 -0.25786403 -0.343377853 1.00000000 0.256738003 -0.17737191 [5,] -0.604872233 -0.38521878 0.009501885 0.25673800 1.000000000 0.05372780 [6,] -0.076195737 -0.01109765 -0.172152051 -0.17737191 0.053727799 1.00000000 [7,] -0.079940284 -0.24182828 -0.072781140 0.02018362 -0.120395821 0.07908546 [8,] -0.370729333 -0.09370512 0.060163204 -0.04358243 0.070311828 0.03322333 [,7] [,8] [1,] -0.07994028 -0.37072933 [2,] -0.24182828 -0.09370512 [3,] -0.07278114 0.06016320 [4,] 0.02018362 -0.04358243 [5,] -0.12039582 0.07031183 [6,] 0.07908546 0.03322333 [7,] 1.00000000 0.08063072 [8,] 0.08063072 1.00000000 $predicted [1] 1.97457448 0.10992875 0.41543500 0.29020903 0.30618010 1.97605074 [7] 0.38276981 0.90961538 1.05288365 1.77439854 7.30683037 0.03561402 [13] 0.45950243 1.74247151 5.61892679 0.57347541 1.30490132 0.93631731 [19] 0.72806344 0.61180255 0.30261712 0.69203478 2.05189728 1.28761232 [25] 0.37081069 0.27662130 1.34304381 0.76119153 0.54476112 0.53100596 [31] 0.51560252 0.69428270 5.00175466 6.03625680 4.51531380 1.69453051 [37] 0.88382002 2.14902234 3.77081616 5.02834996 1.91286530 0.06615484 [43] 0.38922120 2.85676457 4.51531380 6.90916068 0.57753461 0.83032295 [49] 3.00423203 0.65547076 0.35268600 0.62243164 0.42144639 0.35814124 [55] 0.44927129 0.72740568 0.64430931 0.90989839 5.22461524 0.90416274 [61] 2.50738010 0.96204373 0.22263271 0.25598453 0.00000000 0.05450419 [67] 0.05974369 0.38627295 1.95045966 0.36385294 0.46196247 1.58043463 [73] 1.80259126 0.01710755 0.23715725 21.65838809 3.08502784 8.51415983 [79] 2.31533770 9.07016287 8.76800425 5.19532308 2.87854261 4.36975160 [85] 10.21014183 2.98690746 0.10188427 3.98153594 0.38922120 0.27356684 [91] 4.89447224 4.52531369 0.30111597 1.96582239 1.45560096 1.25792869 [97] 0.52971530 1.19968110 3.12938623 1.07045683 2.39897587 1.32776393 [103] 2.01931447 0.69947321 0.81984286 1.08408484 0.70242413 1.90554992 [109] 0.56928044 0.85294817 1.74266665 0.33822684 0.60252773 0.55234847 [115] 1.05664902 1.35660956 3.02620838 0.97621778 2.64676013 3.61107246 [121] 0.22123439 0.11469354 0.12199927 10.14259171 8.63571204 5.86162532 [127] 3.96977862 3.63203322 2.11552371 4.77658684 3.81884358 4.40954186 [133] 3.64239672 1.76478737 2.55318854 4.40428329 3.24706408 2.36671372 $residuals [1] 1.725425524 0.090071253 -1.615434999 -0.290209034 -0.306180104 [6] -0.876050736 -0.382769815 -0.809615377 -0.252883645 -1.374398542 [11] -3.006830370 -1.735614022 -0.059502434 0.057528487 -0.418926791 [16] -1.873475411 0.395098684 -1.436317308 -1.128063441 -1.711802551 [21] -0.602617118 -1.692034784 -1.351897283 -3.187612316 -1.170810689 [26] -1.776621300 -0.943043809 -1.261191526 -0.444761118 -0.631005964 [31] -1.415602515 -0.294282695 0.598245338 1.263743202 3.184686202 [36] 0.305469486 -1.683820023 -1.049022342 1.229183844 -0.428349960 [41] -0.812865297 -0.066154841 0.010778796 -1.656764571 -2.015313798 [46] -1.609160683 -1.277534612 -1.530322949 1.795767972 -1.755470755 [51] -0.352686000 -0.622431640 -1.621446386 -0.558141237 -2.549271288 [56] -1.427405681 -1.944309308 -1.809898394 -1.124615236 -0.804162743 [61] -0.507380103 -0.962043733 -1.022632715 -0.855984529 -1.000000000 [66] -0.054504189 -0.059743690 -0.186272949 -1.450459658 -1.363852943 [71] -0.461962469 -1.880434629 -1.302591255 -1.517107550 -0.037157255 [76] 6.941611909 0.414972163 -6.214159829 -0.815337697 -2.870162870 [81] -6.568004246 -1.495323077 1.921457391 -0.469751603 1.389858166 [86] 1.213092536 -0.001884269 -1.481535945 0.010778796 0.726433158 [91] -1.394472239 -2.125313685 -0.101115968 -1.765822386 1.044399045 [96] -1.057928694 -1.329715297 -0.899681096 -1.929386234 0.429543169 [101] -0.398975866 -1.027763933 -1.219314473 0.500526790 -0.119842856 [106] 0.815915157 -0.402424134 -1.905549920 0.030719565 -0.852948170 [111] -1.242666653 -0.038226841 -0.202527731 -0.752348473 -1.856649025 [116] -0.756609557 -2.226208383 -1.976217775 -0.346760128 -1.511072464 [121] -0.421234389 0.385306461 -0.321999268 0.057408287 3.464287960 [126] -4.061625318 -1.469778625 0.867966777 -0.115523708 -1.376586840 [131] -1.318843584 -0.609541864 -1.242396724 1.335212631 -0.653188544 [136] -0.004283292 -0.547064077 1.433286285 > > # Run the example using grotag_boot > res <- grotag_boot(L1 = bonito$L1, + L2 = bonito$L2, + T1 = bonito$T1, + T2 = bonito$T2, + alpha = 35, beta = 55, + design = list(nu = 1, m = 1,p = 1, sea = 1), + stvalue = list(sigma = 0.9, nu = 0.4, m = -1, p = 0.2, u = 0.4, w = 0.4), + upper = list(sigma = 5, nu = 1, m = 2, p = 0.5, u = 1, w = 1), + lower = list(sigma = 0, nu = 0, m = -2, p = 0.0, u = 0, w = 0), + control = list(maxit = 1e4), + nresamp = 3, na_action = "narm") Error in names(x) <- value : 'names' attribute [7] must be the same length as the vector [0] Calls: grotag_boot -> colnames<- Execution halted * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR See ‘/Users/ripley/R/packages/tests-devel/fishboot.Rcheck/00check.log’ for details. 38.84 real 32.03 user 5.93 sys