* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/PAICE.Rcheck’ * using R Under development (unstable) (2025-11-16 r89026) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) * running under: Fedora Linux 40 (Workstation Edition) * using session charset: UTF-8 * checking for file ‘PAICE/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PAICE’ version ‘1.0.2’ * 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 ‘PAICE’ can be installed ... 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 whether startup messages can be suppressed ... 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 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 ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... OK * checking examples with --run-donttest ... [30m/31m] ERROR Running examples in ‘PAICE-Ex.R’ failed The error most likely occurred in: > ### Name: PAICE-package > ### Title: Phylogeographic Analysis of Island Colonization Events > ### Aliases: PAICE PAICE-package > ### Keywords: package > > ### ** Examples > ## No test: > # Inference of minimum number of inter-island colonization events > data(CmonsData) > data(CmonsNetwork) > col <- colonization(data = CmonsData, network = CmonsNetwork) > col Minimum number of inferred colonization events 13 > summary(col) Summary of data used: Total Islands 5 Populations 37 Individuals 90 Haplotypes 16 Inference of colonization events: c = c1 + c2 + c3 Colonization events by haplotype: c1 c2 c3 OUT 0 0 0 c1 0 0 0 c2 0 1 0 c3 0 0 0 c4 0 0 0 c5 3 0 0 c6 1 0 0 c7 0 1 0 c8 0 0 0 c9 1 0 0 c10 0 0 0 c11 2 0 0 c12 0 0 0 c13 3 0 0 c14 0 0 0 c15 1 0 0 c16 0 0 0 Colonization events by type: c1 c2 c3 11 2 0 Total of colonization events inferred: c = 13 colonization events > > # Asumptotic estimators of colonization events > # 25 replicates used in each sampling variable > set.seed(31) > CmonsRare <- rarecol(data = CmonsData, network = CmonsNetwork, + replicates_field = 25, replicates_genetic = 25, monitor = TRUE, + mode = c(1, 2)) [17/11/25, 21:19:13] 1 genetic replicates [17/11/25, 21:19:32] 17 positions [17/11/25, 21:19:50] 16 positions [17/11/25, 21:20:08] 15 positions [17/11/25, 21:20:25] 14 positions [17/11/25, 21:20:41] 13 positions [17/11/25, 21:20:56] 12 positions [17/11/25, 21:21:11] 11 positions [17/11/25, 21:21:25] 10 positions [17/11/25, 21:21:39] 9 positions [17/11/25, 21:21:51] 8 positions [17/11/25, 21:22:03] 7 positions [17/11/25, 21:22:14] 6 positions [17/11/25, 21:22:25] 5 positions [17/11/25, 21:22:35] 4 positions [17/11/25, 21:22:43] 3 positions [17/11/25, 21:22:51] 2 positions [17/11/25, 21:22:59] 1 positions [17/11/25, 21:23:05] 0 positions [17/11/25, 21:23:05] 2 genetic replicates [17/11/25, 21:23:23] 17 positions [17/11/25, 21:23:41] 16 positions [17/11/25, 21:23:58] 15 positions [17/11/25, 21:24:14] 14 positions [17/11/25, 21:24:29] 13 positions [17/11/25, 21:24:44] 12 positions [17/11/25, 21:24:58] 11 positions [17/11/25, 21:25:11] 10 positions [17/11/25, 21:25:24] 9 positions [17/11/25, 21:25:36] 8 positions [17/11/25, 21:25:47] 7 positions [17/11/25, 21:25:58] 6 positions [17/11/25, 21:26:08] 5 positions [17/11/25, 21:26:18] 4 positions [17/11/25, 21:26:27] 3 positions [17/11/25, 21:26:34] 2 positions [17/11/25, 21:26:41] 1 positions [17/11/25, 21:26:47] 0 positions [17/11/25, 21:26:47] 3 genetic replicates [17/11/25, 21:27:05] 17 positions [17/11/25, 21:27:23] 16 positions [17/11/25, 21:27:40] 15 positions [17/11/25, 21:27:56] 14 positions [17/11/25, 21:28:11] 13 positions [17/11/25, 21:28:26] 12 positions [17/11/25, 21:28:39] 11 positions [17/11/25, 21:28:52] 10 positions [17/11/25, 21:29:05] 9 positions [17/11/25, 21:29:16] 8 positions [17/11/25, 21:29:27] 7 positions [17/11/25, 21:29:38] 6 positions [17/11/25, 21:29:48] 5 positions [17/11/25, 21:29:59] 4 positions [17/11/25, 21:30:08] 3 positions [17/11/25, 21:30:16] 2 positions [17/11/25, 21:30:23] 1 positions [17/11/25, 21:30:29] 0 positions [17/11/25, 21:30:29] 4 genetic replicates [17/11/25, 21:30:47] 17 positions [17/11/25, 21:31:04] 16 positions [17/11/25, 21:31:20] 15 positions [17/11/25, 21:31:37] 14 positions [17/11/25, 21:31:52] 13 positions [17/11/25, 21:32:06] 12 positions [17/11/25, 21:32:20] 11 positions [17/11/25, 21:32:33] 10 positions [17/11/25, 21:32:46] 9 positions [17/11/25, 21:32:57] 8 positions [17/11/25, 21:33:08] 7 positions [17/11/25, 21:33:18] 6 positions [17/11/25, 21:33:29] 5 positions [17/11/25, 21:33:38] 4 positions [17/11/25, 21:33:47] 3 positions [17/11/25, 21:33:54] 2 positions [17/11/25, 21:34:02] 1 positions [17/11/25, 21:34:07] 0 positions [17/11/25, 21:34:07] 5 genetic replicates [17/11/25, 21:34:25] 17 positions [17/11/25, 21:34:40] 16 positions [17/11/25, 21:34:56] 15 positions [17/11/25, 21:35:12] 14 positions [17/11/25, 21:35:28] 13 positions [17/11/25, 21:35:44] 12 positions [17/11/25, 21:35:57] 11 positions [17/11/25, 21:36:09] 10 positions [17/11/25, 21:36:22] 9 positions [17/11/25, 21:36:35] 8 positions [17/11/25, 21:36:46] 7 positions [17/11/25, 21:36:57] 6 positions [17/11/25, 21:37:07] 5 positions [17/11/25, 21:37:16] 4 positions [17/11/25, 21:37:26] 3 positions [17/11/25, 21:37:35] 2 positions [17/11/25, 21:37:42] 1 positions [17/11/25, 21:37:48] 0 positions [17/11/25, 21:37:48] 6 genetic replicates [17/11/25, 21:38:06] 17 positions [17/11/25, 21:38:23] 16 positions [17/11/25, 21:38:40] 15 positions [17/11/25, 21:38:56] 14 positions [17/11/25, 21:39:11] 13 positions [17/11/25, 21:39:25] 12 positions [17/11/25, 21:39:41] 11 positions [17/11/25, 21:39:54] 10 positions [17/11/25, 21:40:07] 9 positions [17/11/25, 21:40:19] 8 positions [17/11/25, 21:40:30] 7 positions [17/11/25, 21:40:42] 6 positions [17/11/25, 21:40:52] 5 positions [17/11/25, 21:41:02] 4 positions [17/11/25, 21:41:12] 3 positions [17/11/25, 21:41:20] 2 positions [17/11/25, 21:41:27] 1 positions [17/11/25, 21:41:34] 0 positions [17/11/25, 21:41:34] 7 genetic replicates [17/11/25, 21:41:54] 17 positions [17/11/25, 21:42:13] 16 positions [17/11/25, 21:42:30] 15 positions [17/11/25, 21:42:47] 14 positions [17/11/25, 21:43:01] 13 positions [17/11/25, 21:43:17] 12 positions [17/11/25, 21:43:34] 11 positions [17/11/25, 21:43:47] 10 positions [17/11/25, 21:44:01] 9 positions [17/11/25, 21:44:14] 8 positions [17/11/25, 21:44:26] 7 positions [17/11/25, 21:44:37] 6 positions [17/11/25, 21:44:48] 5 positions [17/11/25, 21:44:58] 4 positions [17/11/25, 21:45:07] 3 positions [17/11/25, 21:45:15] 2 positions [17/11/25, 21:45:24] 1 positions [17/11/25, 21:45:30] 0 positions [17/11/25, 21:45:30] 8 genetic replicates [17/11/25, 21:45:48] 17 positions [17/11/25, 21:46:05] 16 positions [17/11/25, 21:46:22] 15 positions [17/11/25, 21:46:38] 14 positions [17/11/25, 21:46:55] 13 positions [17/11/25, 21:47:09] 12 positions [17/11/25, 21:47:25] 11 positions [17/11/25, 21:47:40] 10 positions [17/11/25, 21:47:53] 9 positions [17/11/25, 21:48:06] 8 positions [17/11/25, 21:48:18] 7 positions [17/11/25, 21:48:29] 6 positions [17/11/25, 21:48:39] 5 positions [17/11/25, 21:48:49] 4 positions [17/11/25, 21:48:57] 3 positions [17/11/25, 21:49:05] 2 positions [17/11/25, 21:49:12] 1 positions [17/11/25, 21:49:18] 0 positions [17/11/25, 21:49:18] 9 genetic replicates [17/11/25, 21:49:39] 17 positions * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘spelling.R’ OK * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * checking for new files in some other directories ... OK * DONE Status: 1 ERROR See ‘/data/blackswan/ripley/R/packages/tests-devel/PAICE.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 31:25.90, 1826.09 + 12.80