* using log directory 'd:/RCompile/CRANincoming/R-devel/PAICE.Rcheck' * using R Under development (unstable) (2023-10-26 r85419 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 12.3.0 GNU Fortran (GCC) 12.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'PAICE/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'PAICE' version '1.0.1' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Alberto J. Coello ' New submission Possibly misspelled words in DESCRIPTION: Phylogeographic (3:8) Package CITATION file contains call(s) to old-style personList() or as.personList(). Please use c() on person objects instead. Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead. * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'PAICE' can be installed ... OK * checking installed package size ... OK * 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 R 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 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 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 ... ERROR Running examples in 'PAICE-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: PAICE-package > ### Title: Phylogeographic Analysis of Island Colonization Events > ### Aliases: PAICE PAICE-package > ### Keywords: package > > ### ** Examples > > # Inference of minimum number of inter-island colonization events > data(CmonsData) > data(CmonsNetwork) > col <- colonization(data = CmonsData, network = CmonsNetwork) > col Total 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 > ## Note: The code is commented because 'CmonsRare' exists as an example > #set.seed(31) > #CmonsRare <- rarecol(data = CmonsData, network = CmonsNetwork, > # replicates_field = 25, replicates_genetic = 25, monitor = TRUE, > # mode = c(1, 2)) > maxcol <- maxCol(data = CmonsRare, level = 0.95, del = 0.5, method = 1) Waiting for profiling to be done... Waiting for profiling to be done... > maxcol Maximum of estimated colonization events: Mean Min Max Genetic estimator 36.94346 31.62768 45.40657 Field estimator 26.26998 23.67619 29.65297 Minimum and maximum determined by a interval of conficende of 95% > summary(maxcol) Final curve of colonization events in genetic estimator Formula: c = m * positons / (k + positions) + c0 mean min max m 32.677378 28.069277 40.452429 k 18.236241 13.238361 26.863181 c0 4.266078 3.558404 4.954138 Final curve of colonization events in field estimator Formula: c = m * (populations - 1) / (k + populations - 1) mean min max m 26.26998 23.67619 29.65297 k 16.31835 12.67959 21.24158 Interval of conficende of 95% Deleted the 50 % of extreme values > > # Plotting results > par(mfrow = c(2, 2)) > plot(CmonsRare) > par(fig = c(0, 1, 0, 0.5), new = TRUE) > plot(maxcol) Error in x$ParametersGen : $ operator is invalid for atomic vectors Calls: plot -> plot.maxCol -> curve -> eval -> eval -> f_gen Execution halted * checking PDF version of manual ... [13s] OK * checking HTML version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE