* using log directory ‘/Users/ripley/R/packages/tests-devel/doolkit.Rcheck’ * using R Under development (unstable) (2024-04-17 r86441) * using platform: aarch64-apple-darwin23.4.0 * R was compiled by Apple clang version 15.0.0 (clang-1500.3.9.4) GNU Fortran (GCC) 12.2.0 * running under: macOS Sonoma 14.4.1 * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘doolkit/DESCRIPTION’ ... OK * this is package ‘doolkit’ version ‘1.42.2’ * 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 ‘doolkit’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.3Mb sub-directories of 1Mb or more: R 2.0Mb data 1.9Mb extdata 2.3Mb * 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 ... NOTE checkRd: (-1) dkprofile.Rd:64: Lost braces 64 | \doi{10.3389/fphys.2017.00524}{Thiery et al. (2017)} | ^ checkRd: (-1) dne.Rd:45: Lost braces 45 | \doi{10.1002/ajpa.21489}{Bunn et al. (2011)} | ^ checkRd: (-1) dne.Rd:47: Lost braces 47 | \doi{10.1007/s10914-016-9326-0}{Pampush et al. (2016)} | ^ checkRd: (-1) inclin.Rd:28: Lost braces 28 | \doi{10.1371/journal.pone.0066142}{Guy et al. (2013)} | ^ checkRd: (-1) oedist.Rd:43: Lost braces 43 | \doi{10.1371/journal.pone.0066142}{Guy et al. (2013)} | ^ checkRd: (-1) oedist.Rd:45: Lost braces 45 | \doi{10.1371/journal.pone.0138802}{Guy et al. (2015)} | ^ checkRd: (-1) oedist.Rd:47: Lost braces 47 | \doi{10.3389/fphys.2017.00524}{Thiery et al. (2017)} | ^ checkRd: (-1) oedist.Rd:49: Lost braces 49 | \doi{10.1098/rsbl.2019.0671}{Schwartz et al. (2020)} | ^ checkRd: (-1) opc.Rd:36: Lost braces 36 | \doi{10.1038/nature05433}{Evans et al. (2007)} | ^ checkRd: (-1) opcr.Rd:30: Lost braces 30 | \doi{10.1038/nature10880}{Wilson et al. (2012)} | ^ checkRd: (-1) rfi.Rd:34: Lost braces 34 | \doi{10.1016/j.jhevol.2008.08.002}{Boyer (2008)} | ^ checkRd: (-1) rfi.Rd:35: Lost braces 35 | \doi{10.1371/journal.pone.0066142}{Guy et al. (2013)} | ^ checkRd: (-1) rrate.Rd:34: Lost braces 34 | \doi{10.1002/ajpa.23916}{Thiery et al. (2019)} | ^ checkRd: (-1) shape.index.Rd:44: Lost braces 44 | \doi{10.1029/TR013i001p00350}{Horton (1932)} | ^ checkRd: (-1) shape.index.Rd:46: Lost braces 46 | \doi{10.1130/0016-7606(1956)67[597:EODSAS]2.0.CO;2}{Schumm (1956)} | ^ checkRd: (-1) shape.index.Rd:48: Lost braces 48 | \doi{10.2475/ajs.255.2.138}{Chorley et al. (1957)} | ^ * 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 ...sh: line 1: 48262 Abort trap: 6 LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/Users/ripley/R/R-devel/bin/R' --vanilla --encoding=UTF-8 > 'doolkit-Ex.Rout' 2>&1 < 'doolkit-Ex.R' ERROR Running examples in ‘doolkit-Ex.R’ failed The error most likely occurred in: > ### Name: dkborder > ### Title: dkborder > ### Aliases: dkborder > > ### ** Examples > > border <- dkborder(dkmodel$cusp) > > # Map the border in orange: > is_border <- rep(1, Rvcg::nfaces(dkmodel$cusp)) > is_border[border] <- 2 > dkmap(dkmodel$cusp, is_border, col = c("white", "#E69F00"), col.levels = 2, legend = FALSE, + scalebar = FALSE, smooth = FALSE) Warning in normalizePath(texture) : path[1]="/var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T//RtmpHeYikk/working_dir/RtmpypP0q1/filebc86375d5f8a.png": No such file or directory Warning in rgl.material0(color = "white", alpha = 1, lit = FALSE, ambient = "#000000", : RGL: Pixmap load: unable to open file '/var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T//RtmpHeYikk/working_dir/RtmpypP0q1/filebc86375d5f8a.png' for reading > > # Compare with vcgBorder from the R package Rvcg, in blue: > vcgborder <- which(Rvcg::vcgBorder(dkmodel$cusp)$borderit == TRUE) > is_border[vcgborder] <- 3 > dkmap(dkmodel$cusp, is_border, col = c("white", "#E69F00", "#56B4E9"), col.levels = 3, + legend = FALSE, scalebar = FALSE, smooth = FALSE) * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/Users/ripley/R/packages/tests-devel/doolkit.Rcheck/00check.log’ for details. 37.86 real 32.44 user 4.48 sys