• using R version 4.4.0 (2024-04-24)
• using platform: x86_64-apple-darwin20
• R was compiled by     Apple clang version 14.0.0 (clang-1400.0.29.202)     GNU Fortran (GCC) 12.2.0
• running under: macOS Ventura 13.3.1
• using session charset: UTF-8
• 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 ... [10s/11s] OK See the install log for details.
• checking installed package size ... NOTE   installed size is 7.5Mb   sub-directories of 1Mb or more:     R 3.0Mb     data 2.0Mb     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 ... [2s/2s] OK
• checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
• checking whether the package can be unloaded cleanly ... [2s/2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
• checking loading without being on the library search path ... [2s/2s] 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 ... [6s/6s] OK
• checking Rd files ... [0s/0s] 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 ... [1s/1s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking examples ... [6s/6s] ERROR Running examples in ‘doolkit-Ex.R’ failed The error most likely occurred in: > ### Name: dkcrop > ### Title: crop a mesh > ### Aliases: dkcrop > > ### ** Examples > > #Crop above a certain threshold: > mythreshold <- quantile(elev(dkmodel$basin), 0.5) > mypolynetwork <- poly.network(dkmodel$basin, elev(dkmodel$basin), + lwr.limit = mythreshold) > mynewmesh <- dkcrop(dkmodel$basin, mypolynetwork) > dkmap(mynewmesh, elev(mynewmesh))
• checking PDF version of manual ... [6s/6s] OK
• DONE Status: 1 ERROR, 2 NOTEs
• using check arguments '--no-clean-on-error '