* using log directory ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/doolkit.Rcheck’
* using R Under development (unstable) (2025-01-24 r87627)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* 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 ... [9s/14s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-macos-x86_64/doolkit-00install.html' for details.
* checking installed package size ... INFO
  installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R         2.9Mb
    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 ... [2s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/3s] 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/3s] OK
* checking loading without being on the library search path ... [2s/3s] 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/8s] OK
* checking Rd files ... [0s/1s] 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/8s] 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))
> 
> #Crop the sharpest dental elements:
> sharpmesh <- dkcrop(dkmodel$basin, poly.network(dkmodel$basin,
+ Rvcg::vcgCurve(dkmodel$basin)$meanitmax,
+ lwr.limit = quantile(Rvcg::vcgCurve(dkmodel$basin)$meanitmax, 0.8),
+ min.size = 50))
> dkmap(sharpmesh, arc(sharpmesh), col = "arc", col.levels = 20,
+ min.range = -20, max.range = 20)
> #Map of the sharpest elements' elevation, slope and orientation;
> dkmap(sharpmesh, elev(sharpmesh), col = "elev")
* checking PDF version of manual ... [6s/8s] OK
* DONE
Status: 1 ERROR, 1 NOTE
* using check arguments '--no-clean-on-error '

* elapsed time (check, wall clock): 1:37