* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/doremi.Rcheck’
* using R Under development (unstable) (2024-04-27 r86487)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.4 (1)
    Debian flang-new version 18.1.4 (1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘doremi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘doremi’ version ‘1.0.0’
* 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 serialization versions ... OK
* checking whether package ‘doremi’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/doremi-00install.html' for details.
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ 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 ... NOTE
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    New features
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [4s/5s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the package can be unloaded cleanly ... [4s/5s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the namespace can be unloaded cleanly ... [4s/5s] OK
* checking loading without being on the library search path ... [4s/5s] 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 ... [25s/30s] OK
* checking Rd files ... [1s/1s] NOTE
checkRd: (-1) analyze.1order.Rd:49: Lost braces
    49 | Although only the first derivative is used here, using a higher order can enhance derivative estimation (see \doi{10.1080/00273171.2015.1123138}{Chow et al.(2016)})}
       |                                                                                                                                                 ^
checkRd: (-1) analyze.2order.Rd:44: Lost braces
    44 | 2 in second order differential equations), for instance, order=4 might enhance derivative estimation (see \doi{10.1080/00273171.2015.1123138}{Chow et al.(2016)})}
       |                                                                                                                                              ^
checkRd: (-1) calculate.fda.Rd:29: Lost braces
    29 | method described in several sources, such as in \doi{10.1007/b98888}{Ramsay et al. (2009)}
       |                                                                     ^
checkRd: (-1) calculate.fda.Rd:30: Lost braces
    30 | and  \doi{10.1080/00273171.2015.1123138}{Chow et al. (2016)}.
       |                                         ^
checkRd: (-1) calculate.glla.Rd:34: Lost braces
    34 | described in \doi{10.4324/9780203864746}{Boker et al.(2010)}.
       |                                         ^
checkRd: (-1) calculate.gold.Rd:33: Lost braces
    33 | method described in \doi{10.1080/00273171.2010.498294}{Deboeck (2010)}. The code available on this paper was extracted and adapted for non constant time steps.
       |                                                       ^
checkRd: (-1) optimum_param.Rd:47: Lost braces
    47 | Using a higher order can enhance derivative estimation (see \doi{10.1080/00273171.2015.1123138}{Chow et al.(2016)})}
       |                                                                                                ^
checkRd: (-1) rotation.Rd:37: Lost braces
    37 | \doi{10.1016/j.yhbeh.2012.12.007}{(Courvoisier et al., 2013)}.
       |                                  ^
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* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [45s/52s] OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
optimum_param         7.180  0.183   8.456
plot.doremiparam      7.097  0.094   8.371
analyze.2order        6.914  0.207   8.019
generate.panel.2order 4.107  0.042   5.017
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [177s/220s] OK
* checking PDF version of manual ... [6s/9s] OK
* checking HTML version of manual ... [2s/4s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 2 NOTEs