* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/motmot.Rcheck’
* using R Under development (unstable) (2025-02-23 r87804)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (1+b1)
    Debian flang-new version 19.1.7 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘motmot/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motmot’ version ‘2.1.3’
* 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 ‘motmot’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/motmot-00install.html' for details.
* used C compiler: ‘Debian clang version 19.1.7 (1+b1)’
* used C++ compiler: ‘Debian clang version 19.1.7 (1+b1)’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 ... 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/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/3s] 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 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 ... [32s/46s] OK
* checking Rd files ... [1s/1s] NOTE
checkRd: (-1) transformPhylo.MCMC.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.MCMC.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.MCMC.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.MCMC.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.MCMC.Rd:86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.MCMC.Rd:87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ML.Rd:119: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ML.Rd:120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ML.Rd:121: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ML.Rd:122: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ML.Rd:123: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ML.Rd:124: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ML.Rd:125: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ML.Rd:126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ML.Rd:127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ML.Rd:128: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ML.Rd:129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ML.Rd:130: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ML.Rd:131: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ML.Rd:132: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ML.Rd:133: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.Rd:97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.Rd:98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.Rd:99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.Rd:100: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ll.Rd:100: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ll.Rd:101: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ll.Rd:102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ll.Rd:103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ll.Rd:104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ll.Rd:105: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ll.Rd:106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ll.Rd:107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ll.Rd:108: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ll.Rd:109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ll.Rd:110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ll.Rd:111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ll.Rd:112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ll.Rd:113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformPhylo.ll.Rd:114: Lost braces in \itemize; meant \describe ?
* 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 ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [27s/35s] OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
transformPhylo.ML 4.252  0.001   5.193
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [116s/159s] OK
* checking PDF version of manual ... [6s/12s] OK
* checking HTML version of manual ... [2s/4s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 2 NOTEs