* using log directory ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/smartsnp.Rcheck’
* using R Under development (unstable) (2025-02-28 r87848)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.2.0-16) 14.2.0
    GNU Fortran (Debian 14.2.0-16) 14.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘smartsnp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘smartsnp’ version ‘1.1.0’
* 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 whether package ‘smartsnp’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/smartsnp-00install.html' for details.
* used C++ compiler: ‘g++-14 (Debian 14.2.0-16) 14.2.0’
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [0s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/1s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [6s/8s] OK
* checking Rd files ... [0s/0s] NOTE
checkRd: (-1) read_packedancestrymap.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_mva.Rd:7-11: Lost braces
     7 | \item{snp_data}{snp_data}{File name read from working directory.
       |                          ^
checkRd: (-1) smart_mva.Rd:100-101: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_mva.Rd:102-103: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_mva.Rd:104-105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_mva.Rd:106-109: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_mva.Rd:110: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_mva.Rd:111: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_mva.Rd:112: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_mva.Rd:113-114: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_mva.Rd:115: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_mva.Rd:116: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_mva.Rd:117: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_mva.Rd:118: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_mva.Rd:119: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_pca.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_pca.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_pca.Rd:64-67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_permanova.Rd:71-73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_permanova.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_permanova.Rd:75-76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_permanova.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_permanova.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_permanova.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_permdisp.Rd:78-81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_permdisp.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_permdisp.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_permdisp.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_permdisp.Rd:85-86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_permdisp.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_permdisp.Rd:88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smart_permdisp.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly
* 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 LazyData ... INFO
  'LazyData' is specified without a 'data' directory
* 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 examples ... [12s/15s] OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
smart_permanova 4.760  0.106   5.314
smart_mva       3.764  0.156   5.007
* checking PDF version of manual ... [4s/5s] OK
* checking HTML version of manual ... [0s/1s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 NOTE