* using log directory ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/smartsnp.Rcheck’ * using R Under development (unstable) (2024-04-29 r86495) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-13 (Debian 13.2.0-23) 13.2.0 GNU Fortran (Debian 13.2.0-23) 13.2.0 * 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++-13 (Debian 13.2.0-23) 13.2.0’ * 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [0s/1s] OK * checking whether the package can be unloaded cleanly ... [0s/1s] 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 ... [1s/1s] 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 ... [9s/16s] OK * checking Rd files ... [0s/1s] 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 ... NOTE '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 ... [16s/24s] OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed smart_permanova 6.394 0.074 10.414 smart_mva 4.895 0.219 7.213 * checking PDF version of manual ... [5s/13s] OK * checking HTML version of manual ... [1s/2s] OK * checking for non-standard things in the check directory ... OK * DONE Status: 2 NOTEs