* using log directory ‘/srv/hornik/tmp/CRAN/simer.Rcheck’ * using R Under development (unstable) (2023-09-23 r85215) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 16.0.6 (15) GNU Fortran (Debian 13.2.0-4) 13.2.0 * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘simer/DESCRIPTION’ ... OK * this is package ‘simer’ version ‘0.9.0.3’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/9s] NOTE Maintainer: ‘Xiaolei Liu ’ New maintainer: Xiaolei Liu Old maintainer(s): Xiaolei Liu Found the following (possibly) invalid URLs: URL: http://ianimal.pro/ (moved to https://ianimal.pro/) From: README.md Status: 301 Message: Moved Permanently For content that is 'Moved Permanently', please change http to https, add trailing slashes, or replace the old by the new URL. The Date field is over a month old. * 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 ‘simer’ can be installed ... [38s/38s] WARNING Found the following significant warnings: pedigree.cpp:195:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical] pedigree.cpp:200:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical] pedigree.cpp:218:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] pedigree.cpp:218:72: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical] pedigree.cpp:218:16: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical] See ‘/srv/hornik/tmp/CRAN/simer.Rcheck/00install.out’ for details. * used C++ compiler: ‘Debian clang version 16.0.6 (15)’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * 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 R 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 ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking whether startup messages can be suppressed ... [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 ... [13s/13s] OK * checking Rd files ... [0s/0s] OK * 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 ... NOTE Documented arguments not in \usage in documentation object 'print_info': ‘line’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking examples ... [179s/14s] NOTE Examples with CPU (user + system) or elapsed time > 5s user system elapsed mate.4waycro 11.288 0.436 0.433 mate.3waycro 11.338 0.376 0.433 write.file 10.366 0.475 0.571 mate.2waycro 7.613 0.247 0.308 mate.userped 7.612 0.206 0.307 geno.cvt2 5.743 0.257 0.348 mate.assort 5.210 0.210 0.202 Examples with CPU time > 2.5 times elapsed time user system elapsed ratio simer.Data.Ped 3.698 0.139 0.130 29.515 mate.4waycro 11.288 0.436 0.433 27.076 mate.3waycro 11.338 0.376 0.433 27.053 mate.assort 5.210 0.210 0.202 26.832 mate.2waycro 7.613 0.247 0.308 25.519 mate.userped 7.612 0.206 0.307 25.466 mate 3.670 0.166 0.171 22.433 selects 3.923 0.084 0.183 21.896 mate.clone 3.818 0.126 0.181 21.790 reproduces 3.951 0.117 0.187 21.754 mate.randexself 3.789 0.120 0.180 21.717 mate.disassort 3.706 0.180 0.179 21.709 mate.randmate 3.760 0.119 0.179 21.670 mate.backcro 3.769 0.128 0.180 21.650 mate.selfpol 3.753 0.144 0.180 21.650 simer 3.926 0.144 0.188 21.649 mate.dh 3.758 0.127 0.180 21.583 genotype 3.611 0.101 0.172 21.581 write.file 10.366 0.475 0.571 18.986 geno.cvt1 3.620 0.189 0.205 18.580 phenotype 4.210 0.149 0.239 18.238 geno.cvt2 5.743 0.257 0.348 17.241 simer.Data.Bfile2MVP 1.125 0.032 0.213 5.432 simer.Data.MVP2MVP 0.993 0.036 0.211 4.877 * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 WARNING, 4 NOTEs