• using R Under development (unstable) (2025-10-07 r88905)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 21.1.2     flang version 21.1.2
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘phyr/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘phyr’ 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 ‘phyr’ can be installed ... [211s/261s] WARNING Found the following significant warnings:   cor_phylo.cpp:76:14: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]   cor_phylo.cpp:81:14: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]   cor_phylo.cpp:89:14: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations] See the install log for details.
• used C++ compiler: ‘clang version 21.1.2’
• checking installed package size ... OK
• checking package directory ... 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 ... [19s/31s] OK
• checking whether the package can be loaded with stated dependencies ... [18s/30s] OK
• checking whether the package can be unloaded cleanly ... [19s/29s] OK
• checking whether the namespace can be loaded with stated dependencies ... [19s/32s] OK
• checking whether the namespace can be unloaded cleanly ... [19s/31s] OK
• checking loading without being on the library search path ... OK
• checking whether startup messages can be suppressed ... [19s/28s] 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 ... [106s/147s] OK
• checking Rd files ... 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 ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... OK
• checking LazyData ... 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [12s/14s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [12s/19s] OK   Running ‘testthat.R’ [12s/18s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [43s/61s] OK
• checking PDF version of manual ... [9s/12s] OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 WARNING