• using R Under development (unstable) (2025-09-18 r88857)
  • using platform: x86_64-pc-linux-gnu
  • R was compiled by     clang version 21.1.1     flang version 21.1.1
  • 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 ... [233s/374s] 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 21.1.1’
  • 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 ... [21s/63s] OK
  • checking whether the package can be loaded with stated dependencies ... [21s/63s] OK
  • checking whether the package can be unloaded cleanly ... [21s/60s] OK
  • checking whether the namespace can be loaded with stated dependencies ... [20s/69s] OK
  • checking whether the namespace can be unloaded cleanly ... [21s/55s] OK
  • checking loading without being on the library search path ... [5s/15s] OK
  • checking whether startup messages can be suppressed ... [20s/46s] OK
  • checking use of S3 registration ... OK
  • checking dependencies in R code ... NOTE shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
  • checking S3 generic/method consistency ... WARNING shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual.
  • checking replacement functions ... WARNING shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory The argument of a replacement function which corresponds to the right hand side must be named ‘value’.
  • checking foreign function calls ... NOTE shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual.
  • checking R code for possible problems ... ERROR Incorrect (un)loading of package shared object. shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory The system-specific extension for shared objects must not be added. See ?library.dynam.  [112s/166s] NOTE shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory Found the following possibly unsafe calls: shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory See section ‘Good practice’ in ‘?data’. shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
  • checking for missing documentation entries ... WARNING shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.