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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:distinct.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings distinct_1.12.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/distinct.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘distinct/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘distinct’ version ‘1.12.2’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘distinct’ can be installed ... WARNING
Found the following significant warnings:
  /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/types.hpp:42:7: warning: inline variables are a C++17 extension [-Wc++17-extensions]
  /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/types.hpp:47:7: warning: inline variables are a C++17 extension [-Wc++17-extensions]
  /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/types.hpp:52:7: warning: inline variables are a C++17 extension [-Wc++17-extensions]
  /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/types.hpp:57:7: warning: inline variables are a C++17 extension [-Wc++17-extensions]
  /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/types.hpp:62:7: warning: inline variables are a C++17 extension [-Wc++17-extensions]
See ‘/Users/biocbuild/bbs-3.17-bioc/meat/distinct.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘Rfast’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
perm_test_parallel_R: no visible binding for global variable ‘cl_id’
perm_test_parallel_covariates_R: no visible binding for global variable
  ‘cl_id’
plot_cdfs: no visible binding for global variable ‘group’
plot_densities: no visible binding for global variable ‘group’
Undefined global functions or variables:
  cl_id group
* checking Rd files ... OK
* checking Rd metadata ... 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 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
distinct_test 2.793  0.144 101.997
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/distinct.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL distinct
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘distinct’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Perm.cpp -o Perm.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Perm_covariates.cpp -o Perm_covariates.o
In file included from Perm_covariates.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast.h:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/matrix.hpp:15:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/types.hpp:42:7: warning: inline variables are a C++17 extension [-Wc++17-extensions]
                inline static type val;
                ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/types.hpp:47:7: warning: inline variables are a C++17 extension [-Wc++17-extensions]
                inline static type val= NA_INTEGER;
                ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/types.hpp:52:7: warning: inline variables are a C++17 extension [-Wc++17-extensions]
                inline static type val= NA_LOGICAL;
                ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/types.hpp:57:7: warning: inline variables are a C++17 extension [-Wc++17-extensions]
                inline static type val= NA_REAL;
                ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/types.hpp:62:7: warning: inline variables are a C++17 extension [-Wc++17-extensions]
                inline static type val = NA_STRING;
                ^
5 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Perm_covariates_parallel.cpp -o Perm_covariates_parallel.o
In file included from Perm_covariates_parallel.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast.h:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/matrix.hpp:15:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/types.hpp:42:7: warning: inline variables are a C++17 extension [-Wc++17-extensions]
                inline static type val;
                ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/types.hpp:47:7: warning: inline variables are a C++17 extension [-Wc++17-extensions]
                inline static type val= NA_INTEGER;
                ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/types.hpp:52:7: warning: inline variables are a C++17 extension [-Wc++17-extensions]
                inline static type val= NA_LOGICAL;
                ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/types.hpp:57:7: warning: inline variables are a C++17 extension [-Wc++17-extensions]
                inline static type val= NA_REAL;
                ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include/Rfast/types.hpp:62:7: warning: inline variables are a C++17 extension [-Wc++17-extensions]
                inline static type val = NA_STRING;
                ^
5 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Perm_parallel.cpp -o Perm_parallel.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rfast/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o distinct.so Perm.o Perm_covariates.o Perm_covariates_parallel.o Perm_parallel.o RcppExports.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-distinct/00new/distinct/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (distinct)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(distinct)
> test_check("distinct")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 8 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
 19.564   1.074 124.877