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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:distinct.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings distinct_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/distinct.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘distinct/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘distinct’ version ‘1.14.0’
* 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 ... OK
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   8.8Mb
* 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 loading without being on the library search path ... 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 $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
distinct_test 2.678  1.295    82.3
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    2.   └─distinct:::perm_test_parallel_R(...)
    3.     ├─... %dorng% ...
    4.     │ └─base::do.call(`%dopar%`, list(obj, ex), envir = parent.frame())
    5.     └─foreach (local) `<fn>`(...)
    6.       └─e$fun(obj, substitute(ex), parent.frame(), e$data)
    7.         └─parallel::clusterApplyLB(cl, argsList, evalWrapper)
    8.           └─parallel:::dynamicClusterApply(cl, fun, length(x), argfun)
    9.             └─parallel:::recvOneResult(cl)
   10.               ├─parallel:::recvOneData(cl)
   11.               └─parallel:::recvOneData.SOCKcluster(cl)
   12.                 └─base::unserialize(socklist[[n]])
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 7 ]
  Error: Test failures
  Execution halted
* 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 ERROR, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/distinct.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL distinct
###
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘distinct’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rfast/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c Perm.cpp -o Perm.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rfast/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c Perm_covariates.cpp -o Perm_covariates.o
In file included from /home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:16,
                 from /home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast.h:5,
                 from Perm_covariates.cpp:2:
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/helpers.hpp:19: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
   19 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/helpers.hpp:92: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
   92 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/helpers.hpp:105: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  105 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/helpers.hpp:157: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  157 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/helpers.hpp:164: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  164 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/helpers.hpp:175: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  175 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/helpers.hpp:182: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  182 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/helpers.hpp:193: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  193 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/helpers.hpp:200: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  200 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/helpers.hpp:211: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  211 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/helpers.hpp:218: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  218 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/helpers.hpp:228: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  228 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/helpers.hpp:456: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  456 | #pragma omp critical
      | 
In file included from /home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast.h:5,
                 from Perm_covariates.cpp:2:
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:939: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  939 | #pragma omp parallel for
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:944: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  944 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:973: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  973 | #pragma omp parallel for
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:978: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  978 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1006: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
 1006 | #pragma omp parallel for
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1011: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
 1011 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1394: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
 1394 | #pragma omp parallel for
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1416: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
 1416 | #pragma omp parallel for
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1421: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
 1421 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1498: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
 1498 | #pragma omp parallel for
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1520: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
 1520 | #pragma omp parallel for
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1525: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
 1525 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1556: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
 1556 | #pragma omp parallel for
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1579: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
 1579 | #pragma omp parallel for
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1600: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
 1600 | #pragma omp parallel for
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1621: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
 1621 | #pragma omp parallel for
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1762: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
 1762 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1823: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
 1823 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1884: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
 1884 | #pragma omp critical
      | 
In file included from /home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:15,
                 from /home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast.h:5,
                 from Perm_covariates.cpp:2:
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/types.hpp:42:7: warning: inline variables are only available with ‘-std=c++17’ or ‘-std=gnu++17’
   42 |       inline static type val;
      |       ^~~~~~
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/types.hpp:47:7: warning: inline variables are only available with ‘-std=c++17’ or ‘-std=gnu++17’
   47 |       inline static type val= NA_INTEGER;
      |       ^~~~~~
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/types.hpp:52:7: warning: inline variables are only available with ‘-std=c++17’ or ‘-std=gnu++17’
   52 |       inline static type val= NA_LOGICAL;
      |       ^~~~~~
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/types.hpp:57:7: warning: inline variables are only available with ‘-std=c++17’ or ‘-std=gnu++17’
   57 |       inline static type val= NA_REAL;
      |       ^~~~~~
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/types.hpp:62:7: warning: inline variables are only available with ‘-std=c++17’ or ‘-std=gnu++17’
   62 |       inline static type val = NA_STRING;
      |       ^~~~~~
Perm_covariates.cpp: In function ‘arma::vec my_rint_reg(const mat&, const vec&, Rcpp::IntegerVector, const unsigned int&, const unsigned int&, const double&, const unsigned int&)’:
Perm_covariates.cpp:189:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  189 |   for(int i=0;i<p;i++)
      |               ~^~
Perm_covariates.cpp:210:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  210 |   while(i++<maxiters && sum(abs(b2-b1.col(0))) > tol) {
      |         ~~~^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rfast/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c Perm_covariates_parallel.cpp -o Perm_covariates_parallel.o
In file included from /home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:16,
                 from /home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast.h:5,
                 from Perm_covariates_parallel.cpp:2:
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/helpers.hpp:19: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
   19 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/helpers.hpp:92: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
   92 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/helpers.hpp:105: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  105 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/helpers.hpp:157: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  157 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/helpers.hpp:164: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  164 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/helpers.hpp:175: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  175 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/helpers.hpp:182: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  182 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/helpers.hpp:193: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  193 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/helpers.hpp:200: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  200 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/helpers.hpp:211: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  211 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/helpers.hpp:218: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  218 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/helpers.hpp:228: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  228 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/helpers.hpp:456: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  456 | #pragma omp critical
      | 
In file included from /home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast.h:5,
                 from Perm_covariates_parallel.cpp:2:
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:939: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  939 | #pragma omp parallel for
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:944: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  944 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:973: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  973 | #pragma omp parallel for
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:978: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  978 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1006: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
 1006 | #pragma omp parallel for
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1011: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
 1011 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1394: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
 1394 | #pragma omp parallel for
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1416: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
 1416 | #pragma omp parallel for
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1421: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
 1421 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1498: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
 1498 | #pragma omp parallel for
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1520: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
 1520 | #pragma omp parallel for
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1525: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
 1525 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1556: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
 1556 | #pragma omp parallel for
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1579: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
 1579 | #pragma omp parallel for
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1600: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
 1600 | #pragma omp parallel for
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1621: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
 1621 | #pragma omp parallel for
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1762: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
 1762 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1823: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
 1823 | #pragma omp critical
      | 
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:1884: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
 1884 | #pragma omp critical
      | 
In file included from /home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/matrix.hpp:15,
                 from /home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast.h:5,
                 from Perm_covariates_parallel.cpp:2:
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/types.hpp:42:7: warning: inline variables are only available with ‘-std=c++17’ or ‘-std=gnu++17’
   42 |       inline static type val;
      |       ^~~~~~
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/types.hpp:47:7: warning: inline variables are only available with ‘-std=c++17’ or ‘-std=gnu++17’
   47 |       inline static type val= NA_INTEGER;
      |       ^~~~~~
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/types.hpp:52:7: warning: inline variables are only available with ‘-std=c++17’ or ‘-std=gnu++17’
   52 |       inline static type val= NA_LOGICAL;
      |       ^~~~~~
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/types.hpp:57:7: warning: inline variables are only available with ‘-std=c++17’ or ‘-std=gnu++17’
   57 |       inline static type val= NA_REAL;
      |       ^~~~~~
/home/biocbuild/R/R-4.3.1/site-library/Rfast/include/Rfast/types.hpp:62:7: warning: inline variables are only available with ‘-std=c++17’ or ‘-std=gnu++17’
   62 |       inline static type val = NA_STRING;
      |       ^~~~~~
Perm_covariates_parallel.cpp: In function ‘arma::vec my_rint_reg_parallel(const mat&, const vec&, Rcpp::IntegerVector, const unsigned int&, const unsigned int&, const double&, const unsigned int&)’:
Perm_covariates_parallel.cpp:189:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  189 |   for(int i=0;i<p;i++)
      |               ~^~
Perm_covariates_parallel.cpp:210:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  210 |   while(i++<maxiters && sum(abs(b2-b1.col(0))) > tol) {
      |         ~~~^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rfast/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c Perm_parallel.cpp -o Perm_parallel.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rfast/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o distinct.so Perm.o Perm_covariates.o Perm_covariates_parallel.o Perm_parallel.o RcppExports.o -llapack -lblas -lgfortran -lm -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/site-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: aarch64-unknown-linux-gnu (64-bit)

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> library(testthat)
> library(distinct)
> test_check("distinct")
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 7 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_distinct_test.R:12:3'): distinct_test() works faultlessly. ─────
Error in `unserialize(socklist[[n]])`: error reading from connection
Backtrace:
     ▆
  1. └─distinct::distinct_test(...) at test_distinct_test.R:12:2
  2.   └─distinct:::perm_test_parallel_R(...)
  3.     ├─... %dorng% ...
  4.     │ └─base::do.call(`%dopar%`, list(obj, ex), envir = parent.frame())
  5.     └─foreach (local) `<fn>`(...)
  6.       └─e$fun(obj, substitute(ex), parent.frame(), e$data)
  7.         └─parallel::clusterApplyLB(cl, argsList, evalWrapper)
  8.           └─parallel:::dynamicClusterApply(cl, fun, length(x), argfun)
  9.             └─parallel:::recvOneResult(cl)
 10.               ├─parallel:::recvOneData(cl)
 11.               └─parallel:::recvOneData.SOCKcluster(cl)
 12.                 └─base::unserialize(socklist[[n]])

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 7 ]
Error: Test failures
Execution halted