##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:distinct.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings distinct_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/distinct.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘distinct/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘distinct’ version ‘1.11.0’
* 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++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   4.1Mb
* 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 1.263  0.081  66.057
* 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 ...
  ‘distinct.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘distinct.Rmd’ using rmarkdown
Error: processing vignette 'distinct.Rmd' failed with diagnostics:
there is no package called ‘BiocStyle’
--- failed re-building ‘distinct.Rmd’

SUMMARY: processing the following file failed:
  ‘distinct.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/distinct.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL distinct
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘distinct’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast.h:5,
                 from Perm_covariates.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:553: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  553 |                                 #pragma omp parallel for
      | 
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:569: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  569 |                                 #pragma omp parallel for
      | 
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:573: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  573 |                                         #pragma omp critical
      | 
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:633: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  633 |                                 #pragma omp parallel for
      | 
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:650: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  650 |                     #pragma omp parallel for
      | 
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:668: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  668 |                         #pragma omp parallel for
      | 
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:683: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  683 |                     #pragma omp parallel for
      | 
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:698: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  698 |                         #pragma omp parallel for
      | 
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/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast.h:5,
                 from Perm_covariates_parallel.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:553: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  553 |                                 #pragma omp parallel for
      | 
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:569: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  569 |                                 #pragma omp parallel for
      | 
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:573: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
  573 |                                         #pragma omp critical
      | 
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:633: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  633 |                                 #pragma omp parallel for
      | 
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:650: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  650 |                     #pragma omp parallel for
      | 
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:668: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  668 |                         #pragma omp parallel for
      | 
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:683: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  683 |                     #pragma omp parallel for
      | 
/home/biocbuild/bbs-3.17-bioc/R/site-library/Rfast/include/Rfast/matrix.hpp:698: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  698 |                         #pragma omp parallel for
      | 
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/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/lib -L/usr/local/lib -o distinct.so Perm.o Perm_covariates.o Perm_covariates_parallel.o Perm_parallel.o RcppExports.o -llapack -L/home/biocbuild/bbs-3.17-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/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 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
 10.116   0.474  76.768