##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:motifmatchr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings motifmatchr_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/motifmatchr.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifmatchr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifmatchr’ version ‘1.20.0’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘motifmatchr’ can be installed ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 shell scripts ... 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
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/motifmatchr.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL motifmatchr
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘motifmatchr’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c r_interface.cpp -o r_interface.o
In file included from r_interface.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/unordered_map:437:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__hash_table:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:653:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:500:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/function.h:20:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/shared_ptr.h:25:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h:57:5: warning: delete called on 'MOODS::scan::Motif' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor]
    delete __ptr;
    ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h:318:7: note: in instantiation of member function 'std::default_delete<MOODS::scan::Motif>::operator()' requested here
      __ptr_.second()(__tmp);
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h:272:19: note: in instantiation of member function 'std::unique_ptr<MOODS::scan::Motif>::reset' requested here
  ~unique_ptr() { reset(); }
                  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator.h:159:15: note: in instantiation of member function 'std::unique_ptr<MOODS::scan::Motif>::~unique_ptr' requested here
        __p->~_Tp();
              ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator_traits.h:309:13: note: in instantiation of member function 'std::allocator<std::unique_ptr<MOODS::scan::Motif>>::destroy' requested here
        __a.destroy(__p);
            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:450:25: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<std::unique_ptr<MOODS::scan::Motif>>>::destroy<std::unique_ptr<MOODS::scan::Motif>, void>' requested here
        __alloc_traits::destroy(__alloc(), _VSTD::__to_address(--__soon_to_be_end));
                        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:374:29: note: in instantiation of member function 'std::__vector_base<std::unique_ptr<MOODS::scan::Motif>, std::allocator<std::unique_ptr<MOODS::scan::Motif>>>::__destruct_at_end' requested here
    void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
                            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:487:9: note: in instantiation of member function 'std::__vector_base<std::unique_ptr<MOODS::scan::Motif>, std::allocator<std::unique_ptr<MOODS::scan::Motif>>>::clear' requested here
        clear();
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:573:5: note: in instantiation of member function 'std::__vector_base<std::unique_ptr<MOODS::scan::Motif>, std::allocator<std::unique_ptr<MOODS::scan::Motif>>>::~__vector_base' requested here
    ~vector()
    ^
./MOODS/scanner.h:31:11: note: in instantiation of member function 'std::vector<std::unique_ptr<MOODS::scan::Motif>>::~vector' requested here
    class Scanner {
          ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c MOODS/scanner.cpp -o MOODS/scanner.o
In file included from MOODS/scanner.cpp:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:682:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/shared_ptr.h:25:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h:57:5: warning: delete called on 'MOODS::scan::Motif' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor]
    delete __ptr;
    ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h:318:7: note: in instantiation of member function 'std::default_delete<MOODS::scan::Motif>::operator()' requested here
      __ptr_.second()(__tmp);
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h:272:19: note: in instantiation of member function 'std::unique_ptr<MOODS::scan::Motif>::reset' requested here
  ~unique_ptr() { reset(); }
                  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator.h:159:15: note: in instantiation of member function 'std::unique_ptr<MOODS::scan::Motif>::~unique_ptr' requested here
        __p->~_Tp();
              ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator_traits.h:309:13: note: in instantiation of member function 'std::allocator<std::unique_ptr<MOODS::scan::Motif>>::destroy' requested here
        __a.destroy(__p);
            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:450:25: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<std::unique_ptr<MOODS::scan::Motif>>>::destroy<std::unique_ptr<MOODS::scan::Motif>, void>' requested here
        __alloc_traits::destroy(__alloc(), _VSTD::__to_address(--__soon_to_be_end));
                        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:374:29: note: in instantiation of member function 'std::__vector_base<std::unique_ptr<MOODS::scan::Motif>, std::allocator<std::unique_ptr<MOODS::scan::Motif>>>::__destruct_at_end' requested here
    void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
                            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:487:9: note: in instantiation of member function 'std::__vector_base<std::unique_ptr<MOODS::scan::Motif>, std::allocator<std::unique_ptr<MOODS::scan::Motif>>>::clear' requested here
        clear();
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:519:5: note: in instantiation of member function 'std::__vector_base<std::unique_ptr<MOODS::scan::Motif>, std::allocator<std::unique_ptr<MOODS::scan::Motif>>>::~__vector_base' requested here
    vector() _NOEXCEPT_(is_nothrow_default_constructible<allocator_type>::value)
    ^
MOODS/scanner.cpp:28:14: note: in instantiation of member function 'std::vector<std::unique_ptr<MOODS::scan::Motif>>::vector' requested here
    Scanner::Scanner(unsigned int window_size){
             ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c MOODS/motif_h.cpp -o MOODS/motif_h.o
MOODS/motif_h.cpp:256:25: warning: '&' within '^' [-Wbitwise-op-parentheses]
            CODE = MASK & (CODE << SHIFT) ^ alphabet_map[s[ii + i + q - 1]];
                   ~~~~~^~~~~~~~~~~~~~~~~ ~
MOODS/motif_h.cpp:256:25: note: place parentheses around the '&' expression to silence this warning
            CODE = MASK & (CODE << SHIFT) ^ alphabet_map[s[ii + i + q - 1]];
                        ^
                   (                     )
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c MOODS/motif_0.cpp -o MOODS/motif_0.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c MOODS/moods_tools.cpp -o MOODS/moods_tools.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c MOODS/moods_scan.cpp -o MOODS/moods_scan.o
MOODS/moods_scan.cpp:97:14: warning: unused variable 'done' [-Wunused-variable]
        bool done = 0;
             ^
MOODS/moods_scan.cpp:252:33: warning: '&' within '|' [-Wbitwise-op-parentheses]
                    CODE = MASK & (CODE << SHIFT) | alphabet_map[seq[i+j+q-1]];
                           ~~~~~^~~~~~~~~~~~~~~~~ ~
MOODS/moods_scan.cpp:252:33: note: place parentheses around the '&' expression to silence this warning
                    CODE = MASK & (CODE << SHIFT) | alphabet_map[seq[i+j+q-1]];
                                ^
                           (                     )
In file included from MOODS/moods_scan.cpp:3:
In file included from ./MOODS/moods.h:5:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:275:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:653:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:500:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/function.h:20:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/shared_ptr.h:25:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h:57:5: warning: delete called on 'MOODS::scan::Motif' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor]
    delete __ptr;
    ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h:318:7: note: in instantiation of member function 'std::default_delete<MOODS::scan::Motif>::operator()' requested here
      __ptr_.second()(__tmp);
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/unique_ptr.h:272:19: note: in instantiation of member function 'std::unique_ptr<MOODS::scan::Motif>::reset' requested here
  ~unique_ptr() { reset(); }
                  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator.h:159:15: note: in instantiation of member function 'std::unique_ptr<MOODS::scan::Motif>::~unique_ptr' requested here
        __p->~_Tp();
              ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator_traits.h:309:13: note: in instantiation of member function 'std::allocator<std::unique_ptr<MOODS::scan::Motif>>::destroy' requested here
        __a.destroy(__p);
            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:450:25: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<std::unique_ptr<MOODS::scan::Motif>>>::destroy<std::unique_ptr<MOODS::scan::Motif>, void>' requested here
        __alloc_traits::destroy(__alloc(), _VSTD::__to_address(--__soon_to_be_end));
                        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:374:29: note: in instantiation of member function 'std::__vector_base<std::unique_ptr<MOODS::scan::Motif>, std::allocator<std::unique_ptr<MOODS::scan::Motif>>>::__destruct_at_end' requested here
    void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
                            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:487:9: note: in instantiation of member function 'std::__vector_base<std::unique_ptr<MOODS::scan::Motif>, std::allocator<std::unique_ptr<MOODS::scan::Motif>>>::clear' requested here
        clear();
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:573:5: note: in instantiation of member function 'std::__vector_base<std::unique_ptr<MOODS::scan::Motif>, std::allocator<std::unique_ptr<MOODS::scan::Motif>>>::~__vector_base' requested here
    ~vector()
    ^
./MOODS/scanner.h:31:11: note: in instantiation of member function 'std::vector<std::unique_ptr<MOODS::scan::Motif>>::~vector' requested here
    class Scanner {
          ^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c MOODS/moods_parsers.cpp -o MOODS/moods_parsers.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c MOODS/moods_misc.cpp -o MOODS/moods_misc.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c MOODS/match_types.cpp -o MOODS/match_types.o
clang++ -mmacosx-version-min=10.13 -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/usr/local/lib -o motifmatchr.so ./RcppExports.o ./r_interface.o ./MOODS/scanner.o ./MOODS/motif_h.o ./MOODS/motif_0.o ./MOODS/moods_tools.o ./MOODS/moods_scan.o ./MOODS/moods_parsers.o ./MOODS/moods_misc.o ./MOODS/match_types.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-motifmatchr/00new/motifmatchr/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 (motifmatchr)

R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(motifmatchr)

> 
> test_check("motifmatchr")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 50 ]
> 
> proc.time()
   user  system elapsed 
 15.369   0.818  16.215