##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:cfTools.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings cfTools_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/cfTools.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    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 ‘cfTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cfTools’ version ‘1.5.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘cfTools’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/biocbuild/bbs-3.20-bioc/meat/cfTools.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
  installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
* 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 ... 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 ... 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 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
cfSort         17.167  2.447  27.571
CancerDetector  7.079  0.694   7.981
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/cfTools.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL cfTools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘cfTools’ ...
** using non-staged installation via StagedInstall field
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c data_types.cpp -o data_types.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/range/iterator_range.hpp:13,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/range/as_literal.hpp:18,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string.hpp:19,
                 from data_types.cpp:14:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/function/detail/prologue.hpp:19,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string.hpp:23,
                 from data_types.cpp:14:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
      |                                        ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27,
                 from data_types.cpp:2:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
data_types.cpp: In function ‘int get_num_of_non_void_bins(Bins_index&, std::vector<int>&)’:
data_types.cpp:101:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  101 |   for (int i=0; i<bins_of_chr.size(); i++)
      |                 ~^~~~~~~~~~~~~~~~~~~
data_types.cpp: In function ‘int find_bin_of_position(Bins_end_coord&, std::string, unsigned int)’:
data_types.cpp:135:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<unsigned int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  135 |   if (bin_internal_index==coords_bins_of_chr.size()) {
      |       ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
data_types.cpp: In function ‘void print_uint_vec(std::ostream&, std::vector<unsigned int>&, int)’:
data_types.cpp:169:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<unsigned int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  169 |  if (len>v.size() || len==0) len=v.size();
      |      ~~~^~~~~~~~~
data_types.cpp: In function ‘void print_Bins2Values(Bins2Values&)’:
data_types.cpp:235:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  235 |   for (int i=0; i<values.size(); i++)
      |                 ~^~~~~~~~~~~~~~
data_types.cpp: In function ‘void write_Bins2Values(Bins2Values&, std::vector<std::__cxx11::basic_string<char> >&, std::string, bool)’:
data_types.cpp:264:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  264 |  for (i=0; i<columns_names.size()-1; i++)
      |            ~^~~~~~~~~~~~~~~~~~~~~~~
data_types.cpp:285:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  285 |   for (i=0; i<values.size(); i++)
      |             ~^~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c matrix.cpp -o matrix.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/range/iterator_range.hpp:13,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/range/as_literal.hpp:18,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string.hpp:19,
                 from matrix.cpp:15:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/function/detail/prologue.hpp:19,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string.hpp:23,
                 from matrix.cpp:15:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
      |                                        ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27,
                 from matrix.cpp:2:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/chain.hpp:36,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/filtering_streambuf.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/filtering_stream.hpp:22,
                 from matrix.cpp:17:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27,
                 from matrix.cpp:2:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/chain.hpp:36,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/filtering_streambuf.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/filtering_stream.hpp:22,
                 from matrix.cpp:17:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27,
                 from matrix.cpp:2:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/chain.hpp:36,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/filtering_streambuf.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/filtering_stream.hpp:22,
                 from matrix.cpp:17:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27,
                 from matrix.cpp:2:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/chain.hpp:36,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/filtering_streambuf.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/filtering_stream.hpp:22,
                 from matrix.cpp:17:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27,
                 from matrix.cpp:2:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/chain.hpp:36,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/filtering_streambuf.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/filtering_stream.hpp:22,
                 from matrix.cpp:17:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27,
                 from matrix.cpp:2:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/chain.hpp:36,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/filtering_streambuf.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/filtering_stream.hpp:22,
                 from matrix.cpp:17:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27,
                 from matrix.cpp:2:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/chain.hpp:36,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/filtering_streambuf.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/filtering_stream.hpp:22,
                 from matrix.cpp:17:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27,
                 from matrix.cpp:2:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from matrix.cpp:18:
matrix.h: In member function ‘void Matrix_Double::multipy_single_value(double)’:
matrix.h:30:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
   30 |    for (int i=0; i<nrow; i++) {
      |                  ~^~~~~
matrix.h:31:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
   31 |     for (int j=0; j<ncol; j++) {
      |                   ~^~~~~
matrix.h: In member function ‘std::vector<double>* Matrix_Double::get_row_vector(int)’:
matrix.h:40:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
   40 |   if (row_index>=nrow) return(NULL);
      |       ~~~~~~~~~^~~~~~
matrix.h: In member function ‘bool Matrix_Double::set_row_labels(std::vector<int>&)’:
matrix.h:74:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
   74 |     for (int i=0; i<nrow; i++) row_labels.push_back(row_labels_[i]);
      |                   ~^~~~~
matrix.cpp: In constructor ‘Matrix_Double::Matrix_Double(unsigned int, unsigned int, double)’:
matrix.cpp:32:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
   32 |  for (int i=0; i<nrow; i++) {
      |                ~^~~~~
matrix.cpp:35:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
   35 |   for (int j=0; j<ncol; j++)
      |                 ~^~~~~
matrix.cpp: In member function ‘void Matrix_Double::process_one_line_of_mat_file(std::string&, int)’:
matrix.cpp:48:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   48 |  for (int i=0; i<items.size(); i++) {
      |                ~^~~~~~~~~~~~~
matrix.cpp: In member function ‘long int Matrix_Double::append_row_vector(std::vector<double>&, int)’:
matrix.cpp:105:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  105 |  for (int i=0; i<v_.size(); i++) {
      |                ~^~~~~~~~~~
matrix.cpp: In member function ‘bool Matrix_Double::get_element(int, int, double&)’:
matrix.cpp:141:8: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘unsigned int’ [-Wsign-compare]
  141 |   if (i<nrow && j<ncol) {
      |       ~^~~~~
matrix.cpp:141:18: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘unsigned int’ [-Wsign-compare]
  141 |   if (i<nrow && j<ncol) {
      |                 ~^~~~~
matrix.cpp: In member function ‘bool Matrix_Double::set_element(int, int, double)’:
matrix.cpp:157:8: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘unsigned int’ [-Wsign-compare]
  157 |   if (i<nrow && j<ncol) {
      |       ~^~~~~
matrix.cpp:157:18: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘unsigned int’ [-Wsign-compare]
  157 |   if (i<nrow && j<ncol) {
      |                 ~^~~~~
matrix.cpp: In member function ‘bool Matrix_Double::get_column_sum(int, double&)’:
matrix.cpp:172:8: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘unsigned int’ [-Wsign-compare]
  172 |   if (j<ncol) {
      |       ~^~~~~
matrix.cpp:174:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  174 |    for (int k=0; k<nrow; k++) {
      |                  ~^~~~~
matrix.cpp: In member function ‘bool Matrix_Double::get_row_sum(int, double&)’:
matrix.cpp:191:8: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘unsigned int’ [-Wsign-compare]
  191 |   if (i<nrow) {
      |       ~^~~~~
matrix.cpp:193:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  193 |    for (int k=0; k<ncol; k++) {
      |                  ~^~~~~
matrix.cpp: In member function ‘void Matrix_Double::get_unique_row_labels(std::vector<int>&)’:
matrix.cpp:210:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  210 |  for (int i=0; i<row_labels.size(); i++)
      |                ~^~~~~~~~~~~~~~~~~~
matrix.cpp: In member function ‘void Matrix_Double::print_with_additional_column_of_Bins2Value(std::ostream&, Bins2Value&)’:
matrix.cpp:227:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  227 |  for (int i=0; i<nrow; i++) {
      |                ~^~~~~
matrix.cpp:240:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  240 |  for (int i=0; i<unique_row_labels.size(); i++) {
      |                ~^~~~~~~~~~~~~~~~~~~~~~~~~
matrix.cpp:245:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  245 |    for (int j=0; j<ncol; j++) {
      |                  ~^~~~~
matrix.cpp:249:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  249 |    for (int j=0; j<ncol; j++) {
      |                  ~^~~~~
matrix.cpp: In function ‘std::ostream& operator<<(std::ostream&, Matrix_Double&)’:
matrix.cpp:267:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  267 |   for (int i=0; i<mat.get_row_num(); i++) {
      |                 ~^~~~~~~~~~~~~~~~~~
matrix.cpp:271:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  271 |    for (j=0; j<mat.get_column_num()-1; j++) {
      |              ~^~~~~~~~~~~~~~~~~~~~~~~
matrix.cpp: In function ‘double objective_em_supervise(Matrix_Double&, std::vector<double>&)’:
matrix.cpp:288:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  288 |  for (int i=0; i<nrow; i++) {
      |                ~^~~~~
matrix.cpp:290:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  290 |   for (int j=0; j<ncol; j++) {
      |                 ~^~~~~
matrix.cpp: In function ‘void em_supervise(Matrix_Double&, int, std::vector<double>&, Matrix_Double&)’:
matrix.cpp:318:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  318 |  for (int j=0; j<ncol; j++) {
      |                ~^~~~~
matrix.cpp:328:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  328 |   for (int i=0; i<nrow; i++) {
      |                 ~^~~~~
matrix.cpp:330:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  330 |    for (int j=0; j<ncol; j++) {
      |                  ~^~~~~
matrix.cpp:336:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  336 |    for (int j=0; j<ncol; j++) {
      |                  ~^~~~~
matrix.cpp:343:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  343 |   for (int j=0; j<ncol; j++) {
      |                 ~^~~~~
matrix.cpp:345:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  345 |    for (int i=0; i<nrow; i++) {
      |                  ~^~~~~
matrix.cpp:355:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  355 |  for (int i=0; i<nrow; i++) {
      |                ~^~~~~
matrix.cpp:357:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  357 |   for (int j=0; j<ncol; j++) {
      |                 ~^~~~~
matrix.cpp:363:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  363 |   for (int j=0; j<ncol; j++) {
      |                 ~^~~~~
matrix.cpp: In function ‘void em_semisupervise(Matrix_Double&, std::vector<int>&, std::vector<int>&, int, std::vector<double>&, Matrix_Double&, std::vector<double>&, std::vector<double>&)’:
matrix.cpp:411:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  411 |  for (int j=0; j<ncol+1; j++) {
      |                ~^~~~~~~
matrix.cpp:417:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  417 |  for (int i=0; i<nrow; i++)
      |                ~^~~~~
matrix.cpp:426:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  426 |   for (int i=0; i<nrow; i++) {
      |                 ~^~~~~
matrix.cpp:429:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  429 |    for (int j=0; j<ncol; j++) {
      |                  ~^~~~~
matrix.cpp:443:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  443 |    for (int j=0; j<ncol; j++) {
      |                  ~^~~~~
matrix.cpp:454:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  454 |   for (int i=0; i<nrow; i++) {
      |                 ~^~~~~
matrix.cpp:479:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  479 |   for (int j=0; j<ncol; j++) {
      |                 ~^~~~~
matrix.cpp:481:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  481 |    for (int i=0; i<nrow; i++) {
      |                  ~^~~~~
matrix.cpp:488:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  488 |   for (int i=0; i<nrow; i++)
      |                 ~^~~~~
matrix.cpp: In function ‘void readCounts_by_reads_posterior_probability_version_regular(Matrix_Double&, double, Matrix_Double&)’:
matrix.cpp:514:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  514 |  for (int i=0; i<nrow; i++) {
      |                ~^~~~~
matrix.cpp:528:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  528 |   for (int j=0; j<ncol; j++) {
      |                 ~^~~~~
matrix.cpp: In function ‘void readCounts_by_reads_posterior_probability_version_unknownclass(Matrix_Double&, std::vector<double>&, double, Matrix_Double&)’:
matrix.cpp:553:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  553 |  for (int i=0; i<nrow; i++) {
      |                ~^~~~~
matrix.cpp:567:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  567 |   for (int j=0; j<ncol; j++) {
      |                 ~^~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c my_getopt.cpp -o my_getopt.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c read_deconvolution.cpp -o read_deconvolution.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/range/iterator_range.hpp:13,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/range/as_literal.hpp:18,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string.hpp:19,
                 from read_deconvolution.cpp:14:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/function/detail/prologue.hpp:19,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string.hpp:23,
                 from read_deconvolution.cpp:14:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
      |                                        ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27,
                 from read_deconvolution.cpp:2:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/chain.hpp:36,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/filtering_streambuf.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/filtering_stream.hpp:22,
                 from read_deconvolution.cpp:16:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27,
                 from read_deconvolution.cpp:2:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/chain.hpp:36,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/filtering_streambuf.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/filtering_stream.hpp:22,
                 from read_deconvolution.cpp:16:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27,
                 from read_deconvolution.cpp:2:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/chain.hpp:36,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/filtering_streambuf.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/filtering_stream.hpp:22,
                 from read_deconvolution.cpp:16:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27,
                 from read_deconvolution.cpp:2:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/chain.hpp:36,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/filtering_streambuf.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/filtering_stream.hpp:22,
                 from read_deconvolution.cpp:16:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27,
                 from read_deconvolution.cpp:2:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/chain.hpp:36,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/filtering_streambuf.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/filtering_stream.hpp:22,
                 from read_deconvolution.cpp:16:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27,
                 from read_deconvolution.cpp:2:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/chain.hpp:36,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/filtering_streambuf.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/filtering_stream.hpp:22,
                 from read_deconvolution.cpp:16:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27,
                 from read_deconvolution.cpp:2:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/chain.hpp:36,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/filtering_streambuf.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/filtering_stream.hpp:22,
                 from read_deconvolution.cpp:16:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27,
                 from read_deconvolution.cpp:2:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from utils.h:12,
                 from read_deconvolution.cpp:18:
matrix.h: In member function ‘void Matrix_Double::multipy_single_value(double)’:
matrix.h:30:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
   30 |    for (int i=0; i<nrow; i++) {
      |                  ~^~~~~
matrix.h:31:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
   31 |     for (int j=0; j<ncol; j++) {
      |                   ~^~~~~
matrix.h: In member function ‘std::vector<double>* Matrix_Double::get_row_vector(int)’:
matrix.h:40:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
   40 |   if (row_index>=nrow) return(NULL);
      |       ~~~~~~~~~^~~~~~
matrix.h: In member function ‘bool Matrix_Double::set_row_labels(std::vector<int>&)’:
matrix.h:74:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
   74 |     for (int i=0; i<nrow; i++) row_labels.push_back(row_labels_[i]);
      |                   ~^~~~~
read_deconvolution.cpp: In function ‘void read_deconvolution_cpp(std::string, int, double, std::string, std::string, std::string, std::string, int)’:
read_deconvolution.cpp:248:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  248 |   for (int i=0; i<theta.size(); i++) {
      |                 ~^~~~~~~~~~~~~
In file included from read_deconvolution.cpp:25:
template_utils.cpp: In instantiation of ‘void print_vec(std::ostream&, std::vector<T>&, std::string, std::string) [with T = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]’:
read_deconvolution.cpp:196:39:   required from here
template_utils.cpp:18:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   18 |    for (i=0; i<v.size()-1; i++) of << v[i] << delimit;
      |              ~^~~~~~~~~~~
template_utils.cpp: In instantiation of ‘void print_vec(std::ostream&, std::vector<T>&, std::string, std::string) [with T = double; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]’:
read_deconvolution.cpp:199:32:   required from here
template_utils.cpp:18:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
read_deconvolution.cpp:268:22: warning: ‘num_total_reads’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  268 |    double unit = 1e6 / num_total_reads; // default unit is readCountPerMillion
      |                  ~~~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c template_utils.cpp -o template_utils.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c utils.cpp -o utils.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/range/iterator_range.hpp:13,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/range/as_literal.hpp:18,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string.hpp:19,
                 from utils.cpp:17:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/function/detail/prologue.hpp:19,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/algorithm/string.hpp:23,
                 from utils.cpp:17:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
      |                                        ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27,
                 from utils.cpp:2:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/device/file.hpp:24,
                 from utils.cpp:18:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27,
                 from utils.cpp:2:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/device/file.hpp:24,
                 from utils.cpp:18:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27,
                 from utils.cpp:2:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/device/file.hpp:24,
                 from utils.cpp:18:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  508 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27,
                 from utils.cpp:2:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/device/file.hpp:24,
                 from utils.cpp:18:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  521 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27,
                 from utils.cpp:2:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/device/file.hpp:24,
                 from utils.cpp:18:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  604 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27,
                 from utils.cpp:2:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/device/file.hpp:24,
                 from utils.cpp:18:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  613 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27,
                 from utils.cpp:2:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iostreams/device/file.hpp:24,
                 from utils.cpp:18:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  615 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27,
                 from utils.cpp:2:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from utils.cpp:31:
matrix.h: In member function ‘void Matrix_Double::multipy_single_value(double)’:
matrix.h:30:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
   30 |    for (int i=0; i<nrow; i++) {
      |                  ~^~~~~
matrix.h:31:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
   31 |     for (int j=0; j<ncol; j++) {
      |                   ~^~~~~
matrix.h: In member function ‘std::vector<double>* Matrix_Double::get_row_vector(int)’:
matrix.h:40:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
   40 |   if (row_index>=nrow) return(NULL);
      |       ~~~~~~~~~^~~~~~
matrix.h: In member function ‘bool Matrix_Double::set_row_labels(std::vector<int>&)’:
matrix.h:74:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
   74 |     for (int i=0; i<nrow; i++) row_labels.push_back(row_labels_[i]);
      |                   ~^~~~~
utils.cpp: In function ‘void multi_vec_by_number(std::vector<double>&, double)’:
utils.cpp:40:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   40 |   for (int i=0; i<vec.size(); i++) vec[i] *= v;
      |                 ~^~~~~~~~~~~
utils.cpp: In function ‘bool assign_vector_zeros(std::vector<double>&)’:
utils.cpp:47:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   47 |   for (int i=0; i<vec.size(); i++) vec[i] = 0;
      |                 ~^~~~~~~~~~~
utils.cpp: In function ‘void process_one_line_of_wig_file(std::string&, std::string&, std::map<std::__cxx11::basic_string<char>, std::map<int, double> >&)’:
utils.cpp:186:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  186 |   for (int i=0; i<items.size(); i++) {
      |                 ~^~~~~~~~~~~~~
utils.cpp: In function ‘void print_wig_bins_data(Wig_bins_data&, Bins_index&, Bins_info&)’:
utils.cpp:360:53: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  360 |    for (int bin_internal_index=0; bin_internal_index<markers_index_of_a_chr.size(); ++bin_internal_index) {
      |                                   ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils.cpp:369:53: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  369 |    for (int bin_internal_index=0; bin_internal_index<markers_index_of_a_chr.size(); ++bin_internal_index) {
      |                                   ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils.cpp: In function ‘void read_tissue_markers_txt_file(std::string, int, int, Bins2Values&, std::vector<std::__cxx11::basic_string<char> >&)’:
utils.cpp:441:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  441 |   if (value_column_start_index>items.size()) {
      |       ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
utils.cpp: In function ‘void read_paired_values_file_of_bins(std::string, unsigned int, Bins2PairedValues&, std::vector<std::__cxx11::basic_string<char> >&)’:
utils.cpp:588:44: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  588 |    for (int i=value_column_start_index-1; i<items.size(); i++) {
      |                                           ~^~~~~~~~~~~~~
utils.cpp:606:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  606 |   for (int i=value_column_start_index-1; i<items.size(); i++) {
      |                                          ~^~~~~~~~~~~~~
utils.cpp: In function ‘void process_one_line_of_reads_binning_file(std::string&, int, int, int&, std::vector<unsigned int>&, std::vector<int>&)’:
utils.cpp:695:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  695 |  for (int i=0; i<subitems.size(); i++)
      |                ~^~~~~~~~~~~~~~~~
utils.cpp:698:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  698 |  for (int i=0; i<str_methy_status.size(); i++)
      |                ~^~~~~~~~~~~~~~~~~~~~~~~~
utils.cpp: In function ‘void process_one_line_of_reads_binning_file_with_mary_format(std::string&, int&, std::vector<int>&)’:
utils.cpp:729:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  729 |  for (int i=0; i<str_methy_status.size(); i++)
      |                ~^~~~~~~~~~~~~~~~~~~~~~~~
utils.cpp: In function ‘double calc_one_read_prob_by_single_value(double, std::vector<int>&)’:
utils.cpp:752:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  752 |   for (int i=0; i<methy_status.size(); i++) {
      |                 ~^~~~~~~~~~~~~~~~~~~~
utils.cpp: In function ‘int get_mC_from_methy_states(std::vector<int>&)’:
utils.cpp:774:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  774 |   for (int i=0; i<methy_status.size(); i++) {
      |                 ~^~~~~~~~~~~~~~~~~~~~
utils.cpp: In function ‘long unsigned int calc_read_probability_by_marker2beta_from_reads_binning_text_file(std::string, Bins2Values&, Matrix_Double&, Bins2UnsignedIntegers&, Bins2Value&, std::vector<int>&, std::vector<int>&, double)’:
utils.cpp:872:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  872 |    for (int t=0; t<values.size(); t++) {
      |                  ~^~~~~~~~~~~~~~
utils.cpp:826:6: warning: unused variable ‘print_control’ [-Wunused-variable]
  826 |  int print_control=1000000;
      |      ^~~~~~~~~~~~~
utils.cpp: In function ‘double calc_one_read_prob_by_a_paired_value(double, double, double, std::vector<int>&)’:
utils.cpp:1139:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1139 |   for (int i=0; i<methy_status.size(); i++) {
      |                 ~^~~~~~~~~~~~~~~~~~~~
utils.cpp: In function ‘void calc_read_probability_by_bins2pairedvalues(std::string, Bins2PairedValues&, std::vector<std::__cxx11::basic_string<char> >&)’:
utils.cpp:1194:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1194 |  for (int i=0; i<value_names.size(); i++)
      |                ~^~~~~~~~~~~~~~~~~~~
utils.cpp:1233:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1233 |    for (int t=0; t<alphas.size(); t++) {
      |                  ~^~~~~~~~~~~~~~
utils.cpp: In function ‘void get_reads_methy_data_from_reads_binning_file(std::string, std::vector<int>&, std::vector<int>&)’:
utils.cpp:1287:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1287 |   for (int t=0; t<methy_status.size(); t++)
      |                 ~^~~~~~~~~~~~~~~~~~~~
utils.cpp: In function ‘void print_vec_of_uint(std::ostream&, std::vector<unsigned int>&)’:
utils.cpp:1308:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<unsigned int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1308 |    for (i=0; i<v.size()-1; i++) of << v[i] << ",";
      |              ~^~~~~~~~~~~
utils.cpp: In function ‘void print_vec_of_ulong(std::ostream&, std::vector<long unsigned int>&)’:
utils.cpp:1323:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<long unsigned int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1323 |    for (i=0; i<v.size()-1; i++) of << v[i] << ",";
      |              ~^~~~~~~~~~~
utils.cpp: In function ‘void print_map_of_strings(std::ostream&, std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >&)’:
utils.cpp:1333:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1333 |   for (int i=0; i<strs2.size(); i++)
      |                 ~^~~~~~~~~~~~~
utils.cpp: In function ‘void strings2floats(std::string, std::vector<float>&, std::string)’:
utils.cpp:1349:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1349 |   for (int i=0; i<strs.size(); i++)
      |                 ~^~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o cfTools.so RcppExports.o data_types.o matrix.o my_getopt.o read_deconvolution.o template_utils.o utils.o -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/site-library/cfTools/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
* DONE (cfTools)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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
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> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(cfTools)
> 
> test_check("cfTools")


see ?cfToolsData and browseVignettes('cfToolsData') for documentation
loading from cache
see ?cfToolsData and browseVignettes('cfToolsData') for documentation
loading from cache
WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually.

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 215ms/step
WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually.

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 199ms/step
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 14 ]
> 
> proc.time()
   user  system elapsed 
 33.201   3.049  39.738