Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-10-05 11:45 -0400 (Sat, 05 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4466 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4498 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4446 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4445 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 318/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cfTools 1.5.0 (landing page) Ran Hu
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | ||||||||||
To the developers/maintainers of the cfTools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cfTools.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: cfTools |
Version: 1.5.0 |
Command: /home/biocbuild/R/R/bin/R CMD INSTALL cfTools |
StartedAt: 2024-10-04 19:36:51 -0000 (Fri, 04 Oct 2024) |
EndedAt: 2024-10-04 19:38:03 -0000 (Fri, 04 Oct 2024) |
EllapsedTime: 72.3 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### 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:54, 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:54, 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:54, 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:54, 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:54, 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:54, 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:54, 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:54, 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:54, 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:19: 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:33:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 33 | for (int i=0; i<nrow; i++) { | ~^~~~~ matrix.cpp:36:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 36 | 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:49:17: 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] 49 | 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:106:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 106 | for (int i=0; i<v_.size(); i++) { | ~^~~~~~~~~~ matrix.cpp: In member function ‘bool Matrix_Double::get_element(int, int, double&)’: matrix.cpp:142:8: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘unsigned int’ [-Wsign-compare] 142 | if (i<nrow && j<ncol) { | ~^~~~~ matrix.cpp:142:18: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘unsigned int’ [-Wsign-compare] 142 | if (i<nrow && j<ncol) { | ~^~~~~ matrix.cpp: In member function ‘bool Matrix_Double::set_element(int, int, double)’: matrix.cpp:158:8: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘unsigned int’ [-Wsign-compare] 158 | if (i<nrow && j<ncol) { | ~^~~~~ matrix.cpp:158:18: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘unsigned int’ [-Wsign-compare] 158 | if (i<nrow && j<ncol) { | ~^~~~~ matrix.cpp: In member function ‘bool Matrix_Double::get_column_sum(int, double&)’: matrix.cpp:173:8: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘unsigned int’ [-Wsign-compare] 173 | if (j<ncol) { | ~^~~~~ matrix.cpp:175:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 175 | for (int k=0; k<nrow; k++) { | ~^~~~~ matrix.cpp: In member function ‘bool Matrix_Double::get_row_sum(int, double&)’: matrix.cpp:192:8: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘unsigned int’ [-Wsign-compare] 192 | if (i<nrow) { | ~^~~~~ matrix.cpp:194:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 194 | for (int k=0; k<ncol; k++) { | ~^~~~~ matrix.cpp: In member function ‘void Matrix_Double::get_unique_row_labels(std::vector<int>&)’: matrix.cpp:211:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 211 | 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:228:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 228 | for (int i=0; i<nrow; i++) { | ~^~~~~ matrix.cpp:241:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 241 | for (int i=0; i<unique_row_labels.size(); i++) { | ~^~~~~~~~~~~~~~~~~~~~~~~~~ matrix.cpp:246:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 246 | for (int j=0; j<ncol; j++) { | ~^~~~~ matrix.cpp:250:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 250 | for (int j=0; j<ncol; j++) { | ~^~~~~ matrix.cpp: In function ‘std::ostream& operator<<(std::ostream&, Matrix_Double&)’: matrix.cpp:268:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 268 | for (int i=0; i<mat.get_row_num(); i++) { | ~^~~~~~~~~~~~~~~~~~ matrix.cpp:272:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 272 | 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:289:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 289 | for (int i=0; i<nrow; i++) { | ~^~~~~ matrix.cpp:291:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 291 | for (int j=0; j<ncol; j++) { | ~^~~~~ matrix.cpp: In function ‘double em_supervise(Matrix_Double&, int, std::vector<double>&, Matrix_Double&, int)’: matrix.cpp:321:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 321 | for (int j=0; j<ncol; j++) { | ~^~~~~ matrix.cpp:328:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 328 | for (int j = 0; j < ncol; j++) { | ~~^~~~~~ matrix.cpp:333:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 333 | for (int j = 0; j < ncol; j++) { | ~~^~~~~~ matrix.cpp:345:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 345 | for (int i=0; i<nrow; i++) { | ~^~~~~ matrix.cpp:347:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 347 | for (int j=0; j<ncol; j++) { | ~^~~~~ matrix.cpp:353:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 353 | for (int j=0; j<ncol; j++) { | ~^~~~~ matrix.cpp:360:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 360 | for (int j=0; j<ncol; j++) { | ~^~~~~ matrix.cpp:362:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 362 | for (int i=0; i<nrow; i++) { | ~^~~~~ matrix.cpp:372:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 372 | for (int i=0; i<nrow; i++) { | ~^~~~~ matrix.cpp:374:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 374 | for (int j=0; j<ncol; j++) { | ~^~~~~ matrix.cpp:380:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 380 | 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>&, int)’: matrix.cpp:431:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 431 | for (int j=0; j<ncol+1; j++) { | ~^~~~~~~ matrix.cpp:438:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 438 | for (int j = 0; j < ncol+1; j++) { | ~~^~~~~~~~ matrix.cpp:443:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 443 | for (int j = 0; j < ncol+1; j++) { | ~~^~~~~~~~ matrix.cpp:454:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 454 | for (int i=0; i<nrow; i++) | ~^~~~~ matrix.cpp:463:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 463 | for (int i=0; i<nrow; i++) { | ~^~~~~ matrix.cpp:466:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 466 | for (int j=0; j<ncol; j++) { | ~^~~~~ matrix.cpp:480:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 480 | for (int j=0; j<ncol; j++) { | ~^~~~~ matrix.cpp:491:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 491 | for (int i=0; i<nrow; i++) { | ~^~~~~ matrix.cpp:516:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 516 | for (int j=0; j<ncol; j++) { | ~^~~~~ matrix.cpp:518:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 518 | for (int i=0; i<nrow; i++) { | ~^~~~~ matrix.cpp:525:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 525 | 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:551:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 551 | for (int i=0; i<nrow; i++) { | ~^~~~~ matrix.cpp:565:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 565 | 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:590:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 590 | for (int i=0; i<nrow; i++) { | ~^~~~~ matrix.cpp:604:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 604 | 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:54, 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:54, 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:54, 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:54, 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:54, 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:54, 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:54, 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:54, 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, int)’: read_deconvolution.cpp:190:10: warning: unused variable ‘obj’ [-Wunused-variable] 190 | double obj = em_supervise(reads_likelihoods, em_max_iterations, theta, q, random_seed); | ^~~ read_deconvolution.cpp:250:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 250 | for (int i=0; i<theta.size(); i++) { | ~^~~~~~~~~~~~~ read_deconvolution.cpp:246:10: warning: unused variable ‘obj’ [-Wunused-variable] 246 | double obj = em_supervise(reads_likelihoods, em_max_iterations, theta, q, random_seed); | ^~~ 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:271:22: warning: ‘num_total_reads’ may be used uninitialized in this function [-Wmaybe-uninitialized] 271 | 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:54, 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:54, 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:54, 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:54, 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:54, 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:54, 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:54, 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:54, 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)