Ran Hu
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/cfTools |
| git_branch: devel |
| git_last_commit: a99acda |
| git_last_commit_date: 2023-10-24 11:48:38 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:40:25 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 317/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cfTools 1.3.0 (landing page) Ran Hu
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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: 1.3.0 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL cfTools |
| StartedAt: 2024-03-27 19:47:01 -0000 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 19:48:38 -0000 (Wed, 27 Mar 2024) |
| EllapsedTime: 97.6 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL cfTools
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string.hpp:19,
from data_types.cpp:14:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/bind/mem_fn.hpp:25,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mem_fn.hpp:22,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/function/detail/prologue.hpp:19,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/function.hpp:30,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string/split.hpp:16,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string.hpp:23,
from data_types.cpp:14:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string.hpp:19,
from matrix.cpp:15:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/bind/mem_fn.hpp:25,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mem_fn.hpp:22,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/function/detail/prologue.hpp:19,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/function.hpp:30,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string/split.hpp:16,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string.hpp:23,
from matrix.cpp:15:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/chain.hpp:36,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/filtering_streambuf.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/filtering_stream.hpp:22,
from matrix.cpp:17:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/chain.hpp:36,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/filtering_streambuf.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/filtering_stream.hpp:22,
from matrix.cpp:17:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/chain.hpp:36,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/filtering_streambuf.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/filtering_stream.hpp:22,
from matrix.cpp:17:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/chain.hpp:36,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/filtering_streambuf.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/filtering_stream.hpp:22,
from matrix.cpp:17:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/chain.hpp:36,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/filtering_streambuf.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/filtering_stream.hpp:22,
from matrix.cpp:17:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/chain.hpp:36,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/filtering_streambuf.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/filtering_stream.hpp:22,
from matrix.cpp:17:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/chain.hpp:36,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/filtering_streambuf.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/filtering_stream.hpp:22,
from matrix.cpp:17:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/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-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string.hpp:19,
from read_deconvolution.cpp:14:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/bind/mem_fn.hpp:25,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mem_fn.hpp:22,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/function/detail/prologue.hpp:19,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/function.hpp:30,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string/split.hpp:16,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string.hpp:23,
from read_deconvolution.cpp:14:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/chain.hpp:36,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/filtering_streambuf.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/filtering_stream.hpp:22,
from read_deconvolution.cpp:16:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/chain.hpp:36,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/filtering_streambuf.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/filtering_stream.hpp:22,
from read_deconvolution.cpp:16:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/chain.hpp:36,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/filtering_streambuf.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/filtering_stream.hpp:22,
from read_deconvolution.cpp:16:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/chain.hpp:36,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/filtering_streambuf.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/filtering_stream.hpp:22,
from read_deconvolution.cpp:16:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/chain.hpp:36,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/filtering_streambuf.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/filtering_stream.hpp:22,
from read_deconvolution.cpp:16:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/chain.hpp:36,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/filtering_streambuf.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/filtering_stream.hpp:22,
from read_deconvolution.cpp:16:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/chain.hpp:36,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/filtering_streambuf.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/filtering_stream.hpp:22,
from read_deconvolution.cpp:16:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/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-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string.hpp:19,
from utils.cpp:17:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/bind/mem_fn.hpp:25,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mem_fn.hpp:22,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/function/detail/prologue.hpp:19,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/function.hpp:30,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string/split.hpp:16,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string.hpp:23,
from utils.cpp:17:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/device/file.hpp:24,
from utils.cpp:18:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/device/file.hpp:24,
from utils.cpp:18:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/device/file.hpp:24,
from utils.cpp:18:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/device/file.hpp:24,
from utils.cpp:18:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/device/file.hpp:24,
from utils.cpp:18:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/device/file.hpp:24,
from utils.cpp:18:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iostreams/device/file.hpp:24,
from utils.cpp:18:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/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-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/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-devel-2024.03.20/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-devel-2024.03.20/lib -lR
installing to /home/biocbuild/R/R-4.4-devel-2024.03.20/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)