Jiri Hon
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/pqsfinder |
| git_branch: RELEASE_3_13 |
| git_last_commit: 777bb64 |
| git_last_commit_date: 2021-05-19 12:19:51 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:48 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the pqsfinder package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pqsfinder.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1422/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pqsfinder 2.8.0 (landing page) Jiri Hon
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: pqsfinder |
| Version: 2.8.0 |
| Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:pqsfinder.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings pqsfinder_2.8.0.tar.gz |
| StartedAt: 2021-10-14 11:04:52 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 11:07:28 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 156.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pqsfinder.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:pqsfinder.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings pqsfinder_2.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/pqsfinder.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pqsfinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pqsfinder’ version ‘2.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘pqsfinder’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 14.4Mb
sub-directories of 1Mb or more:
lib 11.1Mb
libs 2.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for ‘BH’ is only usable in R >= 3.0.2
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.13-bioc/meat/pqsfinder.Rcheck/00check.log’
for details.
pqsfinder.Rcheck/00install.out
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##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL pqsfinder
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘pqsfinder’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c pqsfinder.cpp -o pqsfinder.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from pqsfinder.cpp:22:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from pqsfinder.cpp:13:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from pqsfinder.cpp:22:
/home/biocbuild/bbs-3.13-bioc/R/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++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from pqsfinder.cpp:13:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from pqsfinder.cpp:22:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from pqsfinder.cpp:13:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from pqsfinder.cpp:22:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from pqsfinder.cpp:13:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from pqsfinder.cpp:22:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from pqsfinder.cpp:13:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from pqsfinder.cpp:22:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
561 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from pqsfinder.cpp:13:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from pqsfinder.cpp:22:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
570 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from pqsfinder.cpp:13:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from pqsfinder.cpp:22:
/home/biocbuild/bbs-3.13-bioc/R/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/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from pqsfinder.cpp:13:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
pqsfinder.cpp: In function ‘void find_all_runs(SEXP, int, std::__cxx11::basic_string<char>::const_iterator, std::__cxx11::basic_string<char>::const_iterator, run_match*, const regex&, const opts_t&, const scoring&, const const_iterator&, size_t, storage&, int&, results&, bool, std::chrono::_V2::system_clock::time_point, int, int, int, int&, bool)’:
pqsfinder.cpp:584:53: warning: ‘loop_len’ may be used uninitialized in this function [-Wmaybe-uninitialized]
584 | pqs_storage, int_cnt, res, (loop_len == 0 ? true : zero_loop),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/cpp_regex_traits.cpp -o boost_regex/cpp_regex_traits.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/cpp_regex_traits.cpp:22:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/cpp_regex_traits.cpp:22:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/cpp_regex_traits.cpp:22:
/home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/cpp_regex_traits.cpp:22:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/cpp_regex_traits.cpp:22:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/cpp_regex_traits.cpp:22:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/cpp_regex_traits.cpp:22:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/cpp_regex_traits.cpp:22:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/cpp_regex_traits.cpp:22:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/cpp_regex_traits.cpp:22:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/cpp_regex_traits.cpp:22:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
561 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/cpp_regex_traits.cpp:22:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/cpp_regex_traits.cpp:22:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
570 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/cpp_regex_traits.cpp:22:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/cpp_regex_traits.cpp:22:
/home/biocbuild/bbs-3.13-bioc/R/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/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/cpp_regex_traits.cpp:22:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/cregex.cpp -o boost_regex/cregex.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/cregex.cpp:22:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/cregex.cpp:22:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/cregex.cpp:22:
/home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/cregex.cpp:22:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/cregex.cpp:22:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/cregex.cpp:22:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/cregex.cpp:22:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/cregex.cpp:22:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/cregex.cpp:22:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/cregex.cpp:22:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/cregex.cpp:22:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
561 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/cregex.cpp:22:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/cregex.cpp:22:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
570 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/cregex.cpp:22:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/cregex.cpp:22:
/home/biocbuild/bbs-3.13-bioc/R/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/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/cregex.cpp:22:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/usinstances.cpp -o boost_regex/usinstances.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/icu.cpp -o boost_regex/icu.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/fileiter.cpp -o boost_regex/fileiter.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from boost_regex/fileiter.cpp:28:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from boost_regex/fileiter.cpp:28:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from boost_regex/fileiter.cpp:28:
/home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from boost_regex/fileiter.cpp:28:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from boost_regex/fileiter.cpp:28:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from boost_regex/fileiter.cpp:28:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from boost_regex/fileiter.cpp:28:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from boost_regex/fileiter.cpp:28:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from boost_regex/fileiter.cpp:28:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from boost_regex/fileiter.cpp:28:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from boost_regex/fileiter.cpp:28:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
561 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from boost_regex/fileiter.cpp:28:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from boost_regex/fileiter.cpp:28:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
570 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from boost_regex/fileiter.cpp:28:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from boost_regex/fileiter.cpp:28:
/home/biocbuild/bbs-3.13-bioc/R/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/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from boost_regex/fileiter.cpp:28:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/regex.cpp -o boost_regex/regex.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/regex.cpp:24:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/regex.cpp:24:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/regex.cpp:24:
/home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/regex.cpp:24:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/regex.cpp:24:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/regex.cpp:24:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/regex.cpp:24:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/regex.cpp:24:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/regex.cpp:24:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/regex.cpp:24:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/regex.cpp:24:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
561 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/regex.cpp:24:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/regex.cpp:24:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
570 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/regex.cpp:24:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/regex.cpp:24:
/home/biocbuild/bbs-3.13-bioc/R/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/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/regex.cpp:24:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/posix_api.cpp -o boost_regex/posix_api.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/posix_api.cpp:23:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/posix_api.cpp:23:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/posix_api.cpp:23:
/home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/posix_api.cpp:23:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/posix_api.cpp:23:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/posix_api.cpp:23:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/posix_api.cpp:23:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/posix_api.cpp:23:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/posix_api.cpp:23:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/posix_api.cpp:23:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/posix_api.cpp:23:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
561 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/posix_api.cpp:23:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/posix_api.cpp:23:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
570 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/posix_api.cpp:23:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/posix_api.cpp:23:
/home/biocbuild/bbs-3.13-bioc/R/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/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/posix_api.cpp:23:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/c_regex_traits.cpp -o boost_regex/c_regex_traits.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
from boost_regex/c_regex_traits.cpp:28:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
from boost_regex/c_regex_traits.cpp:28:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
from boost_regex/c_regex_traits.cpp:28:
/home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
from boost_regex/c_regex_traits.cpp:28:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
from boost_regex/c_regex_traits.cpp:28:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
from boost_regex/c_regex_traits.cpp:28:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
from boost_regex/c_regex_traits.cpp:28:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
from boost_regex/c_regex_traits.cpp:28:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
from boost_regex/c_regex_traits.cpp:28:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
from boost_regex/c_regex_traits.cpp:28:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
from boost_regex/c_regex_traits.cpp:28:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
561 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
from boost_regex/c_regex_traits.cpp:28:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
from boost_regex/c_regex_traits.cpp:28:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
570 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
from boost_regex/c_regex_traits.cpp:28:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
from boost_regex/c_regex_traits.cpp:28:
/home/biocbuild/bbs-3.13-bioc/R/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/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
from boost_regex/c_regex_traits.cpp:28:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/wide_posix_api.cpp -o boost_regex/wide_posix_api.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/wide_posix_api.cpp:25:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/wide_posix_api.cpp:25:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/wide_posix_api.cpp:25:
/home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/wide_posix_api.cpp:25:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/wide_posix_api.cpp:25:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/wide_posix_api.cpp:25:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/wide_posix_api.cpp:25:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/wide_posix_api.cpp:25:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/wide_posix_api.cpp:25:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/wide_posix_api.cpp:25:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/wide_posix_api.cpp:25:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
561 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/wide_posix_api.cpp:25:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/wide_posix_api.cpp:25:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
570 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/wide_posix_api.cpp:25:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/wide_posix_api.cpp:25:
/home/biocbuild/bbs-3.13-bioc/R/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/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/wide_posix_api.cpp:25:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/winstances.cpp -o boost_regex/winstances.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/winstances.cpp:30:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/winstances.cpp:30:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/winstances.cpp:30:
/home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/winstances.cpp:30:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/winstances.cpp:30:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/winstances.cpp:30:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/winstances.cpp:30:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/winstances.cpp:30:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/winstances.cpp:30:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/winstances.cpp:30:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/winstances.cpp:30:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
561 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/winstances.cpp:30:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/winstances.cpp:30:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
570 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/winstances.cpp:30:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/winstances.cpp:30:
/home/biocbuild/bbs-3.13-bioc/R/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/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/winstances.cpp:30:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/w32_regex_traits.cpp -o boost_regex/w32_regex_traits.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/instances.cpp -o boost_regex/instances.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/instances.cpp:30:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/instances.cpp:30:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/instances.cpp:30:
/home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/instances.cpp:30:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/instances.cpp:30:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/instances.cpp:30:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/instances.cpp:30:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/instances.cpp:30:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/instances.cpp:30:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/instances.cpp:30:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/instances.cpp:30:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
561 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/instances.cpp:30:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/instances.cpp:30:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
570 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/instances.cpp:30:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/instances.cpp:30:
/home/biocbuild/bbs-3.13-bioc/R/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/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex.hpp:31,
from boost_regex/instances.cpp:30:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/regex_traits_defaults.cpp -o boost_regex/regex_traits_defaults.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/regex_traits_defaults.cpp:20:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/regex_traits_defaults.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/regex_traits_defaults.cpp:20:
/home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/regex_traits_defaults.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/regex_traits_defaults.cpp:20:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/regex_traits_defaults.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/regex_traits_defaults.cpp:20:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/regex_traits_defaults.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/regex_traits_defaults.cpp:20:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/regex_traits_defaults.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/regex_traits_defaults.cpp:20:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
561 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/regex_traits_defaults.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/regex_traits_defaults.cpp:20:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
570 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/regex_traits_defaults.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/regex_traits_defaults.cpp:20:
/home/biocbuild/bbs-3.13-bioc/R/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/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
from boost_regex/regex_traits_defaults.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/wc_regex_traits.cpp -o boost_regex/wc_regex_traits.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
from boost_regex/wc_regex_traits.cpp:76:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from boost_regex/wc_regex_traits.cpp:23:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
from boost_regex/wc_regex_traits.cpp:76:
/home/biocbuild/bbs-3.13-bioc/R/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++/9/memory:80,
from boost_regex/wc_regex_traits.cpp:23:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
from boost_regex/wc_regex_traits.cpp:76:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from boost_regex/wc_regex_traits.cpp:23:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
from boost_regex/wc_regex_traits.cpp:76:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from boost_regex/wc_regex_traits.cpp:23:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
from boost_regex/wc_regex_traits.cpp:76:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from boost_regex/wc_regex_traits.cpp:23:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
from boost_regex/wc_regex_traits.cpp:76:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
561 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from boost_regex/wc_regex_traits.cpp:23:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
from boost_regex/wc_regex_traits.cpp:76:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
570 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from boost_regex/wc_regex_traits.cpp:23:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
from boost_regex/wc_regex_traits.cpp:76:
/home/biocbuild/bbs-3.13-bioc/R/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/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from boost_regex/wc_regex_traits.cpp:23:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/regex_raw_buffer.cpp -o boost_regex/regex_raw_buffer.o
mkdir -p "/home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-pqsfinder/00new/pqsfinder/lib"
ar rs "/home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a" boost_regex/cpp_regex_traits.o boost_regex/cregex.o boost_regex/usinstances.o boost_regex/icu.o boost_regex/fileiter.o boost_regex/regex.o boost_regex/posix_api.o boost_regex/c_regex_traits.o boost_regex/wide_posix_api.o boost_regex/winstances.o boost_regex/w32_regex_traits.o boost_regex/instances.o boost_regex/regex_traits_defaults.o boost_regex/wc_regex_traits.o boost_regex/regex_debug.o boost_regex/static_mutex.o boost_regex/regex_raw_buffer.o
ar: creating /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o pqsfinder.so RcppExports.o pqsfinder.o /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-pqsfinder/00new/pqsfinder/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pqsfinder)
pqsfinder.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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> library(testthat)
> library(pqsfinder)
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
>
> test_check("pqsfinder")
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
compare pqsfinder_1_4_4_d, pqsfinder_1_4_4_r
run default pqsfinder
Searching on sense strand...
Search status: finished
run pqsfinder using boost regex engine
Searching on sense strand...
Search status: finished
compare pv_d, pv_r
compare pv_d, pqsfinder_1_4_4_d
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: 30% ETTC 00:00:00
Search status: 43% ETTC 00:00:00
Search status: 46% ETTC 00:00:01
Search status: 47% ETTC 00:00:01
Search status: 48% ETTC 00:00:02
Search status: 49% ETTC 00:00:03
Search status: 55% ETTC 00:00:02
Search status: 59% ETTC 00:00:02
Search status: 78% ETTC 00:00:01
Search status: 99% ETTC 00:00:00
Search status: finished
Searching on antisense strand...
Search status: 23% ETTC 00:00:00
Search status: 42% ETTC 00:00:00
Search status: 46% ETTC 00:00:01
Search status: 51% ETTC 00:00:00
Search status: 57% ETTC 00:00:01
Search status: 83% ETTC 00:00:00
Search status: finished
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: 44% ETTC 00:00:00
Search status: finished
Searching on antisense strand...
Search status: 54% ETTC 00:00:00
Search status: finished
Searching on sense strand...
Search status: 44% ETTC 00:00:00
Search status: finished
Searching on antisense strand...
Search status: 54% ETTC 00:00:00
Search status: finished
Searching on sense strand...
Search status: 40% ETTC 00:00:00
Search status: 70% ETTC 00:00:00
Search status: finished
Searching on antisense strand...
Search status: 42% ETTC 00:00:00
Search status: 86% ETTC 00:00:00
Search status: finished
Searching on sense strand...
Search status: 40% ETTC 00:00:00
Search status: 70% ETTC 00:00:00
Search status: finished
Searching on antisense strand...
Search status: 42% ETTC 00:00:00
Search status: 86% ETTC 00:00:00
Search status: finished
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: 3% ETTC 00:00:00
Search status: 4% ETTC 00:00:24
Search status: 7% ETTC 00:00:26
Search status: 9% ETTC 00:00:30
Search status: 11% ETTC 00:00:32
Search status: 13% ETTC 00:00:33
Search status: 16% ETTC 00:00:31
Search status: 17% ETTC 00:00:34
Search status: 20% ETTC 00:00:32
Search status: 22% ETTC 00:00:31
Search status: 24% ETTC 00:00:31
Search status: 25% ETTC 00:00:33
Search status: 25% ETTC 00:00:36
Search status: 27% ETTC 00:00:35
Search status: 29% ETTC 00:00:34
Search status: 31% ETTC 00:00:33
Search status: 33% ETTC 00:00:32
Search status: 34% ETTC 00:00:33
Search status: 36% ETTC 00:00:32
Search status: 38% ETTC 00:00:31
Search status: 39% ETTC 00:00:31
Search status: 39% ETTC 00:00:34
Search status: 40% ETTC 00:00:34
Search status: 43% ETTC 00:00:31
Search status: 47% ETTC 00:00:28
Search status: 48% ETTC 00:00:28
Search status: 49% ETTC 00:00:28
Search status: 52% ETTC 00:00:25
Search status: 55% ETTC 00:00:23
Search status: 56% ETTC 00:00:23
Search status: 59% ETTC 00:00:21
Search status: 61% ETTC 00:00:20
Search status: 63% ETTC 00:00:19
Search status: 65% ETTC 00:00:18
Search status: 68% ETTC 00:00:16
Search status: 73% ETTC 00:00:12
Search status: 75% ETTC 00:00:12
Search status: 79% ETTC 00:00:09
Search status: 80% ETTC 00:00:09
Search status: 82% ETTC 00:00:08
Search status: 86% ETTC 00:00:06
Search status: 89% ETTC 00:00:04
Search status: 91% ETTC 00:00:04
Search status: 93% ETTC 00:00:03
Search status: 96% ETTC 00:00:01
Search status: 97% ETTC 00:00:01
Search status: 99% ETTC 00:00:00
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: 92% ETTC 00:00:00
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: 49% ETTC 00:00:01
Search status: 93% ETTC 00:00:00
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: 74% ETTC 00:00:00
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: 98% ETTC 00:00:00
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: finished
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
Searching on sense strand...
Search status: finished
Searching on antisense strand...
Search status: finished
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 83 ]
>
> proc.time()
user system elapsed
76.975 0.500 77.463
pqsfinder.Rcheck/pqsfinder-Ex.timings
| name | user | system | elapsed | |
| PQSViews | 0.076 | 0.004 | 0.079 | |
| density-PQSViews-method | 0.041 | 0.000 | 0.041 | |
| maxScores-PQSViews-method | 0.026 | 0.000 | 0.026 | |
| maxScores | 0.002 | 0.000 | 0.003 | |
| pqsfinder | 0.058 | 0.000 | 0.057 | |
| score-PQSViews-method | 0.023 | 0.000 | 0.023 | |
| strand-PQSViews-method | 0.021 | 0.004 | 0.025 | |