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CHECK report for pqsfinder on malbec2

This page was generated on 2019-10-16 12:08:48 -0400 (Wed, 16 Oct 2019).

Package 1239/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pqsfinder 2.0.2
Jiri Hon
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/pqsfinder
Branch: RELEASE_3_9
Last Commit: 35f0e7d
Last Changed Date: 2019-10-10 09:09:05 -0400 (Thu, 10 Oct 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: pqsfinder
Version: 2.0.2
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:pqsfinder.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings pqsfinder_2.0.2.tar.gz
StartedAt: 2019-10-16 04:02:37 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:05:32 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 174.2 seconds
RetCode: 0
Status:  OK 
CheckDir: pqsfinder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:pqsfinder.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings pqsfinder_2.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/pqsfinder.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘2.0.2’
* 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 25.5Mb
  sub-directories of 1Mb or more:
    lib   20.9Mb
    libs   4.2Mb
* 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 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-3.9-bioc/meat/pqsfinder.Rcheck/00check.log’
for details.

Installation output

pqsfinder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL pqsfinder
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘pqsfinder’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from pqsfinder.cpp:22:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pqsfinder.cpp:13:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from pqsfinder.cpp:22:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pqsfinder.cpp:13:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from pqsfinder.cpp:22:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pqsfinder.cpp:13:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from pqsfinder.cpp:22:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pqsfinder.cpp:13:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from pqsfinder.cpp:22:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pqsfinder.cpp:13:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from pqsfinder.cpp:22:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pqsfinder.cpp:13:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from pqsfinder.cpp:22:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pqsfinder.cpp:13:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from pqsfinder.cpp:22:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from pqsfinder.cpp:13:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
pqsfinder.cpp: In function ‘void find_all_runs(SEXP, int, std::__cxx11::basic_string::const_iterator, std::__cxx11::basic_string::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]
           pqs_storage, int_cnt, res, (loop_len == 0 ? true : zero_loop),
                                      ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/regex_traits_defaults.cpp:20:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_traits.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/regex_traits.hpp:27,
                 from boost_regex/cpp_regex_traits.cpp:22:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/cregex.cpp:22:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from boost_regex/fileiter.cpp:28:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from boost_regex/fileiter.cpp:28:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from boost_regex/fileiter.cpp:28:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from boost_regex/fileiter.cpp:28:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from boost_regex/fileiter.cpp:28:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from boost_regex/fileiter.cpp:28:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from boost_regex/fileiter.cpp:28:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from boost_regex/fileiter.cpp:28:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from boost_regex/fileiter.cpp:28:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from boost_regex/fileiter.cpp:28:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from boost_regex/fileiter.cpp:28:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from boost_regex/fileiter.cpp:28:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from boost_regex/fileiter.cpp:28:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from boost_regex/fileiter.cpp:28:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from boost_regex/fileiter.cpp:28:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from boost_regex/fileiter.cpp:28:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/regex.cpp:24:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/posix_api.cpp:23:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/wide_posix_api.cpp:25:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/winstances.cpp:30:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/winstances.cpp:30:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/winstances.cpp:30:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/winstances.cpp:30:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/winstances.cpp:30:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/winstances.cpp:30:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/winstances.cpp:30:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/winstances.cpp:30:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/winstances.cpp:30:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/winstances.cpp:30:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/winstances.cpp:30:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/winstances.cpp:30:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/winstances.cpp:30:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/winstances.cpp:30:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/winstances.cpp:30:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/winstances.cpp:30:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/instances.cpp:30:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/instances.cpp:30:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/instances.cpp:30:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/instances.cpp:30:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/instances.cpp:30:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/instances.cpp:30:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/instances.cpp:30:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/instances.cpp:30:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/instances.cpp:30:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/instances.cpp:30:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/instances.cpp:30:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/instances.cpp:30:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/instances.cpp:30:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/instances.cpp:30:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/instances.cpp:30:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex.hpp:32,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex.hpp:31,
                 from boost_regex/instances.cpp:30:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:22,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/c_regex_traits.cpp:28:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:42,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/wc_regex_traits.cpp:76:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from boost_regex/wc_regex_traits.cpp:23:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/wc_regex_traits.cpp:76:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from boost_regex/wc_regex_traits.cpp:23:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/wc_regex_traits.cpp:76:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from boost_regex/wc_regex_traits.cpp:23:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/wc_regex_traits.cpp:76:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from boost_regex/wc_regex_traits.cpp:23:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/wc_regex_traits.cpp:76:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from boost_regex/wc_regex_traits.cpp:23:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/wc_regex_traits.cpp:76:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from boost_regex/wc_regex_traits.cpp:23:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/wc_regex_traits.cpp:76:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from boost_regex/wc_regex_traits.cpp:23:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/regex_workaround.hpp:44,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/regex/v4/c_regex_traits.hpp:26,
                 from boost_regex/wc_regex_traits.cpp:76:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from boost_regex/wc_regex_traits.cpp:23:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/00LOCK-pqsfinder/00new/pqsfinder/lib"
ar rs "/home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a" boost_regex/regex_traits_defaults.o 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/wide_posix_api.o boost_regex/winstances.o boost_regex/w32_regex_traits.o boost_regex/instances.o boost_regex/c_regex_traits.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-3.9-bioc/R/library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o pqsfinder.so RcppExports.o pqsfinder.o /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-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)

Tests output

pqsfinder.Rcheck/tests/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(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, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

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 00:00:02
Search status: 48% ETTC 00:00:03
Search status: 49% ETTC 00:00:04
Search status: 55% ETTC 00:00:03
Search status: 59% ETTC 00:00:03
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 00:00:00
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: 62% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: 53% ETTC 00:00:00
Search status: 96% ETTC 00:00:00
Search status: finished              
Searching on sense strand...
Search status: 62% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: 53% ETTC 00:00:00
Search status: 96% ETTC 00:00:00
Search status: finished              
Searching on sense strand...
Search status: 50% ETTC 00:00:00
Search status: 93% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: 55% ETTC 00:00:00
Search status: 90% ETTC 00:00:00
Search status: finished              
Searching on sense strand...
Search status: 50% ETTC 00:00:00
Search status: 93% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: 55% ETTC 00:00:00
Search status: 90% 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: 2% ETTC 00:01:38
Search status: 5% ETTC 00:00:57
Search status: 6% ETTC 00:01:02
Search status: 10% ETTC 00:00:45
Search status: 10% ETTC 00:00:54
Search status: 12% ETTC 00:00:51
Search status: 17% ETTC 00:00:39
Search status: 17% ETTC 00:00:48
Search status: 18% ETTC 00:00:50
Search status: 19% ETTC 00:00:51
Search status: 20% ETTC 00:00:52
Search status: 23% ETTC 00:00:46
Search status: 24% ETTC 00:00:47
Search status: 27% ETTC 00:00:43
Search status: 29% ETTC 00:00:41
Search status: 31% ETTC 00:00:40
Search status: 34% ETTC 00:00:36
Search status: 37% ETTC 00:00:34
Search status: 40% ETTC 00:00:31
Search status: 42% ETTC 00:00:30
Search status: 43% ETTC 00:00:30
Search status: 46% ETTC 00:00:28
Search status: 49% ETTC 00:00:26
Search status: 50% ETTC 00:00:26
Search status: 51% ETTC 00:00:26
Search status: 53% ETTC 00:00:24
Search status: 56% ETTC 00:00:23
Search status: 58% ETTC 00:00:22
Search status: 61% ETTC 00:00:20
Search status: 63% ETTC 00:00:19
Search status: 67% ETTC 00:00:16
Search status: 69% ETTC 00:00:15
Search status: 71% ETTC 00:00:14
Search status: 73% ETTC 00:00:13
Search status: 74% ETTC 00:00:13
Search status: 79% ETTC 00:00:10
Search status: 82% ETTC 00:00:08
Search status: 83% ETTC 00:00:08
Search status: 85% ETTC 00:00:07
Search status: 88% ETTC 00:00:05
Search status: 90% ETTC 00:00:04
Search status: 91% ETTC 00:00:04
Search status: 92% ETTC 00:00:04
Search status: 94% ETTC 00:00:03
Search status: 96% ETTC 00:00:02
Search status: 98% ETTC 00:00:01
Search status: 99% ETTC 00:00:00
Search status: 100% 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              
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 83 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 88.927   0.131  89.058

Example timings

pqsfinder.Rcheck/pqsfinder-Ex.timings

nameusersystemelapsed
PQSViews0.0540.0000.055
density-PQSViews-method0.0230.0000.036
maxScores-PQSViews-method0.0120.0000.012
maxScores0.0010.0000.001
pqsfinder0.0130.0000.013
score-PQSViews-method0.0130.0000.013
strand-PQSViews-method0.0080.0030.012