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               from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25:0,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:82:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14:0,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:82:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/thread/thread.hpp:13:0,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:83:
./boost/boost/thread/detail/thread_group.hpp: In member function ‘boost::thread* boost::thread_group::create_thread(F)’:
./boost/boost/thread/detail/thread_group.hpp:78:18: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
             std::auto_ptr<thread> new_thread(new thread(threadfunc));
                  ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from ./boost/boost/iostreams/detail/config/codecvt.hpp:62,
                 from ./boost/boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
In file included from ./boost/boost/scoped_ptr.hpp:14:0,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: ‘template<class> 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++/6/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/filesystem/path.hpp:29,
                 from ./boost/boost/filesystem/operations.hpp:25,
                 from pwiz/utility/misc/SHA1.cpp:18:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/smart_ptr/scoped_ptr.hpp:21,
                 from ./boost/boost/scoped_ptr.hpp:14,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from pwiz/utility/misc/SHA1.cpp:17:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: ‘template<class> 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++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25:0,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from ./pwiz/utility/misc/String.hpp:29,
                 from ./pwiz/utility/misc/Std.hpp:31,
                 from pwiz/utility/misc/SHA1Calculator.cpp:33:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14:0,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/utility/misc/SHA1Calculator.cpp:33:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:32:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: ‘template<class> 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++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25:0,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/function/detail/prologue.hpp:18,
                 from ./boost/boost/function.hpp:24,
                 from ./boost/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from ./boost/boost/algorithm/string/find_iterator.hpp:24,
                 from ./boost/boost/algorithm/string/iter_find.hpp:27,
                 from ./boost/boost/algorithm/string/split.hpp:16,
                 from ./boost/boost/algorithm/string.hpp:23,
                 from pwiz/utility/misc/String.hpp:29,
                 from pwiz/utility/misc/Filesystem.hpp:29,
                 from pwiz/utility/misc/unit.hpp:30,
                 from pwiz/utility/misc/sha1calc.cpp:25:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/scoped_ptr.hpp:14:0,
                 from ./boost_aux/boost/nowide/fstream.hpp:14,
                 from ./pwiz/utility/misc/Stream.hpp:30,
                 from ./pwiz/utility/misc/Std.hpp:32,
                 from pwiz/utility/misc/sha1calc.cpp:26:
./boost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c random_access_gzFile.cpp -o random_access_gzFile.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/libs/thread/src/pthread/once.cpp -o boost/libs/thread/src/pthread/once.o
In file included from ./boost/boost/bind/mem_fn.hpp:25:0,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/bind/bind.hpp:26,
                 from ./boost/boost/bind.hpp:22,
                 from ./boost/boost/thread/pthread/once_atomic.hpp:19,
                 from ./boost/boost/thread/once.hpp:20,
                 from boost/libs/thread/src/pthread/./once_atomic.cpp:9,
                 from boost/libs/thread/src/pthread/once.cpp:8:
./boost/boost/get_pointer.hpp:27:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/get_pointer.hpp:14,
                 from ./boost/boost/bind/mem_fn.hpp:25,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/bind/bind.hpp:26,
                 from ./boost/boost/bind.hpp:22,
                 from ./boost/boost/thread/pthread/once_atomic.hpp:19,
                 from ./boost/boost/thread/once.hpp:20,
                 from boost/libs/thread/src/pthread/./once_atomic.cpp:9,
                 from boost/libs/thread/src/pthread/once.cpp:8:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/libs/thread/src/pthread/thread.cpp -o boost/libs/thread/src/pthread/thread.o
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
./boost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
./boost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: ‘template<class> 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++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
./boost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
./boost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
./boost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
./boost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/shared_ptr.hpp:17:0,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
./boost/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
./boost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./boost/boost/bind/mem_fn.hpp:25:0,
                 from ./boost/boost/mem_fn.hpp:22,
                 from ./boost/boost/bind/bind.hpp:26,
                 from ./boost/boost/bind.hpp:22,
                 from ./boost/boost/thread/detail/thread.hpp:30,
                 from ./boost/boost/thread/thread_only.hpp:22,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
./boost/boost/get_pointer.hpp: At global scope:
./boost/boost/get_pointer.hpp:27:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
                 from ./boost/boost/config/no_tr1/memory.hpp:21,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:23,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from ./boost/boost/date_time/time_clock.hpp:17,
                 from ./boost/boost/thread/thread_time.hpp:9,
                 from ./boost/boost/thread/lock_types.hpp:18,
                 from ./boost/boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rampR.cpp -o rampR.o
gcc -I/usr/local/lib/R/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_mzR.c -o R_init_mzR.o
g++ -std=gnu++11 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o mzR.so cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/fileiter.o ./boost/libs/regex/src/regex_raw_buffer.o ./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o ./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/regex_traits_defaults.o ./boost/libs/regex/src/winstances.o ./boost/libs/regex/src/wc_regex_traits.o ./boost/libs/regex/src/c_regex_traits.o ./boost/libs/regex/src/cpp_regex_traits.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/regex/src/w32_regex_traits.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/RAMPAdapter.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o ./RcppExports.o ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o rampR.o R_init_mzR.o -L/opt/lib/hdf5-18/lib/ -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lnetcdf -lhdf5_hl -lhdf5 -lpthread -lsz -lz -ldl -lm -lcurl -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/mzR/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (mzR)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘ropls’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (ropls)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘pkgmaker’ ...
** package ‘pkgmaker’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
Creating meta registry in package 'pkgmaker' ... OK
Creating registry 'extra_handler' in package 'pkgmaker' ... OK
Creating registry 'extra_action' in package 'pkgmaker' ... OK
Registering extra handler 'install.packages' [function] ... OK
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (pkgmaker)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘affy’ ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -I/usr/local/lib/R/include -DNDEBUG -DHAVE_ZLIB=1  -I"/usr/local/lib/R/site-library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c chipbackground.c -o chipbackground.o
gcc -I/usr/local/lib/R/include -DNDEBUG -DHAVE_ZLIB=1  -I"/usr/local/lib/R/site-library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c getall_locations.c -o getall_locations.o
gcc -I/usr/local/lib/R/include -DNDEBUG -DHAVE_ZLIB=1  -I"/usr/local/lib/R/site-library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mas5calls.c -o mas5calls.o
gcc -I/usr/local/lib/R/include -DNDEBUG -DHAVE_ZLIB=1  -I"/usr/local/lib/R/site-library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rma2.c -o rma2.o
gcc -I/usr/local/lib/R/include -DNDEBUG -DHAVE_ZLIB=1  -I"/usr/local/lib/R/site-library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rma_common.c -o rma_common.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/affy/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (affy)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘foreach’ ...
** package ‘foreach’ successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (foreach)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘hgu133plus2.db’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (hgu133plus2.db)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘hgu133a.db’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (hgu133a.db)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘GSEABase’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (GSEABase)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘gdata’ ...
** package ‘gdata’ successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (gdata)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘MassSpecWavelet’ ...
** libs
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c convolve2.c -o convolve2.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o MassSpecWavelet.so convolve2.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/MassSpecWavelet/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (MassSpecWavelet)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘sandwich’ ...
** package ‘sandwich’ successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (sandwich)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘kohonen’ ...
** package ‘kohonen’ successfully unpacked and MD5 sums checked
** libs
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bdk.c -o bdk.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c map.c -o map.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c som.c -o som.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c supersom.c -o supersom.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c xyf.c -o xyf.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o kohonen.so bdk.o map.o som.o supersom.o xyf.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/kohonen/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (kohonen)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘ChemmineR’ ...
** libs
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c DisjointSets.cpp -o DisjointSets.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c cluster.cc -o cluster.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c cstrsplit.cc -o cstrsplit.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c desc.cc -o desc.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fingerprints.cc -o fingerprints.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c formats.cc -o formats.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c molecule.cc -o molecule.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c r_wrap.cc -o r_wrap.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c script.cc -o script.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c similarity.cc -o similarity.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o ChemmineR.so DisjointSets.o cluster.o cstrsplit.o desc.o fingerprints.o formats.o molecule.o r_wrap.o script.o similarity.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/ChemmineR/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (ChemmineR)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘e1071’ ...
** package ‘e1071’ successfully unpacked and MD5 sums checked
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
** libs
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Rsvm.c -o Rsvm.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c cmeans.c -o cmeans.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c cshell.c -o cshell.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c floyd.c -o floyd.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c svm.cpp -o svm.o
svm.cpp: In function ‘svm_model* svm_load_model(const char*)’:
svm.cpp:2788:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
   fscanf(fp,"%80s",cmd);
                        ^
svm.cpp:2792:25: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
    fscanf(fp,"%80s",cmd);
                         ^
svm.cpp:2817:25: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
    fscanf(fp,"%80s",cmd);
                         ^
svm.cpp:2841:33: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
    fscanf(fp,"%d",&param.degree);
                                 ^
svm.cpp:2843:33: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
    fscanf(fp,"%lf",&param.gamma);
                                 ^
svm.cpp:2845:33: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
    fscanf(fp,"%lf",&param.coef0);
                                 ^
svm.cpp:2847:36: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
    fscanf(fp,"%d",&model->nr_class);
                                    ^
svm.cpp:2849:29: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
    fscanf(fp,"%d",&model->l);
                             ^
svm.cpp:2855:36: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fp,"%lf",&model->rho[i]);
                                    ^
svm.cpp:2862:37: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fp,"%d",&model->label[i]);
                                     ^
svm.cpp:2869:38: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fp,"%lf",&model->probA[i]);
                                      ^
svm.cpp:2876:38: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fp,"%lf",&model->probB[i]);
                                      ^
svm.cpp:2883:35: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fp,"%d",&model->nSV[i]);
                                   ^
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o e1071.so Rsvm.o cmeans.o cshell.o floyd.o init.o svm.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/e1071/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (e1071)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘topGO’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (topGO)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘globaltest’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (globaltest)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘edgeR’ ...
** libs
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_add_prior_count.cpp -o R_add_prior_count.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_add_repeat_matrices.cpp -o R_add_repeat_matrices.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_ave_log_cpm.cpp -o R_ave_log_cpm.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_calculate_cpm.cpp -o R_calculate_cpm.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_check_counts.cpp -o R_check_counts.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_check_poisson_bound.cpp -o R_check_poisson_bound.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_compute_apl.cpp -o R_compute_apl.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_compute_nbdev.cpp -o R_compute_nbdev.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_get_one_way_fitted.cpp -o R_get_one_way_fitted.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_initialize_levenberg.cpp -o R_initialize_levenberg.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_levenberg.cpp -o R_levenberg.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_loess_by_col.cpp -o R_loess_by_col.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_one_group.cpp -o R_one_group.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_simple_good_turing.cpp -o R_simple_good_turing.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c add_prior.cpp -o add_prior.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c adj_coxreid.cpp -o adj_coxreid.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fmm_spline.c -o fmm_spline.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glm_levenberg.cpp -o glm_levenberg.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c glm_one_group.cpp -o glm_one_group.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.cpp -o init.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c interpolator.cpp -o interpolator.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c matvec_check.cpp -o matvec_check.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nbdev.cpp -o nbdev.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o edgeR.so R_add_prior_count.o R_add_repeat_matrices.o R_ave_log_cpm.o R_calculate_cpm.o R_check_counts.o R_check_poisson_bound.o R_compute_apl.o R_compute_nbdev.o R_exact_test_by_deviance.o R_get_one_way_fitted.o R_initialize_levenberg.o R_levenberg.o R_loess_by_col.o R_maximize_interpolant.o R_one_group.o R_process_hairpin_reads.o R_simple_good_turing.o add_prior.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o init.o interpolator.o matvec_check.o nbdev.o -L/usr/local/lib/R/lib -lRlapack -L/usr/local/lib/R/lib -lRblas -lgfortran -lm -lquadmath -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/edgeR/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (edgeR)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘HTMLUtils’ ...
** package ‘HTMLUtils’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (HTMLUtils)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘safe’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (safe)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘KEGGREST’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (KEGGREST)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘pracma’ ...
** package ‘pracma’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** demo
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (pracma)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘Rmpfr’ ...
** package ‘Rmpfr’ successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking mpfr.h usability... yes
checking mpfr.h presence... yes
checking for mpfr.h... yes
checking gmp.h usability... yes
checking gmp.h presence... yes
checking for gmp.h... yes
checking for __gmpz_init in -lgmp... yes
checking for mpfr_init in -lmpfr... yes
checking for mpfr_digamma in -lmpfr... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Ops.c -o Ops.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Summary.c -o Summary.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c convert.c -o convert.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utils.c -o utils.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o Rmpfr.so Ops.o Summary.o convert.o init.o utils.o -lmpfr -lgmp -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/Rmpfr/libs
** R
** demo
** inst
** preparing package for lazy loading
Creating a generic function for ‘factorial’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘diag’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘diag<-’ from package ‘base’ in package ‘Rmpfr’
Creating a new generic function for ‘cbind’ in package ‘Rmpfr’
Creating a new generic function for ‘rbind’ in package ‘Rmpfr’
Creating a generic function for ‘colSums’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘colMeans’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘rowSums’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘rowMeans’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘norm’ from package ‘base’ in package ‘Rmpfr’
in method for ‘show’ with signature ‘"integrateR"’: no definition for class “integrateR”
Creating a new generic function for ‘pmin’ in package ‘Rmpfr’
Creating a new generic function for ‘pmax’ in package ‘Rmpfr’
Creating a generic function for ‘atan2’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘beta’ from package ‘base’ in package ‘Rmpfr’
Creating a generic function for ‘lbeta’ from package ‘base’ in package ‘Rmpfr’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (Rmpfr)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘ALS’ ...
** package ‘ALS’ successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (ALS)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘doParallel’ ...
** package ‘doParallel’ successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (doParallel)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘rngtools’ ...
** package ‘rngtools’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (rngtools)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘vsn’ ...
** libs
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c vsn.c -o vsn.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c vsn2.c -o vsn2.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o vsn.so init.o vsn.o vsn2.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/vsn/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (vsn)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘gage’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (gage)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘GSVA’ ...
** libs
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c kernel_estimation.c -o kernel_estimation.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ks_test.c -o ks_test.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c register_cmethods.c -o register_cmethods.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o GSVA.so kernel_estimation.o ks_test.o register_cmethods.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/GSVA/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GSVA)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘gplots’ ...
** package ‘gplots’ successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (gplots)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘maxLik’ ...
** package ‘maxLik’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (maxLik)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘ChemometricsWithR’ ...
** package ‘ChemometricsWithR’ successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (ChemometricsWithR)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘bioassayR’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘organism’ in package ‘bioassayR’
Creating a new generic function for ‘organism<-’ in package ‘bioassayR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (bioassayR)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘biosigner’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (biosigner)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘pathview’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (pathview)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘RankProd’ ...
** R
** data
** inst
** preparing package for lazy loading
[1] "this is the new version of the RankProd package"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (RankProd)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘mzID’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (mzID)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘doRNG’ ...
** package ‘doRNG’ successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (doRNG)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘tofsims’ ...
** libs
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c LapackEigen.cpp -o LapackEigen.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c c_importer.cpp -o c_importer.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nn.cpp -o nn.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c readRawPhi.cpp -o readRawPhi.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c tofsims_init.c -o tofsims_init.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utilities.cpp -o utilities.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o tofsims.so LapackEigen.o RcppExports.o c_importer.o nn.o readRawPhi.o tofsims_init.o utilities.o -llapack -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/tofsims/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (tofsims)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘MSnbase’ ...
** libs
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Spectrum1_class.c -o Spectrum1_class.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Spectrum2_class.c -o Spectrum2_class.o
g++  -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
gcc -I/usr/local/lib/R/include -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utils.c -o utils.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o MSnbase.so RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/MSnbase/libs
** R
** data
*** moving datasets to lazyload DB
Creating a new generic function for ‘smooth’ in package ‘MSnbase’
Creating a new generic function for ‘trimws’ in package ‘MSnbase’
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
** inst
** preparing package for lazy loading
Creating a new generic function for ‘smooth’ in package ‘MSnbase’
Creating a new generic function for ‘trimws’ in package ‘MSnbase’
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (MSnbase)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘PADOG’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (PADOG)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘xcms’ ...
** libs
rm -f massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o binners.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c massifquant/Tracker.cpp -o massifquant/Tracker.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c massifquant/SegProc.cpp -o massifquant/SegProc.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c obiwarp/mat.cpp -o obiwarp/mat.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c obiwarp/vec.cpp -o obiwarp/vec.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
g++  -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c xcms_obiwarp.cpp -o xcms_obiwarp.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fastMatch.c -o fastMatch.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mzClust_hclust.c -o mzClust_hclust.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mzROI.c -o mzROI.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c util.c -o util.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c xcms.c -o xcms.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c binners.c -o binners.o
g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o xcms.so massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o binners.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/xcms/libs
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘sigma’ in package ‘xcms’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (xcms)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘EGSEA’ ...
** R
** inst
** preparing package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (EGSEA)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘proFIA’ ...
** libs
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c FIABandsExtractionCentroid.c -o FIABandsExtractionCentroid.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c UtilFunc.c -o UtilFunc.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fastMatchPpm.c -o fastMatchPpm.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o proFIA.so FIABandsExtractionCentroid.o UtilFunc.o fastMatchPpm.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/proFIA/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (proFIA)

The downloaded source packages are in
	‘/tmp/RtmpkY3Cfm/downloaded_packages’
Old packages: 'AnnotationDbi', 'AnnotationHub', 'GenomeInfoDb', 'mgcv',
  'S4Vectors', 'SummarizedExperiment', 'VariantAnnotation'
> 
> # just in case there were warnings, we want to see them
> # without having to scroll up:
> warnings()
NULL
> 
> if (!is.null(warnings()))
+ {
+     w <- capture.output(warnings())
+     if (length(grep("is not available|had non-zero exit status", w)))
+         quit("no", 1L)
+ }
> 
> suppressWarnings(BiocInstaller::biocValid(fix=TRUE, ask=FALSE))

* sessionInfo()

R Under development (unstable) (2017-02-05 r72121)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.25.3

loaded via a namespace (and not attached):
[1] compiler_3.4.0 tools_3.4.0   

* Out-of-date packages
                     Package                LibPath                        
AnnotationDbi        "AnnotationDbi"        "/usr/local/lib/R/site-library"
AnnotationHub        "AnnotationHub"        "/usr/local/lib/R/site-library"
GenomeInfoDb         "GenomeInfoDb"         "/usr/local/lib/R/site-library"
S4Vectors            "S4Vectors"            "/usr/local/lib/R/site-library"
SummarizedExperiment "SummarizedExperiment" "/usr/local/lib/R/site-library"
VariantAnnotation    "VariantAnnotation"    "/usr/local/lib/R/site-library"
                     Installed Built   ReposVer 
AnnotationDbi        "1.37.2"  "3.4.0" "1.37.3" 
AnnotationHub        "2.7.11"  "3.4.0" "2.7.13" 
GenomeInfoDb         "1.11.6"  "3.4.0" "1.11.9" 
S4Vectors            "0.13.13" "3.4.0" "0.13.14"
SummarizedExperiment "1.5.4"   "3.4.0" "1.5.6"  
VariantAnnotation    "1.21.15" "3.4.0" "1.21.17"
                     Repository                                              
AnnotationDbi        "https://bioconductor.org/packages/3.5/bioc/src/contrib"
AnnotationHub        "https://bioconductor.org/packages/3.5/bioc/src/contrib"
GenomeInfoDb         "https://bioconductor.org/packages/3.5/bioc/src/contrib"
S4Vectors            "https://bioconductor.org/packages/3.5/bioc/src/contrib"
SummarizedExperiment "https://bioconductor.org/packages/3.5/bioc/src/contrib"
VariantAnnotation    "https://bioconductor.org/packages/3.5/bioc/src/contrib"

update with biocLite()

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.25.3), R Under development (unstable)
  (2017-02-05 r72121).
Installing package(s) ‘AnnotationDbi’, ‘AnnotationHub’, ‘GenomeInfoDb’,
  ‘S4Vectors’, ‘SummarizedExperiment’, ‘VariantAnnotation’
also installing the dependencies ‘GenomeInfoDbData’, ‘DelayedArray’

trying URL 'https://bioconductor.org/packages/3.5/data/annotation/src/contrib/GenomeInfoDbData_0.99.0.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/DelayedArray_0.1.6.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/AnnotationDbi_1.37.3.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/AnnotationHub_2.7.13.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/GenomeInfoDb_1.11.9.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/S4Vectors_0.13.14.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/SummarizedExperiment_1.5.6.tar.gz'
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Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘GenomeInfoDbData’ ...
** data
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (GenomeInfoDbData)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘S4Vectors’ ...
** libs
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c AEbufs.c -o AEbufs.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c DataFrame_class.c -o DataFrame_class.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Hits_class.c -o Hits_class.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Linteger_class.c -o Linteger_class.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c List_class.c -o List_class.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_S4Vectors.c -o R_init_S4Vectors.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Rle_class.c -o Rle_class.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Rle_utils.c -o Rle_utils.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SEXP_utils.c -o SEXP_utils.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SimpleList_class.c -o SimpleList_class.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c anyMissing.c -o anyMissing.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c eval_utils.c -o eval_utils.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c hash_utils.c -o hash_utils.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c int_utils.c -o int_utils.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c logical_utils.c -o logical_utils.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c safe_arithm.c -o safe_arithm.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sort_utils.c -o sort_utils.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c str_utils.c -o str_utils.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c subsetting_utils.c -o subsetting_utils.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c vector_utils.c -o vector_utils.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o Linteger_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o eval_utils.o hash_utils.o int_utils.o logical_utils.o safe_arithm.o sort_utils.o str_utils.o subsetting_utils.o vector_utils.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/S4Vectors/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘S4Vectors’
Creating a new generic function for ‘expand.grid’ in package ‘S4Vectors’
Creating a generic function for ‘%in%’ from package ‘base’ in package ‘S4Vectors’
Creating a new generic function for ‘findMatches’ in package ‘S4Vectors’
Creating a generic function for ‘setequal’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘as.factor’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘tabulate’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘cov’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘cor’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘substr’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘substring’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘sub’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘gsub’ from package ‘base’ in package ‘S4Vectors’
in method for ‘coerce’ with signature ‘"data.table","DataFrame"’: no definition for class “data.table”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (S4Vectors)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘DelayedArray’ ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘apply’ in package ‘DelayedArray’
Creating a generic function for ‘dlogis’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘plogis’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘qlogis’ from package ‘stats’ in package ‘DelayedArray’
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (DelayedArray)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘AnnotationDbi’ ...
** R
** inst
** preparing package for lazy loading
in method for ‘initialize’ with signature ‘"L2Rlink"’: no definition for class “L2Rlink”
in method for ‘toString’ with signature ‘"L2Rlink"’: no definition for class “L2Rlink”
in method for ‘show’ with signature ‘"L2Rlink"’: no definition for class “L2Rlink”
in method for ‘rev’ with signature ‘"L2Rlink"’: no definition for class “L2Rlink”
Creating a new generic function for ‘packageName’ in package ‘AnnotationDbi’
Creating a generic function for ‘ls’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘eapply’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘exists’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘sample’ from package ‘base’ in package ‘AnnotationDbi’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (AnnotationDbi)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘GenomeInfoDb’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (GenomeInfoDb)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘AnnotationHub’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (AnnotationHub)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘SummarizedExperiment’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (SummarizedExperiment)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘VariantAnnotation’ ...
** libs
gcc -I/usr/local/lib/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I"/usr/local/lib/R/site-library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I/usr/local/lib/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I"/usr/local/lib/R/site-library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I/usr/local/lib/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I"/usr/local/lib/R/site-library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
gcc -I/usr/local/lib/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I"/usr/local/lib/R/site-library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XVector_stubs.c -o XVector_stubs.o
gcc -I/usr/local/lib/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I"/usr/local/lib/R/site-library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dna_hash.c -o dna_hash.o
gcc -I/usr/local/lib/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I"/usr/local/lib/R/site-library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rle.c -o rle.o
gcc -I/usr/local/lib/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I"/usr/local/lib/R/site-library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c strhash.c -o strhash.o
gcc -I/usr/local/lib/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I"/usr/local/lib/R/site-library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utilities.c -o utilities.o
gcc -I/usr/local/lib/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I"/usr/local/lib/R/site-library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c vcffile.c -o vcffile.o
gcc -I/usr/local/lib/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I"/usr/local/lib/R/site-library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c vcftype.c -o vcftype.o
gcc -I/usr/local/lib/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I"/usr/local/lib/R/site-library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c writevcf.c -o writevcf.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o VariantAnnotation.so Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o writevcf.o /usr/local/lib/R/site-library/Rsamtools/usrlib//libbam.a /usr/local/lib/R/site-library/Rsamtools/usrlib//libbcf.a /usr/local/lib/R/site-library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/VariantAnnotation/libs
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘tabulate’ in package ‘VariantAnnotation’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (VariantAnnotation)

The downloaded source packages are in
	‘/tmp/RtmpkY3Cfm/downloaded_packages’
Updating packages 'mgcv'
trying URL 'https://cran.rstudio.com/src/contrib/mgcv_1.8-17.tar.gz'
Content type 'application/x-gzip' length 849787 bytes (829 KB)
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downloaded 829 KB

Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* installing *source* package ‘mgcv’ ...
** package ‘mgcv’ successfully unpacked and MD5 sums checked
** libs
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c coxph.c -o coxph.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c discrete.c -o discrete.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gdi.c -o gdi.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c magic.c -o magic.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mat.c -o mat.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c matrix.c -o matrix.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mgcv.c -o mgcv.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c misc.c -o misc.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mvn.c -o mvn.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c qp.c -o qp.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c soap.c -o soap.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sparse-smooth.c -o sparse-smooth.o
gcc -I/usr/local/lib/R/include -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c tprs.c -o tprs.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o mgcv.so coxph.o discrete.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o mvn.o qp.o soap.o sparse-smooth.o tprs.o -L/usr/local/lib/R/lib -lRlapack -L/usr/local/lib/R/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/mgcv/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
* DONE (mgcv)

The downloaded source packages are in
	‘/tmp/RtmpkY3Cfm/downloaded_packages’
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Removing intermediate container a07aff0c3645
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[container-bioc_devel_protmetcore] $ docker tag d28a02a84863 docker-registry-v2.local:30750/bioconductor/devel_protmetcore2:latest
[container-bioc_devel_protmetcore] $ docker inspect d28a02a84863
[container-bioc_devel_protmetcore] $ docker push docker-registry-v2.local:30750/bioconductor/devel_protmetcore2:devel
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[container-bioc_devel_protmetcore] $ docker push docker-registry-v2.local:30750/bioconductor/devel_protmetcore2:latest
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Warning: you have no plugins providing access control for builds, so falling back to legacy behavior of permitting any downstream builds to be triggered
Triggering a new build of container-bioc_devel_metabolomics
Finished: SUCCESS