Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:49 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the RBGL package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RBGL.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1507/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RBGL 1.68.0 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: RBGL |
Version: 1.68.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:RBGL.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings RBGL_1.68.0.tar.gz |
StartedAt: 2021-10-14 11:14:22 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 11:14:52 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 30.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: RBGL.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:RBGL.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings RBGL_1.68.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/RBGL.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘RBGL/DESCRIPTION’ ... OK * this is package ‘RBGL’ version ‘1.68.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘RBGL’ can be installed ... WARNING Found the following significant warnings: interfaces.cpp:81:17: warning: catching polymorphic type ‘struct boost::not_a_dag’ by value [-Wcatch-value=] See ‘/home/biocbuild/bbs-3.13-bioc/meat/RBGL.Rcheck/00install.out’ for details. * checking installed package size ... NOTE installed size is 14.5Mb sub-directories of 1Mb or more: libs 12.0Mb old_boost 1.8Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘methods’ A package should be listed in only one of these fields. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/home/biocbuild/bbs-3.13-bioc/R/library/RBGL/libs/RBGL.so’: Found ‘abort’, possibly from ‘abort’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.13-bioc/meat/RBGL.Rcheck/00check.log’ for details.
RBGL.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL RBGL ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘RBGL’ ... ** using staged installation ** libs g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c bbc.cpp -o bbc.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from bbc.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_<Pred>::************ | ^ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from bbc.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from bbc.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from bbc.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from bbc.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from bbc.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from bbc.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from bbc.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from bbc.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from bbc.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr<Y> & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from bbc.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from bbc.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr<Y> && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from bbc.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from bbc.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from bbc.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from bbc.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from bbc.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from bbc.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead. 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’ 23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’ 13 | BOOST_HEADER_DEPRECATED("<iterator>") | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c cliques.cpp -o cliques.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from cliques.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_<Pred>::************ | ^ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from cliques.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from cliques.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from cliques.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from cliques.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from cliques.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from cliques.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from cliques.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from cliques.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from cliques.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr<Y> & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from cliques.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from cliques.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr<Y> && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from cliques.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from cliques.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from cliques.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from cliques.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from cliques.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from cliques.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead. 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’ 23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’ 13 | BOOST_HEADER_DEPRECATED("<iterator>") | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c clusteringCoef.cpp -o clusteringCoef.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from clusteringCoef.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_<Pred>::************ | ^ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from clusteringCoef.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from clusteringCoef.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from clusteringCoef.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from clusteringCoef.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from clusteringCoef.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from clusteringCoef.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from clusteringCoef.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from clusteringCoef.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from clusteringCoef.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr<Y> & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from clusteringCoef.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from clusteringCoef.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr<Y> && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from clusteringCoef.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from clusteringCoef.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from clusteringCoef.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from clusteringCoef.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from clusteringCoef.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from clusteringCoef.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead. 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’ 23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’ 13 | BOOST_HEADER_DEPRECATED("<iterator>") | ^~~~~~~~~~~~~~~~~~~~~~~ clusteringCoef.cpp: In function ‘SEXPREC* graphGenerator(SEXP, SEXP, SEXP)’: clusteringCoef.cpp:394:40: warning: ‘u’ may be used uninitialized in this function [-Wmaybe-uninitialized] 394 | Graph_ud::vertex_descriptor v, u, w=Graph_ud::null_vertex(); | ^ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c dominatorTree.cpp -o dominatorTree.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from dominatorTree.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_<Pred>::************ | ^ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from dominatorTree.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from dominatorTree.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from dominatorTree.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from dominatorTree.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from dominatorTree.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from dominatorTree.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from dominatorTree.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from dominatorTree.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from dominatorTree.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr<Y> & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from dominatorTree.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from dominatorTree.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr<Y> && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from dominatorTree.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from dominatorTree.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from dominatorTree.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from dominatorTree.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from dominatorTree.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from dominatorTree.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead. 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’ 23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’ 13 | BOOST_HEADER_DEPRECATED("<iterator>") | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c edmonds_optimum_branching.cpp -o edmonds_optimum_branching.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_<Pred>::************ | ^ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr<Y> & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr<Y> && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from edmonds_optimum_branching.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead. 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’ 23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’ 13 | BOOST_HEADER_DEPRECATED("<iterator>") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from edmonds_optimum_branching.hpp:94, from edmonds_optimum_branching.cpp:3: edmonds_optimum_branching_impl.hpp: In function ‘void edmonds_optimum_branching(TEdgeListGraph&, TVertexIndexMap, TWeightMap, TInputIterator, TInputIterator, TOutputIterator)’: edmonds_optimum_branching_impl.hpp:520:71: warning: typedef ‘EdgeIter’ locally defined but not used [-Wunused-local-typedefs] 520 | typedef typename graph_traits<TEdgeListGraph>::edge_iterator EdgeIter; | ^~~~~~~~ edmonds_optimum_branching_impl.hpp:521:71: warning: typedef ‘weight_t’ locally defined but not used [-Wunused-local-typedefs] 521 | typedef typename property_traits<TWeightMap>::value_type weight_t; | ^~~~~~~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c hcs.cpp -o hcs.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from hcs.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_<Pred>::************ | ^ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from hcs.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from hcs.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from hcs.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from hcs.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from hcs.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from hcs.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from hcs.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from hcs.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from hcs.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr<Y> & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from hcs.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from hcs.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr<Y> && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from hcs.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from hcs.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from hcs.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from hcs.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from hcs.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from hcs.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead. 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’ 23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’ 13 | BOOST_HEADER_DEPRECATED("<iterator>") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from mincut.hpp:4, from hcs.cpp:2: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp: In function ‘typename boost::graph_traits<G>::edges_size_type boost::min_cut(VertexListGraph&, OutputIterator, OutputIterator) [with VertexListGraph = const R_adjacency_list<boost::undirectedS, double>; OutputIterator = std::back_insert_iterator<std::vector<long unsigned int> >]’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp:33:44: warning: ‘p’ may be used uninitialized in this function [-Wmaybe-uninitialized] 33 | typename Traits::vertex_descriptor p; | ^ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c incrConnComp.cpp -o incrConnComp.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from incrConnComp.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_<Pred>::************ | ^ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from incrConnComp.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from incrConnComp.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from incrConnComp.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from incrConnComp.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from incrConnComp.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from incrConnComp.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from incrConnComp.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from incrConnComp.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from incrConnComp.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr<Y> & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from incrConnComp.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from incrConnComp.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr<Y> && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from incrConnComp.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from incrConnComp.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from incrConnComp.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from incrConnComp.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from incrConnComp.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from incrConnComp.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead. 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’ 23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’ 13 | BOOST_HEADER_DEPRECATED("<iterator>") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from incrConnComp.cpp:2: incrConnComp.cpp: In function ‘SEXPREC* BGL_incr_comp_internal(SEXP, SEXP, SEXP, E_IC_METHOD)’: incrConnComp.cpp:74:32: warning: unused variable ‘child_index’ [-Wunused-variable] 74 | BOOST_FOREACH(VertexIndex child_index, components[current_index]) { | ^~~~~~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/foreach.hpp:1114:14: note: in definition of macro ‘BOOST_FOREACH’ 1114 | for (VAR = BOOST_FOREACH_DEREF(COL); !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue) = true) | ^~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c interfaces.cpp -o interfaces.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from interfaces.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_<Pred>::************ | ^ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from interfaces.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from interfaces.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from interfaces.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from interfaces.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from interfaces.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from interfaces.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from interfaces.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from interfaces.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from interfaces.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr<Y> & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from interfaces.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from interfaces.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr<Y> && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from interfaces.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from interfaces.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from interfaces.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from interfaces.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from interfaces.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from interfaces.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead. 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’ 23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’ 13 | BOOST_HEADER_DEPRECATED("<iterator>") | ^~~~~~~~~~~~~~~~~~~~~~~ interfaces.cpp: In function ‘SEXPREC* BGL_tsort_D(SEXP, SEXP, SEXP)’: interfaces.cpp:81:17: warning: catching polymorphic type ‘struct boost::not_a_dag’ by value [-Wcatch-value=] 81 | catch ( not_a_dag ) | ^~~~~~~~~ interfaces.cpp:57:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs] 57 | typedef graph_traits < Graph_dd >::edge_descriptor Edge; | ^~~~ interfaces.cpp:61:62: warning: typedef ‘Color’ locally defined but not used [-Wunused-local-typedefs] 61 | typedef property_map<Graph_dd, vertex_color_t>::type Color; | ^~~~~ interfaces.cpp: In function ‘SEXPREC* BGL_bfs_D(SEXP, SEXP, SEXP, SEXP, SEXP)’: interfaces.cpp:98:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs] 98 | typedef graph_traits < Graph_dd >::edge_descriptor Edge; | ^~~~ interfaces.cpp:99:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs] 99 | typedef graph_traits < Graph_dd >::vertex_descriptor Vertex; | ^~~~~~ interfaces.cpp: In function ‘SEXPREC* BGL_dfs_D(SEXP, SEXP, SEXP, SEXP)’: interfaces.cpp:142:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs] 142 | typedef graph_traits < Graph_dd >::edge_descriptor Edge; | ^~~~ interfaces.cpp:143:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs] 143 | typedef graph_traits < Graph_dd >::vertex_descriptor Vertex; | ^~~~~~ interfaces.cpp: In function ‘SEXPREC* BGL_connected_components_U(SEXP, SEXP, SEXP, SEXP)’: interfaces.cpp:198:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs] 198 | typedef graph_traits < Graph_ud >::edge_descriptor Edge; | ^~~~ interfaces.cpp:199:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs] 199 | typedef graph_traits < Graph_ud >::vertex_descriptor Vertex; | ^~~~~~ interfaces.cpp: In function ‘SEXPREC* BGL_strong_components_D(SEXP, SEXP, SEXP, SEXP)’: interfaces.cpp:225:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs] 225 | typedef graph_traits < Graph_dd >::edge_descriptor Edge; | ^~~~ interfaces.cpp:226:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs] 226 | typedef graph_traits < Graph_dd >::vertex_descriptor Vertex; | ^~~~~~ interfaces.cpp: In function ‘SEXPREC* BGL_biconnected_components_U(SEXP, SEXP, SEXP, SEXP)’: interfaces.cpp:252:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs] 252 | typedef graph_traits < Graph_ud >::edge_descriptor Edge; | ^~~~ interfaces.cpp:253:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs] 253 | typedef graph_traits < Graph_ud >::vertex_descriptor Vertex; | ^~~~~~ interfaces.cpp: In function ‘SEXPREC* BGL_articulation_points_U(SEXP, SEXP, SEXP, SEXP)’: interfaces.cpp:295:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs] 295 | typedef graph_traits < Graph_ud >::edge_descriptor Edge; | ^~~~ interfaces.cpp: In function ‘SEXPREC* BGL_edge_connectivity_U(SEXP, SEXP, SEXP, SEXP)’: interfaces.cpp:320:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs] 320 | typedef graph_traits < Graph_ud >::vertex_descriptor Vertex; | ^~~~~~ interfaces.cpp: In function ‘SEXPREC* BGL_sequential_vertex_coloring(SEXP, SEXP, SEXP)’: interfaces.cpp:360:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs] 360 | typedef graph_traits < Graph_ud >::edge_descriptor Edge; | ^~~~ interfaces.cpp:361:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs] 361 | typedef graph_traits < Graph_ud >::vertex_descriptor Vertex; | ^~~~~~ In file included from interfaces.cpp:7: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp: In function ‘typename boost::graph_traits<G>::degree_size_type boost::edge_connectivity(VertexListGraph&, OutputIterator) [with VertexListGraph = R_adjacency_list<boost::undirectedS, double>; OutputIterator = std::back_insert_iterator<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int> > >]’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp:33:44: warning: ‘p’ may be used uninitialized in this function [-Wmaybe-uninitialized] 33 | typename Traits::vertex_descriptor p; | ^ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c minST.cpp -o minST.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from minST.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_<Pred>::************ | ^ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from minST.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from minST.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from minST.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from minST.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from minST.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from minST.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from minST.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from minST.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from minST.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr<Y> & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from minST.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from minST.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr<Y> && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from minST.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from minST.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from minST.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from minST.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from minST.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from minST.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead. 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’ 23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’ 13 | BOOST_HEADER_DEPRECATED("<iterator>") | ^~~~~~~~~~~~~~~~~~~~~~~ minST.cpp: In function ‘SEXPREC* BGL_KMST_D(SEXP, SEXP, SEXP, SEXP)’: minST.cpp:14:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs] 14 | typedef graph_traits < Graph_dd >::vertex_descriptor Vertex; | ^~~~~~ minST.cpp: In function ‘SEXPREC* BGL_KMST_U(SEXP, SEXP, SEXP, SEXP)’: minST.cpp:48:62: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs] 48 | typedef graph_traits < Graph_ud >::vertex_descriptor Vertex; | ^~~~~~ minST.cpp: In function ‘SEXPREC* BGL_PRIM_U(SEXP, SEXP, SEXP, SEXP)’: minST.cpp:81:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs] 81 | typedef graph_traits < Graph_ud >::edge_descriptor Edge; | ^~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from minST.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘void boost::detail::kruskal_mst_impl(const Graph&, OutputIterator, Rank, Parent, Weight) [with Graph = R_adjacency_list<boost::directedS, double>; OutputIterator = std::back_insert_iterator<std::vector<boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > >; Rank = boost::iterator_property_map<__gnu_cxx::__normal_iterator<long unsigned int*, std::vector<long unsigned int> >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, long unsigned int>, long unsigned int, long unsigned int&>; Parent = boost::iterator_property_map<__gnu_cxx::__normal_iterator<long unsigned int*, std::vector<long unsigned int> >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, long unsigned int>, long unsigned int, long unsigned int&>; Weight = boost::adj_list_edge_property_map<boost::directed_tag, double, const double&, long unsigned int, const boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>]’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: ‘*((void*)& ei +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 80 | if (edges BOOST_GRAPH_MEMBER first | ^~ In file included from minST.cpp:2: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/kruskal_min_spanning_tree.hpp:78:55: note: ‘*((void*)& ei +48)’ was declared here 78 | typename graph_traits< Graph >::edge_iterator ei, eiend; | ^~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:32, from RBGL.hpp:38, from minST.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/edge.hpp:27:71: warning: ‘*((void*)& ei +40)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 27 | inline edge_base(Vertex s, Vertex d) : m_source(s), m_target(d) {} | ^ In file included from minST.cpp:2: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/kruskal_min_spanning_tree.hpp:78:55: note: ‘*((void*)& ei +40)’ was declared here 78 | typename graph_traits< Graph >::edge_iterator ei, eiend; | ^~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c mincut.cpp -o mincut.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from mincut.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_<Pred>::************ | ^ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from mincut.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from mincut.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from mincut.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from mincut.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from mincut.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from mincut.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from mincut.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from mincut.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from mincut.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr<Y> & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from mincut.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from mincut.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr<Y> && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from mincut.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from mincut.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from mincut.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from mincut.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from mincut.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from mincut.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead. 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’ 23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’ 13 | BOOST_HEADER_DEPRECATED("<iterator>") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from mincut.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘SEXPREC* BGL_max_flow_internal(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, E_MF_METHOD)’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: ‘*((void*)& ei +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 80 | if (edges BOOST_GRAPH_MEMBER first | ^~ mincut.cpp:99:19: note: ‘*((void*)& ei +48)’ was declared here 99 | edge_iterator ei, e_end; | ^~ mincut.cpp:103:33: warning: ‘*((void*)& ei +40)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 103 | INTEGER(eList)[i++] = source(*ei, flow_g); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from mincut.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:147:48: warning: ‘*((void*)(& ei)+32).__gnu_cxx::__normal_iterator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > >*, std::vector<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > >, std::allocator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > > > > >::_M_current’ may be used uninitialized in this function [-Wmaybe-uninitialized] 147 | &(*this->base()).get_property()); | ^ mincut.cpp:99:19: note: ‘*((void*)(& ei)+32).__gnu_cxx::__normal_iterator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > >*, std::vector<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > >, std::allocator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > > > > >::_M_current’ was declared here 99 | edge_iterator ei, e_end; | ^~ In file included from mincut.hpp:4, from mincut.cpp:2: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp: In function ‘typename boost::graph_traits<G>::edges_size_type boost::min_cut(VertexListGraph&, OutputIterator, OutputIterator) [with VertexListGraph = R_adjacency_list<boost::undirectedS, double>; OutputIterator = std::back_insert_iterator<std::vector<long unsigned int> >]’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/edge_connectivity.hpp:33:44: warning: ‘p’ may be used uninitialized in this function [-Wmaybe-uninitialized] 33 | typename Traits::vertex_descriptor p; | ^ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c ordering.cpp -o ordering.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from ordering.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_<Pred>::************ | ^ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from ordering.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from ordering.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from ordering.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from ordering.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from ordering.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from ordering.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from ordering.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from ordering.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from ordering.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr<Y> & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from ordering.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from ordering.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr<Y> && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from ordering.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from ordering.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from ordering.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from ordering.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from ordering.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from ordering.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead. 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’ 23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’ 13 | BOOST_HEADER_DEPRECATED("<iterator>") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:29, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/sparse_ordering.hpp:24, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/cuthill_mckee_ordering.hpp:15, from ordering.cpp:3: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from ordering.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from ordering.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:36:1: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ ordering.cpp: In function ‘SEXPREC* BGL_min_degree_ordering(SEXP, SEXP, SEXP, SEXP)’: ordering.cpp:133:53: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs] 133 | typedef graph_traits<Graph_dd>::vertex_descriptor Vertex; | ^~~~~~ ordering.cpp: In function ‘SEXPREC* BGL_king_ordering(SEXP, SEXP, SEXP, SEXP)’: ordering.cpp:182:48: warning: variable ‘id’ set but not used [-Wunused-but-set-variable] 182 | property_map<Graph_dd, vertex_index_t>::type id = get(vertex_index, g); | ^~ ordering.cpp:176:53: warning: typedef ‘Vertex’ locally defined but not used [-Wunused-local-typedefs] 176 | typedef graph_traits<Graph_dd>::vertex_descriptor Vertex; | ^~~~~~ ordering.cpp: In function ‘SEXPREC* BGL_sloan_ordering(SEXP, SEXP, SEXP, SEXP, SEXP)’: ordering.cpp:232:47: warning: typedef ‘Pair’ locally defined but not used [-Wunused-local-typedefs] 232 | typedef std::pair<std::size_t, std::size_t> Pair; | ^~~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c planar.cpp -o planar.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from planar.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_<Pred>::************ | ^ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from planar.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from planar.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from planar.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from planar.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from planar.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from planar.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from planar.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from planar.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from planar.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr<Y> & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from planar.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from planar.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr<Y> && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from planar.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from planar.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from planar.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from planar.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from planar.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from planar.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead. 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’ 23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’ 13 | BOOST_HEADER_DEPRECATED("<iterator>") | ^~~~~~~~~~~~~~~~~~~~~~~ planar.cpp: In function ‘SEXPREC* planarFaceTraversal(SEXP, SEXP, SEXP)’: planar.cpp:161:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<long unsigned int>, std::allocator<std::vector<long unsigned int> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 161 | for ( int i = 0; i < v_vis.f_vis.size(); i++ ) | ~~^~~~~~~~~~~~~~~~~~~~ planar.cpp:165:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<long unsigned int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 165 | for ( int j = 0; j < v_vis.f_vis[i].size(); j++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~~ planar.cpp: In function ‘SEXPREC* planarCanonicalOrdering(SEXP, SEXP, SEXP)’: planar.cpp:256:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<long unsigned int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 256 | for ( int i = 0; i < ordering.size(); i++ ) | ~~^~~~~~~~~~~~~~~~~ planar.cpp:225:34: warning: variable ‘oi_end’ set but not used [-Wunused-but-set-variable] 225 | Vertex_Vec_t::iterator oi, oi_end = ordering.end(); | ^~~~~~ planar.cpp: In function ‘SEXPREC* isStraightLineDrawing(SEXP, SEXP, SEXP, SEXP)’: planar.cpp:369:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘boost::detail::adj_list_gen<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int>, boost::property<boost::edge_index_t, int> >, boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int>, boost::property<boost::edge_index_t, int>, boost::no_property, boost::listS>::config::vertices_size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 369 | for ( int i = 0, j = 0; i < num_vertices(g); i++ ) | ~~^~~~~~~~~~~~~~~~~ planar.cpp: In function ‘SEXPREC* isKuratowskiSubgraph(SEXP, SEXP, SEXP)’: planar.cpp:429:36: warning: variable ‘ki_end’ set but not used [-Wunused-but-set-variable] 429 | Edge_Vec_t::iterator ki, ki_end = kuratowski_edges.end(); | ^~~~~~ planar.cpp:461:6: warning: unused variable ‘i’ [-Wunused-variable] 461 | int i, j = 0; | ^ In file included from planar.cpp:6: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/chrobak_payne_drawing.hpp: In function ‘void boost::chrobak_payne_straight_line_drawing(const Graph&, PlanarEmbedding, ForwardIterator, ForwardIterator, GridPositionMap, VertexIndexMap) [with Graph = boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int>, boost::property<boost::edge_index_t, int> >; PlanarEmbedding = boost::iterator_property_map<__gnu_cxx::__normal_iterator<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int> >*, std::vector<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int> > > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int>, long unsigned int> >; ForwardIterator = __gnu_cxx::__normal_iterator<long unsigned int*, std::vector<long unsigned int> >; GridPositionMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator<coord_t*, std::vector<coord_t> >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int>, long unsigned int> >; VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int>, long unsigned int>]’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/chrobak_payne_drawing.hpp:207:22: warning: ‘next_to_rightmost’ may be used uninitialized in this function [-Wmaybe-uninitialized] 207 | vertex_t next_to_rightmost; | ^~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/boyer_myrvold_planar_test.hpp:12, from planar.cpp:3: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/planar_detail/boyer_myrvold_impl.hpp: In member function ‘void boost::boyer_myrvold_impl<Graph, VertexIndexMap, StoreOldHandlesPolicy, StoreEmbeddingPolicy>::extract_kuratowski_subgraph(OutputIterator, EdgeIndexMap) [with OutputIterator = std::back_insert_iterator<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int> > >; EdgeIndexMap = boost::adj_list_edge_property_map<boost::undirected_tag, int, const int&, long unsigned int, const boost::property<boost::edge_index_t, int>, boost::edge_index_t>; Graph = boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int>, boost::property<boost::edge_index_t, int> >; VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int>, long unsigned int>; StoreOldHandlesPolicy = boost::graph::detail::store_old_handles; StoreEmbeddingPolicy = boost::graph::detail::no_embedding]’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/planar_detail/boyer_myrvold_impl.hpp:1616:22: warning: ‘bicomp_root’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1616 | while (child != parent) | ~~~~~~^~~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:21, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/planar_detail/boyer_myrvold_impl.hpp:19, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/boyer_myrvold_planar_test.hpp:12, from planar.cpp:3: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/named_function_params.hpp: In static member function ‘static bool boost::maximum_cardinality_matching_verifier<Graph, MateMap, VertexIndexMap>::verify_matching(const Graph&, MateMap, VertexIndexMap) [with Graph = R_adjacency_list<boost::undirectedS, int>; MateMap = long unsigned int*; VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, long unsigned int>]’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/named_function_params.hpp:192:64: warning: ‘*((void*)& occ +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 192 | bgl_named_params(T v, const Base& b) : m_value(v), m_base(b) {} | ^ In file included from planar.cpp:11: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/max_cardinality_matching.hpp:778:52: note: ‘*((void*)& occ +16)’ was declared here 778 | detail::odd_components_counter< v_size_t > occ(num_odd_components); | ^~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c registerSigHandlers.cpp -o registerSigHandlers.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_<Pred>::************ | ^ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr<Y> & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr<Y> && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from registerSigHandlers.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead. 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’ 23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’ 13 | BOOST_HEADER_DEPRECATED("<iterator>") | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c shortestPath.cpp -o shortestPath.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from shortestPath.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_<Pred>::************ | ^ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from shortestPath.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from shortestPath.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from shortestPath.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from shortestPath.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from shortestPath.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from shortestPath.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from shortestPath.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from shortestPath.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from shortestPath.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr<Y> & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from shortestPath.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from shortestPath.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr<Y> && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from shortestPath.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from shortestPath.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from shortestPath.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from shortestPath.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from shortestPath.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from shortestPath.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead. 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’ 23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’ 13 | BOOST_HEADER_DEPRECATED("<iterator>") | ^~~~~~~~~~~~~~~~~~~~~~~ shortestPath.cpp: In function ‘SEXPREC* BGL_dijkstra_shortest_paths_D(SEXP, SEXP, SEXP, SEXP, SEXP)’: shortestPath.cpp:17:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs] 17 | typedef graph_traits < Graph_dd >::edge_descriptor Edge; | ^~~~ shortestPath.cpp: In function ‘SEXPREC* BGL_dag_shortest_paths(SEXP, SEXP, SEXP, SEXP, SEXP)’: shortestPath.cpp:136:60: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs] 136 | typedef graph_traits < Graph_dd >::edge_descriptor Edge; | ^~~~ shortestPath.cpp: In function ‘SEXPREC* BGL_floyd_warshall_all_pairs_shortest_paths_D(SEXP, SEXP, SEXP, SEXP)’: shortestPath.cpp:177:81: warning: typedef ‘Graph’ locally defined but not used [-Wunused-local-typedefs] 177 | property< edge_weight_t, double, property< edge_weight2_t, double > > > Graph; | ^~~~~ shortestPath.cpp:180:39: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs] 180 | typedef std::pair < int, int >Edge; | ^~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from shortestPath.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘bool boost::bellman_ford_shortest_paths(EdgeListGraph&, Size, WeightMap, PredecessorMap, DistanceMap, BinaryFunction, BinaryPredicate, BellmanFordVisitor) [with EdgeListGraph = boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_distance_t, double, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double> >, boost::no_property, boost::listS>; Size = long unsigned int; WeightMap = boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double> >, boost::edge_weight_t>; PredecessorMap = boost::dummy_property_map; DistanceMap = boost::vec_adj_list_vertex_property_map<boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_distance_t, double, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double> >, boost::no_property, boost::listS>, boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_distance_t, double, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double> >, boost::no_property, boost::listS>*, double, double&, boost::vertex_distance_t>; BinaryFunction = boost::closed_plus<double>; BinaryPredicate = std::less<double>; BellmanFordVisitor = boost::bellman_visitor<>]’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: ‘*((void*)& i +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 80 | if (edges BOOST_GRAPH_MEMBER first | ^~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28, from shortestPath.cpp:4: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:104:37: note: ‘*((void*)& i +48)’ was declared here 104 | typename GTraits::edge_iterator i, end; | ^ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from shortestPath.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘bool boost::bellman_ford_shortest_paths(EdgeListGraph&, Size, WeightMap, PredecessorMap, DistanceMap, BinaryFunction, BinaryPredicate, BellmanFordVisitor) [with EdgeListGraph = boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::no_property, boost::property<boost::edge_weight_t, double, boost::no_property> >; Size = int; WeightMap = boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>; PredecessorMap = long unsigned int*; DistanceMap = double*; BinaryFunction = boost::closed_plus<double>; BinaryPredicate = std::less<double>; BellmanFordVisitor = boost::bellman_visitor<>]’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: ‘*((void*)& i +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 80 | if (edges BOOST_GRAPH_MEMBER first | ^~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28, from shortestPath.cpp:4: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:104:37: note: ‘*((void*)& i +48)’ was declared here 104 | typename GTraits::edge_iterator i, end; | ^ In file included from RBGL.hpp:17, from shortestPath.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:129:65: warning: ‘*((void*)& i +40)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 129 | inline const T& get(const T* pa, std::ptrdiff_t k) { return pa[k]; } | ~~^ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28, from shortestPath.cpp:4: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:104:37: note: ‘*((void*)& i +40)’ was declared here 104 | typename GTraits::edge_iterator i, end; | ^ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:104:37: warning: ‘*((void*)(& i)+32).__gnu_cxx::__normal_iterator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >::_M_current’ may be used uninitialized in this function [-Wmaybe-uninitialized] In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from shortestPath.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘bool boost::floyd_warshall_all_pairs_shortest_paths(const VertexAndEdgeListGraph&, DistanceMatrix&, const WeightMap&, const BinaryPredicate&, const BinaryFunction&, const Infinity&, const Zero&) [with VertexAndEdgeListGraph = R_adjacency_list<boost::directedS, double>; DistanceMatrix = Basic2DMatrix<double>; WeightMap = boost::adj_list_edge_property_map<boost::directed_tag, double, const double&, long unsigned int, const boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>; BinaryPredicate = std::less<double>; BinaryFunction = boost::closed_plus<double>; Infinity = double; Zero = double]’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: ‘*((void*)& first +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 80 | if (edges BOOST_GRAPH_MEMBER first | ^~ In file included from shortestPath.cpp:7: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/floyd_warshall_shortest.hpp:101:68: note: ‘*((void*)& first +48)’ was declared here 101 | typename graph_traits< VertexAndEdgeListGraph >::edge_iterator first, last; | ^~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/floyd_warshall_shortest.hpp:113:14: warning: ‘*((void*)& first +40)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 113 | if (d[source(*first, g)][target(*first, g)] != inf) | ~^ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from shortestPath.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘SEXPREC* BGL_bellman_ford_shortest_paths(SEXP, SEXP, SEXP, SEXP, SEXP)’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: ‘*((void*)& ei +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 80 | if (edges BOOST_GRAPH_MEMBER first | ^~ shortestPath.cpp:101:50: note: ‘*((void*)& ei +48)’ was declared here 101 | graph_traits< EdgeGraph >::edge_iterator ei, ei_end; | ^~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from shortestPath.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘bool boost::johnson_all_pairs_shortest_paths(VertexAndEdgeListGraph&, DistanceMatrix&, VertexID, Weight, const BinaryPredicate&, const BinaryFunction&, const Infinity&, DistanceZero) [with VertexAndEdgeListGraph = R_adjacency_list<boost::directedS, double>; DistanceMatrix = Basic2DMatrix<double>; VertexID = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, long unsigned int>; Weight = boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>; BinaryPredicate = std::less<double>; BinaryFunction = boost::closed_plus<double>; Infinity = double; DistanceZero = double]’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: ‘*((void*)& e +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 80 | if (edges BOOST_GRAPH_MEMBER first | ^~ In file included from shortestPath.cpp:4: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:101:37: note: ‘*((void*)& e +48)’ was declared here 101 | typename Traits2::edge_iterator e, e_end; | ^ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_array.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/d_ary_heap.hpp:20, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/named_function_params.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/dijkstra_shortest_paths.hpp:20, from shortestPath.cpp:3: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_array.hpp:201:18: warning: ‘*((void*)& e +40)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 201 | return px[i]; | ~~^ In file included from shortestPath.cpp:4: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:101:37: note: ‘*((void*)& e +40)’ was declared here 101 | typename Traits2::edge_iterator e, e_end; | ^ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:101:37: warning: ‘*((void*)(& e)+32).__gnu_cxx::__normal_iterator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double> > >*, std::vector<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double> > >, std::allocator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double> > > > > >::_M_current’ may be used uninitialized in this function [-Wmaybe-uninitialized] In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from shortestPath.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: ‘*((void*)& e +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 80 | if (edges BOOST_GRAPH_MEMBER first | ^~ In file included from shortestPath.cpp:4: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:84:41: note: ‘*((void*)& e +48)’ was declared here 84 | typename Traits1::edge_iterator e, e_end; | ^ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:89:41: warning: ‘*((void*)& e +40)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 89 | boost::tie(e2, z) = add_edge( | ~~~~~~~~^ 90 | get(id1, source(*e, g1)) + 1, get(id1, target(*e, g1)) + 1, g2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:84:41: warning: ‘*((void*)(& e)+32).__gnu_cxx::__normal_iterator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >::_M_current’ may be used uninitialized in this function [-Wmaybe-uninitialized] 84 | typename Traits1::edge_iterator e, e_end; | ^ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c sna.cpp -o sna.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from sna.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_<Pred>::************ | ^ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from sna.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from sna.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from sna.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from sna.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from sna.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from sna.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from sna.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from sna.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from sna.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr<Y> & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from sna.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from sna.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr<Y> && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from sna.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from sna.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from sna.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from sna.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from sna.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from sna.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead. 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’ 23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’ 13 | BOOST_HEADER_DEPRECATED("<iterator>") | ^~~~~~~~~~~~~~~~~~~~~~~ sna.cpp: In function ‘SEXPREC* lambdaSets(SEXP, SEXP, SEXP, SEXP)’: sna.cpp:161:9: warning: variable ‘res_cap’ set but not used [-Wunused-but-set-variable] 161 | res_cap = get(edge_residual_capacity, flow_g); | ^~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from sna.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘bool boost::bellman_ford_shortest_paths(EdgeListGraph&, Size, WeightMap, PredecessorMap, DistanceMap, BinaryFunction, BinaryPredicate, BellmanFordVisitor) [with EdgeListGraph = boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_distance_t, double, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::no_property, boost::listS>; Size = long unsigned int; WeightMap = boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::edge_weight_t>; PredecessorMap = boost::dummy_property_map; DistanceMap = boost::vec_adj_list_vertex_property_map<boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_distance_t, double, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::no_property, boost::listS>, boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS, boost::property<boost::vertex_distance_t, double, boost::no_property>, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_weight2_t, double, boost::no_property> >, boost::no_property, boost::listS>*, double, double&, boost::vertex_distance_t>; BinaryFunction = boost::closed_plus<double>; BinaryPredicate = std::less<double>; BellmanFordVisitor = boost::bellman_visitor<>]’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: ‘*((void*)& i +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 80 | if (edges BOOST_GRAPH_MEMBER first | ^~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:28, from sna.cpp:3: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/bellman_ford_shortest_paths.hpp:104:37: note: ‘*((void*)& i +48)’ was declared here 104 | typename GTraits::edge_iterator i, end; | ^ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from RBGL.hpp:38, from sna.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘bool boost::johnson_all_pairs_shortest_paths(VertexAndEdgeListGraph&, DistanceMatrix&, VertexID, Weight, const BinaryPredicate&, const BinaryFunction&, const Infinity&, DistanceZero) [with VertexAndEdgeListGraph = R_adjacency_list<boost::undirectedS, double>; DistanceMatrix = Basic2DMatrix<double>; VertexID = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, long unsigned int>; Weight = boost::adj_list_edge_property_map<boost::undirected_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>; BinaryPredicate = std::less<double>; BinaryFunction = boost::closed_plus<double>; Infinity = double; DistanceZero = double]’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: ‘*((void*)& e +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 80 | if (edges BOOST_GRAPH_MEMBER first | ^~ In file included from sna.cpp:3: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:101:37: note: ‘*((void*)& e +48)’ was declared here 101 | typename Traits2::edge_iterator e, e_end; | ^ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/shared_array_property_map.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:27, from sna.cpp:3: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_array.hpp:201:18: warning: ‘*((void*)& e +40)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 201 | return px[i]; | ~~^ In file included from sna.cpp:3: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/johnson_all_pairs_shortest.hpp:101:37: note: ‘*((void*)& e +40)’ was declared here 101 | typename Traits2::edge_iterator e, e_end; | ^ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c transitive_closure.cpp -o transitive_closure.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:29, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:29, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:30, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:36:1: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/graph_traits.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_<Pred>::************ | ^ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:29, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:29, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:29, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:29, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr<Y> & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:29, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr<Y> && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:29, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/graph_concepts.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/depth_first_search.hpp:18, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/strong_components.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:29, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:30, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead. 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’ 23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’ 13 | BOOST_HEADER_DEPRECATED("<iterator>") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:21, from transitive_closure.cpp:16: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/bind.hpp:26, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind.hpp:29, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:34, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/transitive_closure.hpp:21, from transitive_closure.cpp:16: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘SEXPREC* BGL_transitive_closure_D(SEXP, SEXP, SEXP)’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adj_list_edge_iterator.hpp:80:13: warning: ‘*((void*)& ei +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 80 | if (edges BOOST_GRAPH_MEMBER first | ^~ transitive_closure.cpp:43:33: note: ‘*((void*)& ei +48)’ was declared here 43 | Graph_dd::edge_iterator ei, e_end; | ^~ transitive_closure.cpp:46:33: warning: ‘*((void*)& ei +40)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 46 | INTEGER(eList)[i++] = source(*ei, TC); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c wavefront.cpp -o wavefront.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:22, from RBGL.hpp:17, from wavefront.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_<Pred>::************ | ^ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from wavefront.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from wavefront.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from wavefront.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from wavefront.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from wavefront.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from wavefront.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from wavefront.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from wavefront.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from wavefront.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr<Y> & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from wavefront.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from wavefront.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr<Y> && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from wavefront.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from wavefront.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from wavefront.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from wavefront.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from wavefront.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602, from RBGL.hpp:17, from wavefront.cpp:1: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead. 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’ 23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’ 13 | BOOST_HEADER_DEPRECATED("<iterator>") | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o RBGL.so bbc.o cliques.o clusteringCoef.o dominatorTree.o edmonds_optimum_branching.o hcs.o incrConnComp.o interfaces.o minST.o mincut.o ordering.o planar.o registerSigHandlers.o shortestPath.o sna.o transitive_closure.o wavefront.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-RBGL/00new/RBGL/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ‘RBGL.Rnw’ ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (RBGL)
RBGL.Rcheck/tests/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > BiocGenerics:::testPackage("RBGL") Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min RUNIT TEST PROTOCOL -- Thu Oct 14 11:14:48 2021 *********************************************** Number of test functions: 1 Number of errors: 0 Number of failures: 0 1 Test Suite : RBGL RUnit Tests - 1 test function, 0 errors, 0 failures Number of test functions: 1 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 0.658 0.041 0.680
RBGL.Rcheck/RBGL-Ex.timings
name | user | system | elapsed | |
FileDep | 0.291 | 0.039 | 0.332 | |
astarSearch | 0.043 | 0.000 | 0.043 | |
bandwidth | 0.01 | 0.00 | 0.01 | |
bellman.ford.sp | 0.028 | 0.003 | 0.033 | |
bfs | 0.016 | 0.001 | 0.017 | |
biConnComp | 0.006 | 0.000 | 0.007 | |
boyerMyrvoldPlanarityTest | 0.005 | 0.000 | 0.007 | |
chrobakPayneStraightLineDrawing | 0.020 | 0.006 | 0.026 | |
clusteringCoef | 0.004 | 0.000 | 0.005 | |
clusteringCoefAppr | 0.004 | 0.000 | 0.005 | |
coloring | 0.003 | 0.000 | 0.004 | |
connectedComp | 0.005 | 0.004 | 0.010 | |
dag.sp | 0.005 | 0.000 | 0.005 | |
dijkstra.sp | 0.016 | 0.001 | 0.016 | |
dominatorTree | 0.003 | 0.000 | 0.004 | |
edgeConn | 0.003 | 0.000 | 0.004 | |
edmondsMaxCardinalityMatching | 0.002 | 0.004 | 0.007 | |
edmondsOptimumBranching | 0.004 | 0.000 | 0.004 | |
extractPath | 0.000 | 0.002 | 0.002 | |
floyd.warshall.all.pairs.sp | 0.003 | 0.002 | 0.005 | |
gprofile | 0.003 | 0.000 | 0.003 | |
graphGenerator | 0.001 | 0.000 | 0.000 | |
highlyConnSG | 0.002 | 0.003 | 0.005 | |
incrConnComp | 0.002 | 0.002 | 0.004 | |
is.triangulated | 0.005 | 0.002 | 0.006 | |
isKuratowskiSubgraph | 0.003 | 0.001 | 0.005 | |
isStraightLineDrawing | 0.003 | 0.002 | 0.005 | |
isomorphism | 0.006 | 0.000 | 0.006 | |
johnson.all.pairs.sp | 0.004 | 0.000 | 0.005 | |
kCliques | 0.004 | 0.000 | 0.004 | |
kCores | 0.028 | 0.000 | 0.028 | |
lambdaSets | 0.009 | 0.000 | 0.010 | |
layout | 0.000 | 0.000 | 0.001 | |
makeBiconnectedPlanar | 0.008 | 0.000 | 0.008 | |
makeConnected | 0.005 | 0.000 | 0.005 | |
makeMaximalPlanar | 0.006 | 0.000 | 0.005 | |
maxClique | 0.006 | 0.001 | 0.007 | |
maxFlow | 0.004 | 0.003 | 0.006 | |
minCut | 0.004 | 0.000 | 0.003 | |
mstree.kruskal | 0.012 | 0.000 | 0.012 | |
mstree.prim | 0.001 | 0.003 | 0.004 | |
ordering | 0.005 | 0.001 | 0.006 | |
planarCanonicalOrdering | 0.003 | 0.000 | 0.004 | |
planarFaceTraversal | 0.008 | 0.000 | 0.007 | |
removeSelfLoops | 0.002 | 0.004 | 0.005 | |
separates | 0.006 | 0.000 | 0.006 | |
sp.between | 0.011 | 0.004 | 0.013 | |
strongComp | 0.007 | 0.000 | 0.007 | |
transClosure | 0.004 | 0.000 | 0.005 | |
transitivity | 0.003 | 0.000 | 0.003 | |
tsort | 0.003 | 0.000 | 0.003 | |
wavefront | 0.003 | 0.000 | 0.004 | |