| Back to Multiple platform build/check report for BioC 3.13 |
|
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 |
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###
### 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
###
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* 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
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##############################################################################
###
### 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 | |