| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-09 11:40:46 -0400 (Thu, 09 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4748 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4484 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4514 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 596/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Tilo Buschmann
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the DNABarcodes package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DNABarcodes.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: DNABarcodes |
| Version: 1.34.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:DNABarcodes.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings DNABarcodes_1.34.0.tar.gz |
| StartedAt: 2024-05-09 06:55:00 -0000 (Thu, 09 May 2024) |
| EndedAt: 2024-05-09 06:55:57 -0000 (Thu, 09 May 2024) |
| EllapsedTime: 57.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DNABarcodes.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:DNABarcodes.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings DNABarcodes_1.34.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/DNABarcodes.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DNABarcodes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DNABarcodes’ version ‘1.34.0’
* 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 ‘DNABarcodes’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... OK
Not all R platforms support C++17
* checking installed package size ... NOTE
installed size is 9.4Mb
sub-directories of 1Mb or more:
libs 9.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Problems with news in ‘NEWS’:
Cannot process chunk/lines:
First development version for introduction to Bioconductor
Cannot process chunk/lines:
This is the first public release.
* checking code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
create.dnabarcodes 5.852 0.025 3.159
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/DNABarcodes.Rcheck/00check.log’
for details.
DNABarcodes.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL DNABarcodes
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘DNABarcodes’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++17
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c DNABarcodes_init.c -o DNABarcodes_init.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c analyse_barcodes.cpp -o analyse_barcodes.o
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from analyse_barcodes.cpp:10:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from analyse_barcodes.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from analyse_barcodes.cpp:10:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from analyse_barcodes.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from analyse_barcodes.cpp:10:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
508 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from analyse_barcodes.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from analyse_barcodes.cpp:10:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
521 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from analyse_barcodes.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from analyse_barcodes.cpp:10:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
604 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from analyse_barcodes.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from analyse_barcodes.cpp:10:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
613 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from analyse_barcodes.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from analyse_barcodes.cpp:10:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
615 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from analyse_barcodes.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c barcode_set_distances.cpp -o barcode_set_distances.o
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from barcode_set_distances.cpp:10:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from barcode_set_distances.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from barcode_set_distances.cpp:10:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from barcode_set_distances.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from barcode_set_distances.cpp:10:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
508 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from barcode_set_distances.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from barcode_set_distances.cpp:10:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
521 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from barcode_set_distances.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from barcode_set_distances.cpp:10:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
604 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from barcode_set_distances.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from barcode_set_distances.cpp:10:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
613 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from barcode_set_distances.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from barcode_set_distances.cpp:10:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
615 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from barcode_set_distances.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c cachedistance.cpp -o cachedistance.o
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from cachedistance.cpp:7:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from cachedistance.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from cachedistance.cpp:7:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from cachedistance.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from cachedistance.cpp:7:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
508 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from cachedistance.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from cachedistance.cpp:7:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
521 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from cachedistance.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from cachedistance.cpp:7:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
604 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from cachedistance.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from cachedistance.cpp:7:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
613 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from cachedistance.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from cachedistance.cpp:7:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
615 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from cachedistance.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/apply.hpp:24,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array_optimization.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array_wrapper.hpp:21,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array.hpp:26,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/ublas/storage.hpp:22,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/ublas/vector.hpp:21,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/ublas/matrix.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/ublas/symmetric.hpp:16,
from cachedistance.h:16,
from cachedistance.cpp:8:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp: At global scope:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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>::************
| ^
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c chromosome.cpp -o chromosome.o
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from chromosome.h:6,
from chromosome.cpp:3:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from distance.h:8,
from chromosome.h:6,
from chromosome.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from chromosome.h:6,
from chromosome.cpp:3:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from distance.h:8,
from chromosome.h:6,
from chromosome.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from chromosome.h:6,
from chromosome.cpp:3:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
508 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from distance.h:8,
from chromosome.h:6,
from chromosome.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from chromosome.h:6,
from chromosome.cpp:3:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
521 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from distance.h:8,
from chromosome.h:6,
from chromosome.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from chromosome.h:6,
from chromosome.cpp:3:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
604 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from distance.h:8,
from chromosome.h:6,
from chromosome.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from chromosome.h:6,
from chromosome.cpp:3:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
613 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from distance.h:8,
from chromosome.h:6,
from chromosome.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from chromosome.h:6,
from chromosome.cpp:3:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
615 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from distance.h:8,
from chromosome.h:6,
from chromosome.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/foreach.hpp:76,
from chromosome.cpp:15:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp: At global scope:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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>::************
| ^
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c code_falsification.cpp -o code_falsification.o
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from chromosome.h:6,
from code_falsification.cpp:11:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from code_falsification.cpp:5:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from chromosome.h:6,
from code_falsification.cpp:11:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from code_falsification.cpp:5:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from chromosome.h:6,
from code_falsification.cpp:11:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
508 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from code_falsification.cpp:5:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from chromosome.h:6,
from code_falsification.cpp:11:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
521 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from code_falsification.cpp:5:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from chromosome.h:6,
from code_falsification.cpp:11:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
604 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from code_falsification.cpp:5:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from chromosome.h:6,
from code_falsification.cpp:11:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
613 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from code_falsification.cpp:5:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from chromosome.h:6,
from code_falsification.cpp:11:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
615 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from code_falsification.cpp:5:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/foreach.hpp:76,
from code_falsification.cpp:26:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp: At global scope:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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>::************
| ^
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c conway.cpp -o conway.o
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from conway.h:8,
from conway.cpp:3:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from distance.h:8,
from conway.h:8,
from conway.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from conway.h:8,
from conway.cpp:3:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from distance.h:8,
from conway.h:8,
from conway.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from conway.h:8,
from conway.cpp:3:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
508 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from distance.h:8,
from conway.h:8,
from conway.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from conway.h:8,
from conway.cpp:3:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
521 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from distance.h:8,
from conway.h:8,
from conway.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from conway.h:8,
from conway.cpp:3:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
604 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from distance.h:8,
from conway.h:8,
from conway.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from conway.h:8,
from conway.cpp:3:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
613 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from distance.h:8,
from conway.h:8,
from conway.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from conway.h:8,
from conway.cpp:3:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
615 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from distance.h:8,
from conway.h:8,
from conway.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/foreach.hpp:76,
from conway.cpp:11:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp: At global scope:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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>::************
| ^
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c create_distance_func.cpp -o create_distance_func.o
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from create_distance_func.cpp:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from create_distance_func.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from create_distance_func.cpp:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from create_distance_func.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from create_distance_func.cpp:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
508 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from create_distance_func.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from create_distance_func.cpp:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
521 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from create_distance_func.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from create_distance_func.cpp:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
604 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from create_distance_func.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from create_distance_func.cpp:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
613 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from create_distance_func.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from create_distance_func.cpp:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
615 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from create_distance_func.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/apply.hpp:24,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array_optimization.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array_wrapper.hpp:21,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array.hpp:26,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/ublas/storage.hpp:22,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/ublas/vector.hpp:21,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/ublas/matrix.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/ublas/symmetric.hpp:16,
from cachedistance.h:16,
from create_distance_func.cpp:9:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp: At global scope:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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>::************
| ^
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c create_dnabarcodes.cpp -o create_dnabarcodes.o
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/foreach.hpp:76,
from create_dnabarcodes.cpp:13:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from create_dnabarcodes.cpp:17:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from create_dnabarcodes.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from create_dnabarcodes.cpp:17:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from create_dnabarcodes.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from create_dnabarcodes.cpp:17:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
508 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from create_dnabarcodes.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from create_dnabarcodes.cpp:17:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
521 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from create_dnabarcodes.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from create_dnabarcodes.cpp:17:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
604 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from create_dnabarcodes.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from create_dnabarcodes.cpp:17:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
613 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from create_dnabarcodes.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from create_dnabarcodes.cpp:17:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
615 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from create_dnabarcodes.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/graph/adjacency_list.hpp:22,
from maxclique.h:12,
from maxclique_pattabiraman_heuristic.h:10,
from create_dnabarcodes.cpp:26:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
75 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from create_dnabarcodes.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c create_pool.cpp -o create_pool.o
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/foreach.hpp:76,
from create_pool.cpp:6:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from create_pool.cpp:12:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from create_pool.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from create_pool.cpp:12:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from create_pool.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from create_pool.cpp:12:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
508 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from create_pool.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from create_pool.cpp:12:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
521 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from create_pool.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from create_pool.cpp:12:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
604 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from create_pool.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from create_pool.cpp:12:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
613 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from create_pool.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from create_pool.cpp:12:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
615 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from create_pool.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c demultiplex.cpp -o demultiplex.o
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from demultiplex.cpp:9:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from demultiplex.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from demultiplex.cpp:9:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from demultiplex.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from demultiplex.cpp:9:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
508 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from demultiplex.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from demultiplex.cpp:9:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
521 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from demultiplex.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from demultiplex.cpp:9:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
604 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from demultiplex.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from demultiplex.cpp:9:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
613 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from demultiplex.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from demultiplex.cpp:9:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
615 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from demultiplex.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c distance_for_R.cpp -o distance_for_R.o
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from distance_for_R.cpp:9:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from distance_for_R.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from distance_for_R.cpp:9:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from distance_for_R.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from distance_for_R.cpp:9:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
508 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from distance_for_R.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from distance_for_R.cpp:9:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
521 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from distance_for_R.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from distance_for_R.cpp:9:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
604 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from distance_for_R.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from distance_for_R.cpp:9:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
613 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from distance_for_R.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from distance_for_R.cpp:9:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
615 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from distance_for_R.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c genericchromosome.cpp -o genericchromosome.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c greedyevolution.cpp -o greedyevolution.o
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from greedyevolution.h:8,
from greedyevolution.cpp:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from greedyevolution.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from greedyevolution.h:8,
from greedyevolution.cpp:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from greedyevolution.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from greedyevolution.h:8,
from greedyevolution.cpp:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
508 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from greedyevolution.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from greedyevolution.h:8,
from greedyevolution.cpp:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
521 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from greedyevolution.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from greedyevolution.h:8,
from greedyevolution.cpp:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
604 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from greedyevolution.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from greedyevolution.h:8,
from greedyevolution.cpp:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
613 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from greedyevolution.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from greedyevolution.h:8,
from greedyevolution.cpp:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
615 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from greedyevolution.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/foreach.hpp:76,
from greedyevolution.cpp:12:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp: At global scope:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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>::************
| ^
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c hammingdistance.cpp -o hammingdistance.o
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from hammingdistance.cpp:7:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from hammingdistance.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from hammingdistance.cpp:7:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from hammingdistance.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from hammingdistance.cpp:7:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
508 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from hammingdistance.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from hammingdistance.cpp:7:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
521 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from hammingdistance.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from hammingdistance.cpp:7:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
604 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from hammingdistance.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from hammingdistance.cpp:7:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
613 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from hammingdistance.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from hammingdistance.cpp:7:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
615 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from hammingdistance.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c helpers.cpp -o helpers.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c levenshteindistance.cpp -o levenshteindistance.o
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from levenshteindistance.cpp:7:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from levenshteindistance.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from levenshteindistance.cpp:7:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from levenshteindistance.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from levenshteindistance.cpp:7:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
508 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from levenshteindistance.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from levenshteindistance.cpp:7:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
521 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from levenshteindistance.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from levenshteindistance.cpp:7:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
604 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from levenshteindistance.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from levenshteindistance.cpp:7:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
613 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from levenshteindistance.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from levenshteindistance.cpp:7:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
615 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from levenshteindistance.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c maxclique_pattabiraman_heuristic.cpp -o maxclique_pattabiraman_heuristic.o
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/graph/adjacency_list.hpp:22,
from maxclique.h:12,
from maxclique_pattabiraman_heuristic.h:10,
from maxclique_pattabiraman_heuristic.cpp:6:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/scoped_ptr.hpp:75:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
75 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from maxclique_pattabiraman_heuristic.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/graph/graph_traits.hpp:25,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/graph/adjacency_list.hpp:24,
from maxclique.h:12,
from maxclique_pattabiraman_heuristic.h:10,
from maxclique_pattabiraman_heuristic.cpp:6:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/property_map/property_map.hpp:598,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
from maxclique.h:12,
from maxclique_pattabiraman_heuristic.h:10,
from maxclique_pattabiraman_heuristic.cpp:6:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from maxclique_pattabiraman_heuristic.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/property_map/property_map.hpp:598,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
from maxclique.h:12,
from maxclique_pattabiraman_heuristic.h:10,
from maxclique_pattabiraman_heuristic.cpp:6:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from maxclique_pattabiraman_heuristic.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/property_map/property_map.hpp:598,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
from maxclique.h:12,
from maxclique_pattabiraman_heuristic.h:10,
from maxclique_pattabiraman_heuristic.cpp:6:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
508 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from maxclique_pattabiraman_heuristic.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/property_map/property_map.hpp:598,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
from maxclique.h:12,
from maxclique_pattabiraman_heuristic.h:10,
from maxclique_pattabiraman_heuristic.cpp:6:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
521 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from maxclique_pattabiraman_heuristic.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/property_map/property_map.hpp:598,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
from maxclique.h:12,
from maxclique_pattabiraman_heuristic.h:10,
from maxclique_pattabiraman_heuristic.cpp:6:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
604 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from maxclique_pattabiraman_heuristic.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/property_map/property_map.hpp:598,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
from maxclique.h:12,
from maxclique_pattabiraman_heuristic.h:10,
from maxclique_pattabiraman_heuristic.cpp:6:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
613 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from maxclique_pattabiraman_heuristic.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/property_map/property_map.hpp:598,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
from maxclique.h:12,
from maxclique_pattabiraman_heuristic.h:10,
from maxclique_pattabiraman_heuristic.cpp:6:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
615 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from maxclique_pattabiraman_heuristic.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c phaseshiftdist.cpp -o phaseshiftdist.o
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from phaseshiftdist.cpp:10:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from phaseshiftdist.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from phaseshiftdist.cpp:10:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from phaseshiftdist.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from phaseshiftdist.cpp:10:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
508 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from phaseshiftdist.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from phaseshiftdist.cpp:10:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
521 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from phaseshiftdist.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from phaseshiftdist.cpp:10:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
604 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from phaseshiftdist.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from phaseshiftdist.cpp:10:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
613 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from phaseshiftdist.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from phaseshiftdist.cpp:10:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
615 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from phaseshiftdist.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/foreach.hpp:76,
from phaseshiftdist.cpp:23:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp: At global scope:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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>::************
| ^
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c sequence.cpp -o sequence.o
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/foreach.hpp:76,
from sequence.cpp:3:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from sequence.cpp:13:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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++/10.3.1/memory:83,
from sequence.cpp:10:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from sequence.cpp:13:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/memory:83,
from sequence.cpp:10:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from sequence.cpp:13:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
508 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/memory:83,
from sequence.cpp:10:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from sequence.cpp:13:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
521 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/memory:83,
from sequence.cpp:10:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from sequence.cpp:13:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
604 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/memory:83,
from sequence.cpp:10:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from sequence.cpp:13:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
613 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/memory:83,
from sequence.cpp:10:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from sequence.cpp:13:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
615 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/memory:83,
from sequence.cpp:10:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c sequencelevenshteindistance.cpp -o sequencelevenshteindistance.o
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from sequencelevenshteindistance.cpp:3:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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++/10.3.1/memory:83,
from sequence.h:13,
from sequencelevenshteindistance.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from sequencelevenshteindistance.cpp:3:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/memory:83,
from sequence.h:13,
from sequencelevenshteindistance.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from sequencelevenshteindistance.cpp:3:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
508 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/memory:83,
from sequence.h:13,
from sequencelevenshteindistance.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from sequencelevenshteindistance.cpp:3:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
521 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/memory:83,
from sequence.h:13,
from sequencelevenshteindistance.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from sequencelevenshteindistance.cpp:3:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
604 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/memory:83,
from sequence.h:13,
from sequencelevenshteindistance.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from sequencelevenshteindistance.cpp:3:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
613 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/memory:83,
from sequence.h:13,
from sequencelevenshteindistance.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from sequencelevenshteindistance.cpp:3:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
615 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/memory:83,
from sequence.h:13,
from sequencelevenshteindistance.cpp:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c sequencepool.cpp -o sequencepool.o
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from sequencepool.cpp:11:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from sequencepool.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from sequencepool.cpp:11:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from sequencepool.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from sequencepool.cpp:11:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
508 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from sequencepool.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from sequencepool.cpp:11:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
521 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from sequencepool.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from sequencepool.cpp:11:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
604 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from sequencepool.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from sequencepool.cpp:11:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
613 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from sequencepool.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from sequence.h:19,
from distance.h:14,
from sequencepool.cpp:11:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
615 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
from sequencepool.cpp:4:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/foreach.hpp:76,
from sequencepool.cpp:16:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp: At global scope:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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>::************
| ^
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o DNABarcodes.so DNABarcodes_init.o RcppExports.o analyse_barcodes.o barcode_set_distances.o cachedistance.o chromosome.o code_falsification.o conway.o create_distance_func.o create_dnabarcodes.o create_pool.o demultiplex.o distance_for_R.o genericchromosome.o greedyevolution.o hammingdistance.o helpers.o levenshteindistance.o maxclique_pattabiraman_heuristic.o phaseshiftdist.o sequence.o sequencelevenshteindistance.o sequencepool.o -fopenmp -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-DNABarcodes/00new/DNABarcodes/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
Package 'DNABarcodes' is deprecated and will be removed from
Bioconductor version 3.20
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
Package 'DNABarcodes' is deprecated and will be removed from
Bioconductor version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (DNABarcodes)
DNABarcodes.Rcheck/DNABarcodes-Ex.timings
| name | user | system | elapsed | |
| DNABarcodes-package | 1.207 | 0.005 | 0.698 | |
| analyse.barcodes | 0.013 | 0.000 | 0.012 | |
| barcode.set.distances | 0.026 | 0.000 | 0.023 | |
| create.dnabarcodes | 5.852 | 0.025 | 3.159 | |
| create.pool | 0.024 | 0.012 | 0.028 | |
| demultiplex | 1.625 | 0.048 | 1.730 | |
| distance | 0.000 | 0.000 | 0.001 | |