##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL seqbias
###
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##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘seqbias’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c sam.c -o sam.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c bam_plbuf.c -o bam_plbuf.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c bam_aux.c -o bam_aux.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c common.c -o common.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c miscmath.c -o miscmath.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c pos_table.c -o pos_table.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c kmer_matrix.cpp -o kmer_matrix.o
In file included from yaml-cpp/yaml.h:9:0,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
./yaml-cpp/parser.h:45:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Scanner> m_pScanner;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:9:0,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
./yaml-cpp/parser.h:46:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Directives> m_pDirectives;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
./yaml-cpp/iterator.h:20:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
./yaml-cpp/iterator.h:36:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:10:0,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
./yaml-cpp/node.h:43:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:10:0,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
./yaml-cpp/node.h:115:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:13:0,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
./yaml-cpp/emitter.h:98:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr <EmitterState> m_pState;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c logger.cpp -o logger.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c motif.cpp -o motif.o
In file included from yaml-cpp/yaml.h:9:0,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
./yaml-cpp/parser.h:45:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Scanner> m_pScanner;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:9:0,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
./yaml-cpp/parser.h:46:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Directives> m_pDirectives;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
./yaml-cpp/iterator.h:20:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
./yaml-cpp/iterator.h:36:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:10:0,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
./yaml-cpp/node.h:43:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:10:0,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
./yaml-cpp/node.h:115:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:13:0,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
./yaml-cpp/emitter.h:98:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr <EmitterState> m_pState;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c seqbias.cpp -o seqbias.o
In file included from yaml-cpp/yaml.h:9:0,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
./yaml-cpp/parser.h:45:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Scanner> m_pScanner;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:9:0,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
./yaml-cpp/parser.h:46:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Directives> m_pDirectives;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
./yaml-cpp/iterator.h:20:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
./yaml-cpp/iterator.h:36:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:10:0,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
./yaml-cpp/node.h:43:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:10:0,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
./yaml-cpp/node.h:115:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:13:0,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
./yaml-cpp/emitter.h:98:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr <EmitterState> m_pState;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c sequencing_bias.cpp -o sequencing_bias.o
In file included from yaml-cpp/yaml.h:9:0,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
./yaml-cpp/parser.h:45:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Scanner> m_pScanner;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:9:0,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
./yaml-cpp/parser.h:46:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Directives> m_pDirectives;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
./yaml-cpp/iterator.h:20:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
./yaml-cpp/iterator.h:36:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:10:0,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
./yaml-cpp/node.h:43:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:10:0,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
./yaml-cpp/node.h:115:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:13:0,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
./yaml-cpp/emitter.h:98:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr <EmitterState> m_pState;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c twobitseq.cpp -o twobitseq.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/aliasmanager.cpp -o yaml-cpp/aliasmanager.o
In file included from ./yaml-cpp/node.h:12:0,
from yaml-cpp/aliasmanager.cpp:2:
./yaml-cpp/iterator.h:20:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/aliasmanager.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
from yaml-cpp/aliasmanager.cpp:2:
./yaml-cpp/iterator.h:36:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/aliasmanager.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/aliasmanager.cpp:2:0:
./yaml-cpp/node.h:43:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/aliasmanager.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/aliasmanager.cpp:2:0:
./yaml-cpp/node.h:115:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/aliasmanager.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/directives.cpp -o yaml-cpp/directives.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/emitfromevents.cpp -o yaml-cpp/emitfromevents.o
In file included from yaml-cpp/emitfromevents.cpp:2:0:
./yaml-cpp/emitter.h:98:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr <EmitterState> m_pState;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitfromevents.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
In file included from yaml-cpp/emitter.cpp:1:0:
./yaml-cpp/emitter.h:98:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr <EmitterState> m_pState;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/emitterstate.h:9:0,
from yaml-cpp/emitter.cpp:2:
yaml-cpp/ptr_stack.h:29:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
void push(std::auto_ptr<T> t) {
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/emitterstate.h:9:0,
from yaml-cpp/emitter.cpp:2:
yaml-cpp/ptr_stack.h:33:7: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<T> pop() {
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/emitterstate.h:9:0,
from yaml-cpp/emitter.cpp:2:
yaml-cpp/ptr_stack.h: In member function ‘std::auto_ptr<_Up> ptr_stack<T>::pop()’:
yaml-cpp/ptr_stack.h:34:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<T> t(m_data.back());
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/emitterstate.h:10:0,
from yaml-cpp/emitter.cpp:2:
yaml-cpp/setting.h: At global scope:
yaml-cpp/setting.h:24:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr <SettingChangeBase> set(const T& value);
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/emitterstate.h:10:0,
from yaml-cpp/emitter.cpp:2:
yaml-cpp/setting.h:59:14: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
inline std::auto_ptr <SettingChangeBase> Setting<T>::set(const T& value) {
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/emitterstate.h:10:0,
from yaml-cpp/emitter.cpp:2:
yaml-cpp/setting.h: In member function ‘std::auto_ptr<YAML::SettingChangeBase> YAML::Setting<T>::set(const T&)’:
yaml-cpp/setting.h:60:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr <SettingChangeBase> pChange(new SettingChange<T> (this));
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/emitterstate.h:10:0,
from yaml-cpp/emitter.cpp:2:
yaml-cpp/setting.h: At global scope:
yaml-cpp/setting.h:84:18: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
void push(std::auto_ptr <SettingChangeBase> pSettingChange) {
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
In file included from yaml-cpp/emitterstate.h:9:0,
from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/ptr_stack.h:29:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
void push(std::auto_ptr<T> t) {
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/emitterstate.h:9:0,
from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/ptr_stack.h:33:7: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<T> pop() {
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/emitterstate.h:9:0,
from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/ptr_stack.h: In member function ‘std::auto_ptr<T> ptr_stack<T>::pop()’:
yaml-cpp/ptr_stack.h:34:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<T> t(m_data.back());
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/emitterstate.h:10:0,
from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/setting.h: At global scope:
yaml-cpp/setting.h:24:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr <SettingChangeBase> set(const T& value);
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/emitterstate.h:10:0,
from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/setting.h:59:14: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
inline std::auto_ptr <SettingChangeBase> Setting<T>::set(const T& value) {
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/emitterstate.h:10:0,
from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/setting.h: In member function ‘std::auto_ptr<YAML::SettingChangeBase> YAML::Setting<T>::set(const T&)’:
yaml-cpp/setting.h:60:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr <SettingChangeBase> pChange(new SettingChange<T> (this));
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/emitterstate.h:10:0,
from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/setting.h: At global scope:
yaml-cpp/setting.h:84:18: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
void push(std::auto_ptr <SettingChangeBase> pSettingChange) {
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
yaml-cpp/emitterstate.cpp: In member function ‘void YAML::EmitterState::BeginGroup(YAML::GROUP_TYPE)’:
yaml-cpp/emitterstate.cpp:51:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Group> pGroup(new Group(type));
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
yaml-cpp/emitterstate.cpp: In member function ‘void YAML::EmitterState::EndGroup(YAML::GROUP_TYPE)’:
yaml-cpp/emitterstate.cpp:71:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Group> pFinishedGroup = m_groups.pop();
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
In file included from ./yaml-cpp/node.h:12:0,
from yaml-cpp/iterator.cpp:1:
./yaml-cpp/iterator.h:20:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/iterator.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
from yaml-cpp/iterator.cpp:1:
./yaml-cpp/iterator.h:36:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/iterator.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/iterator.cpp:1:0:
./yaml-cpp/node.h:43:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/iterator.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/iterator.cpp:1:0:
./yaml-cpp/node.h:115:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/iterator.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
yaml-cpp/iterator.cpp:11:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
Iterator::Iterator(std::auto_ptr<IterPriv> pData): m_pData(pData)
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/iterator.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/nodebuilder.cpp -o yaml-cpp/nodebuilder.o
In file included from ./yaml-cpp/node.h:12:0,
from yaml-cpp/nodebuilder.cpp:3:
./yaml-cpp/iterator.h:20:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from yaml-cpp/nodebuilder.h:10,
from yaml-cpp/nodebuilder.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
from yaml-cpp/nodebuilder.cpp:3:
./yaml-cpp/iterator.h:36:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from yaml-cpp/nodebuilder.h:10,
from yaml-cpp/nodebuilder.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/nodebuilder.cpp:3:0:
./yaml-cpp/node.h:43:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from yaml-cpp/nodebuilder.h:10,
from yaml-cpp/nodebuilder.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/nodebuilder.cpp:3:0:
./yaml-cpp/node.h:115:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from yaml-cpp/nodebuilder.h:10,
from yaml-cpp/nodebuilder.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/node.cpp -o yaml-cpp/node.o
In file included from ./yaml-cpp/node.h:12:0,
from yaml-cpp/node.cpp:1:
./yaml-cpp/iterator.h:20:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
from yaml-cpp/node.cpp:1:
./yaml-cpp/iterator.h:36:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/node.cpp:1:0:
./yaml-cpp/node.h:43:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/node.cpp:1:0:
./yaml-cpp/node.h:115:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/nodeownership.h:10:0,
from yaml-cpp/node.cpp:4:
yaml-cpp/ptr_vector.h:31:23: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr<T> t) {
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/node.cpp:10:0:
./yaml-cpp/emitter.h:98:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr <EmitterState> m_pState;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
yaml-cpp/node.cpp:54:7: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Node::Clone() const
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
yaml-cpp/node.cpp: In member function ‘std::auto_ptr<YAML::Node> YAML::Node::Clone() const’:
yaml-cpp/node.cpp:56:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> pNode(new Node);
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
yaml-cpp/node.cpp: In member function ‘YAML::Iterator YAML::Node::begin() const’:
yaml-cpp/node.cpp:148:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_seqData.begin())));
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
yaml-cpp/node.cpp:150:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_mapData.begin())));
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
yaml-cpp/node.cpp: In member function ‘YAML::Iterator YAML::Node::end() const’:
yaml-cpp/node.cpp:166:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_seqData.end())));
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
yaml-cpp/node.cpp:168:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_mapData.end())));
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/nodeownership.cpp -o yaml-cpp/nodeownership.o
In file included from yaml-cpp/nodeownership.h:10:0,
from yaml-cpp/nodeownership.cpp:1:
yaml-cpp/ptr_vector.h:31:23: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr<T> t) {
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/nodeownership.h:10,
from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
from yaml-cpp/nodeownership.cpp:2:
./yaml-cpp/iterator.h:20:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/nodeownership.h:10,
from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
from yaml-cpp/nodeownership.cpp:2:
./yaml-cpp/iterator.h:36:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/nodeownership.h:10,
from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/nodeownership.cpp:2:0:
./yaml-cpp/node.h:43:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/nodeownership.h:10,
from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/nodeownership.cpp:2:0:
./yaml-cpp/node.h:115:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/nodeownership.h:10,
from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
yaml-cpp/nodeownership.cpp: In member function ‘YAML::Node& YAML::NodeOwnership::_Create()’:
yaml-cpp/nodeownership.cpp:18:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
m_nodes.push_back(std::auto_ptr<Node>(new Node));
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/nodeownership.h:10,
from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/null.cpp -o yaml-cpp/null.o
In file included from ./yaml-cpp/node.h:12:0,
from yaml-cpp/null.cpp:2:
./yaml-cpp/iterator.h:20:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/null.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
from yaml-cpp/null.cpp:2:
./yaml-cpp/iterator.h:36:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/null.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/null.cpp:2:0:
./yaml-cpp/node.h:43:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/null.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/null.cpp:2:0:
./yaml-cpp/node.h:115:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/null.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
In file included from yaml-cpp/parser.cpp:1:0:
./yaml-cpp/parser.h:45:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Scanner> m_pScanner;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/parser.cpp:1:0:
./yaml-cpp/parser.h:46:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Directives> m_pDirectives;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
from yaml-cpp/parser.cpp:5:
./yaml-cpp/iterator.h:20:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
from yaml-cpp/parser.cpp:5:
./yaml-cpp/iterator.h:36:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/parser.cpp:5:0:
./yaml-cpp/node.h:43:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/parser.cpp:5:0:
./yaml-cpp/node.h:115:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/scanner.h:15:0,
from yaml-cpp/parser.cpp:7:
yaml-cpp/ptr_vector.h:31:23: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr<T> t) {
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/parser.cpp:8:0:
yaml-cpp/singledocparser.h:56:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<CollectionStack> m_pCollectionStack;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
In file included from yaml-cpp/scanner.h:15:0,
from yaml-cpp/scanner.cpp:1:
yaml-cpp/ptr_vector.h:31:23: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr<T> t) {
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/scanner.h:15,
from yaml-cpp/scanner.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
yaml-cpp/scanner.cpp: In member function ‘void YAML::Scanner::StartStream()’:
yaml-cpp/scanner.cpp:237:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IndentMarker> pIndent(new IndentMarker(-1, IndentMarker::NONE));
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/scanner.h:15,
from yaml-cpp/scanner.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
yaml-cpp/scanner.cpp: In member function ‘YAML::Scanner::IndentMarker* YAML::Scanner::PushIndentTo(int, YAML::Scanner::IndentMarker::INDENT_TYPE)’:
yaml-cpp/scanner.cpp:284:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IndentMarker> pIndent(new IndentMarker(column, type));
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/scanner.h:15,
from yaml-cpp/scanner.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
In file included from yaml-cpp/scanner.h:15:0,
from yaml-cpp/scanscalar.cpp:2:
yaml-cpp/ptr_vector.h:31:23: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr<T> t) {
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/scanner.h:15,
from yaml-cpp/scanscalar.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
In file included from yaml-cpp/scanner.h:15:0,
from yaml-cpp/scantag.cpp:1:
yaml-cpp/ptr_vector.h:31:23: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr<T> t) {
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/scanner.h:15,
from yaml-cpp/scantag.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
In file included from yaml-cpp/scanner.h:15:0,
from yaml-cpp/scantoken.cpp:1:
yaml-cpp/ptr_vector.h:31:23: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr<T> t) {
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/scanner.h:15,
from yaml-cpp/scantoken.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
In file included from yaml-cpp/scanner.h:15:0,
from yaml-cpp/simplekey.cpp:1:
yaml-cpp/ptr_vector.h:31:23: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr<T> t) {
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/scanner.h:15,
from yaml-cpp/simplekey.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/singledocparser.cpp -o yaml-cpp/singledocparser.o
In file included from yaml-cpp/singledocparser.cpp:1:0:
yaml-cpp/singledocparser.h:56:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr<CollectionStack> m_pCollectionStack;
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from yaml-cpp/singledocparser.h:13,
from yaml-cpp/singledocparser.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
In file included from yaml-cpp/singledocparser.cpp:2:0:
yaml-cpp/collectionstack.h: In member function ‘void YAML::CollectionStack::PopCollectionType(YAML::CollectionType::value)’:
yaml-cpp/collectionstack.h:28:48: warning: unused parameter ‘type’ [-Wunused-parameter]
void PopCollectionType(CollectionType::value type) { assert(type == GetCurCollectionType()); collectionStack.pop(); }
^˜˜˜
In file included from yaml-cpp/scanner.h:15:0,
from yaml-cpp/singledocparser.cpp:6:
yaml-cpp/ptr_vector.h: At global scope:
yaml-cpp/ptr_vector.h:31:23: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr<T> t) {
^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
from yaml-cpp/singledocparser.h:13,
from yaml-cpp/singledocparser.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o seqbias.so sam.o bam_plbuf.o bam_aux.o common.o miscmath.o pos_table.o kmer_matrix.o logger.o motif.o seqbias.o sequencing_bias.o twobitseq.o yaml-cpp/aliasmanager.o yaml-cpp/conversion.o yaml-cpp/directives.o yaml-cpp/emitfromevents.o yaml-cpp/emitter.o yaml-cpp/emitterstate.o yaml-cpp/emitterutils.o yaml-cpp/exp.o yaml-cpp/iterator.o yaml-cpp/nodebuilder.o yaml-cpp/node.o yaml-cpp/nodeownership.o yaml-cpp/null.o yaml-cpp/ostream.o yaml-cpp/parser.o yaml-cpp/regex.o yaml-cpp/scanner.o yaml-cpp/scanscalar.o yaml-cpp/scantag.o yaml-cpp/scantoken.o yaml-cpp/simplekey.o yaml-cpp/singledocparser.o yaml-cpp/stream.o yaml-cpp/tag.o -L/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib -Wl,-rpath,/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib -lhts -lz -lm -lbz2 -llzma -lpthread -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-seqbias/00new/seqbias/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (seqbias)
