##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL seqbias
###
##############################################################################
##############################################################################
* 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/aliasmanager.cpp:2:0:
./yaml-cpp/node.h:43:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/aliasmanager.cpp:2:0:
./yaml-cpp/node.h:115:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
void push(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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::pop()’:
yaml-cpp/ptr_stack.h:34:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
inline std::auto_ptr Setting::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 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::Setting::set(const T&)’:
yaml-cpp/setting.h:60:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr pChange(new SettingChange (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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
void push(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
void push(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 ptr_stack::pop()’:
yaml-cpp/ptr_stack.h:34:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
inline std::auto_ptr Setting::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 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::Setting::set(const T&)’:
yaml-cpp/setting.h:60:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr pChange(new SettingChange (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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
void push(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/iterator.cpp:1:0:
./yaml-cpp/node.h:43:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/iterator.cpp:1:0:
./yaml-cpp/node.h:115:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 class auto_ptr;
^~~~~~~~
yaml-cpp/iterator.cpp:11:26: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
Iterator::Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/nodebuilder.cpp:3:0:
./yaml-cpp/node.h:43:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/nodebuilder.cpp:3:0:
./yaml-cpp/node.h:115:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/node.cpp:1:0:
./yaml-cpp/node.h:43:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/node.cpp:1:0:
./yaml-cpp/node.h:115:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr 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 class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/node.cpp:10:0:
./yaml-cpp/emitter.h:98:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 class auto_ptr;
^~~~~~~~
yaml-cpp/node.cpp:54:7: warning: ‘template 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 class auto_ptr;
^~~~~~~~
yaml-cpp/node.cpp: In member function ‘std::auto_ptr YAML::Node::Clone() const’:
yaml-cpp/node.cpp:56:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
return Iterator(std::auto_ptr(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 class auto_ptr;
^~~~~~~~
yaml-cpp/node.cpp:150:26: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
return Iterator(std::auto_ptr(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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
return Iterator(std::auto_ptr(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 class auto_ptr;
^~~~~~~~
yaml-cpp/node.cpp:168:26: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
return Iterator(std::auto_ptr(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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/nodeownership.cpp:2:0:
./yaml-cpp/node.h:43:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/nodeownership.cpp:2:0:
./yaml-cpp/node.h:115:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 class auto_ptr;
^~~~~~~~
yaml-cpp/nodeownership.cpp: In member function ‘YAML::Node& YAML::NodeOwnership::_Create()’:
yaml-cpp/nodeownership.cpp:18:26: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
m_nodes.push_back(std::auto_ptr(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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/null.cpp:2:0:
./yaml-cpp/node.h:43:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
std::auto_ptr 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 