##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf seqbias.buildbin-libdir && mkdir seqbias.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=seqbias.buildbin-libdir seqbias_1.42.0.tar.gz
###
##############################################################################
##############################################################################
install for i386
* installing *source* package 'seqbias' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sam.c -o sam.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bam_plbuf.c -o bam_plbuf.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bam_aux.c -o bam_aux.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c common.c -o common.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c miscmath.c -o miscmath.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c pos_table.c -o pos_table.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c kmer_matrix.cpp -o kmer_matrix.o
In file included from yaml-cpp/yaml.h:9,
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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/yaml.h:9,
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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/yaml.h:10,
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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/yaml.h:10,
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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/yaml.h:13,
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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c logger.cpp -o logger.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c motif.cpp -o motif.o
In file included from yaml-cpp/yaml.h:9,
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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/yaml.h:9,
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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/yaml.h:10,
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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/yaml.h:10,
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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/yaml.h:13,
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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c seqbias.cpp -o seqbias.o
In file included from yaml-cpp/yaml.h:9,
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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/yaml.h:9,
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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included 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/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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included 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/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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/yaml.h:13,
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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
seqbias.cpp: In function 'void R_init_seqbias(DllInfo*)':
seqbias.cpp:493:45: warning: cast between incompatible function types from 'SEXPREC* (*)(SEXP, SEXP, SEXP, SEXP, SEXP)' {aka 'SEXPREC* (*)(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)'} to 'DL_FUNC' {aka 'void* (*)()'} [-Wcast-function-type]
{ "seqbias_fit", (DL_FUNC) &seqbias_fit, 5 },
^~~~~~~~~~~
seqbias.cpp:494:45: warning: cast between incompatible function types from 'SEXPREC* (*)(SEXP, SEXP, SEXP, SEXP, SEXP)' {aka 'SEXPREC* (*)(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)'} to 'DL_FUNC' {aka 'void* (*)()'} [-Wcast-function-type]
{ "seqbias_predict", (DL_FUNC) &seqbias_predict, 5 },
^~~~~~~~~~~~~~~
seqbias.cpp:495:45: warning: cast between incompatible function types from 'SEXPREC* (*)(SEXP, SEXP)' {aka 'SEXPREC* (*)(SEXPREC*, SEXPREC*)'} to 'DL_FUNC' {aka 'void* (*)()'} [-Wcast-function-type]
{ "seqbias_load", (DL_FUNC) &seqbias_load, 2 },
^~~~~~~~~~~~
seqbias.cpp:496:45: warning: cast between incompatible function types from 'SEXPREC* (*)(SEXP, SEXP)' {aka 'SEXPREC* (*)(SEXPREC*, SEXPREC*)'} to 'DL_FUNC' {aka 'void* (*)()'} [-Wcast-function-type]
{ "seqbias_save", (DL_FUNC) &seqbias_save, 2 },
^~~~~~~~~~~~
seqbias.cpp:497:48: warning: cast between incompatible function types from 'SEXPREC* (*)(SEXP)' {aka 'SEXPREC* (*)(SEXPREC*)'} to 'DL_FUNC' {aka 'void* (*)()'} [-Wcast-function-type]
{ "seqbias_open_bam", (DL_FUNC) &seqbias_open_bam, 1 },
^~~~~~~~~~~~~~~~
seqbias.cpp:498:48: warning: cast between incompatible function types from 'SEXPREC* (*)(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)' {aka 'SEXPREC* (*)(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)'} to 'DL_FUNC' {aka 'void* (*)()'} [-Wcast-function-type]
{ "seqbias_count_reads", (DL_FUNC) &seqbias_count_reads, 7 },
^~~~~~~~~~~~~~~~~~~
seqbias.cpp:499:60: warning: cast between incompatible function types from 'SEXPREC* (*)(SEXP, SEXP)' {aka 'SEXPREC* (*)(SEXPREC*, SEXPREC*)'} to 'DL_FUNC' {aka 'void* (*)()'} [-Wcast-function-type]
{ "seqbias_alloc_kmer_matrix", (DL_FUNC) &seqbias_alloc_kmer_matrix, 2 },
^~~~~~~~~~~~~~~~~~~~~~~~~
seqbias.cpp:500:60: warning: cast between incompatible function types from 'SEXPREC* (*)(SEXP, SEXP, SEXP, SEXP)' {aka 'SEXPREC* (*)(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)'} to 'DL_FUNC' {aka 'void* (*)()'} [-Wcast-function-type]
{ "seqbias_tally_kmers", (DL_FUNC) &seqbias_tally_kmers, 4 },
^~~~~~~~~~~~~~~~~~~
seqbias.cpp:501:60: warning: cast between incompatible function types from 'SEXPREC* (*)(SEXP, SEXP)' {aka 'SEXPREC* (*)(SEXPREC*, SEXPREC*)'} to 'DL_FUNC' {aka 'void* (*)()'} [-Wcast-function-type]
{ "sebqias_dataframe_from_kmer_matrix", (DL_FUNC) &seqbias_dataframe_from_kmer_matrix, 2 },
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sequencing_bias.cpp -o sequencing_bias.o
In file included 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:
./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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included 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:
./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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included 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/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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included 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/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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/yaml.h:13,
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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c twobitseq.cpp -o twobitseq.o
C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/aliasmanager.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/conversion.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/directives.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/emitfromevents.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/emitter.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/emitterstate.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/emitterutils.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/exp.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/iterator.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/nodebuilder.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/node.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/nodeownership.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/null.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/ostream.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/parser.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/regex.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/scanner.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/scanscalar.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/scantag.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/scantoken.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/simplekey.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/singledocparser.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/stream.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/tag.o: file format not recognized
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o seqbias.dll tmp.def 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 C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/i386/libhts.a -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
yaml-cpp/aliasmanager.o: file not recognized: file format not recognized
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'seqbias'
* removing 'C:/Users/biocbuild/bbs-3.14-bioc/meat/seqbias.buildbin-libdir/seqbias'
