############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/seqbias_1.40.0.tar.gz && rm -rf seqbias.buildbin-libdir && mkdir seqbias.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=seqbias.buildbin-libdir seqbias_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL seqbias_1.40.0.zip && rm seqbias_1.40.0.tar.gz seqbias_1.40.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 585k 100 585k 0 0 1920k 0 --:--:-- --:--:-- --:--:-- 1924k 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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] Iterator(std::auto_ptr 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr 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 class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] Iterator(std::auto_ptr 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr 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 class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] Iterator(std::auto_ptr 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr 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 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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] Iterator(std::auto_ptr 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr 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 class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-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/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/aliasmanager.cpp -o yaml-cpp/aliasmanager.o In file included from ./yaml-cpp/node.h:12, 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/aliasmanager.cpp:2: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./yaml-cpp/node.h:12, 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/aliasmanager.cpp:2: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/aliasmanager.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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/aliasmanager.cpp:2: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/aliasmanager.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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/aliasmanager.cpp:2: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/directives.cpp -o yaml-cpp/directives.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/emitfromevents.cpp -o yaml-cpp/emitfromevents.o In file included from yaml-cpp/emitfromevents.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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/emitter.h:14, from yaml-cpp/emitfromevents.cpp:2: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o In file included from yaml-cpp/emitter.cpp:1: ./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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/emitter.h:14, from yaml-cpp/emitter.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:9, 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/emitter.h:14, from yaml-cpp/emitter.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:9, 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/emitter.h:14, from yaml-cpp/emitter.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:9, 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/emitter.h:14, from yaml-cpp/emitter.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:10, 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/emitter.h:14, from yaml-cpp/emitter.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:10, 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/emitter.h:14, from yaml-cpp/emitter.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:10, 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/emitter.h:14, from yaml-cpp/emitter.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:10, 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/emitter.h:14, from yaml-cpp/emitter.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o In file included from yaml-cpp/emitterstate.h:9, 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_stack.h:9, from yaml-cpp/emitterstate.h:9, from yaml-cpp/emitterstate.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:9, 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_stack.h:9, from yaml-cpp/emitterstate.h:9, from yaml-cpp/emitterstate.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:9, 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_stack.h:9, from yaml-cpp/emitterstate.h:9, from yaml-cpp/emitterstate.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:10, 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_stack.h:9, from yaml-cpp/emitterstate.h:9, from yaml-cpp/emitterstate.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:10, 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_stack.h:9, from yaml-cpp/emitterstate.h:9, from yaml-cpp/emitterstate.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:10, 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_stack.h:9, from yaml-cpp/emitterstate.h:9, from yaml-cpp/emitterstate.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:10, 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_stack.h:9, from yaml-cpp/emitterstate.h:9, from yaml-cpp/emitterstate.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_stack.h:9, from yaml-cpp/emitterstate.h:9, from yaml-cpp/emitterstate.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_stack.h:9, from yaml-cpp/emitterstate.h:9, from yaml-cpp/emitterstate.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o In file included from ./yaml-cpp/node.h:12, 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/iterator.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./yaml-cpp/node.h:12, 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/iterator.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/iterator.cpp:1: ./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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/iterator.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/iterator.cpp:1: ./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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/iterator.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/iterator.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/nodebuilder.cpp -o yaml-cpp/nodebuilder.o In file included from ./yaml-cpp/node.h:12, 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from yaml-cpp/nodebuilder.h:10, from yaml-cpp/nodebuilder.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./yaml-cpp/node.h:12, 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from yaml-cpp/nodebuilder.h:10, from yaml-cpp/nodebuilder.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/nodebuilder.cpp:3: ./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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from yaml-cpp/nodebuilder.h:10, from yaml-cpp/nodebuilder.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/nodebuilder.cpp:3: ./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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from yaml-cpp/nodebuilder.h:10, from yaml-cpp/nodebuilder.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/node.cpp -o yaml-cpp/node.o In file included from ./yaml-cpp/node.h:12, 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/node.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./yaml-cpp/node.h:12, 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/node.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/node.cpp:1: ./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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/node.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/node.cpp:1: ./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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/node.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/nodeownership.h:10, 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/node.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/node.cpp:10: ./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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/node.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/node.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/node.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/node.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/node.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/node.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/node.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/nodeownership.cpp -o yaml-cpp/nodeownership.o In file included from yaml-cpp/nodeownership.h:10, 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_vector.h:9, from yaml-cpp/nodeownership.h:10, from yaml-cpp/nodeownership.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./yaml-cpp/node.h:12, 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_vector.h:9, from yaml-cpp/nodeownership.h:10, from yaml-cpp/nodeownership.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./yaml-cpp/node.h:12, 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_vector.h:9, from yaml-cpp/nodeownership.h:10, from yaml-cpp/nodeownership.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/nodeownership.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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_vector.h:9, from yaml-cpp/nodeownership.h:10, from yaml-cpp/nodeownership.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/nodeownership.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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_vector.h:9, from yaml-cpp/nodeownership.h:10, from yaml-cpp/nodeownership.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_vector.h:9, from yaml-cpp/nodeownership.h:10, from yaml-cpp/nodeownership.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/null.cpp -o yaml-cpp/null.o In file included from ./yaml-cpp/node.h:12, 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/null.cpp:2: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./yaml-cpp/node.h:12, 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/null.cpp:2: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/null.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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/null.cpp:2: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/null.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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/null.cpp:2: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o In file included from yaml-cpp/parser.cpp:1: ./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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/parser.h:12, from yaml-cpp/parser.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/parser.cpp:1: ./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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/parser.h:12, from yaml-cpp/parser.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./yaml-cpp/node.h:12, from yaml-cpp/parser.cpp:5: ./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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/parser.h:12, from yaml-cpp/parser.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./yaml-cpp/node.h:12, from yaml-cpp/parser.cpp:5: ./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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/parser.h:12, from yaml-cpp/parser.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/parser.cpp:5: ./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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/parser.h:12, from yaml-cpp/parser.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/parser.cpp:5: ./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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/parser.h:12, from yaml-cpp/parser.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/scanner.h:15, from yaml-cpp/parser.cpp:7: 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/parser.h:12, from yaml-cpp/parser.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/parser.cpp:8: yaml-cpp/singledocparser.h:56:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr m_pCollectionStack; ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from ./yaml-cpp/parser.h:12, from yaml-cpp/parser.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o In file included from yaml-cpp/regex.cpp:1: yaml-cpp/regex.h: In constructor 'YAML::RegEx::RegEx(const string&, YAML::REGEX_OP)': yaml-cpp/regex.h:21:8: warning: '.YAML::RegEx::m_z' may be used uninitialized in this function [-Wmaybe-uninitialized] class RegEx ^~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o In file included from yaml-cpp/scanner.h:15, from yaml-cpp/scanner.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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_vector.h:9, from yaml-cpp/scanner.h:15, from yaml-cpp/scanner.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ yaml-cpp/scanner.cpp: In member function 'void YAML::Scanner::StartStream()': yaml-cpp/scanner.cpp:237:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr pIndent(new IndentMarker(-1, IndentMarker::NONE)); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_vector.h:9, from yaml-cpp/scanner.h:15, from yaml-cpp/scanner.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr pIndent(new IndentMarker(column, type)); ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_vector.h:9, from yaml-cpp/scanner.h:15, from yaml-cpp/scanner.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o In file included from yaml-cpp/scanner.h:15, from yaml-cpp/scanscalar.cpp:2: 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_vector.h:9, from yaml-cpp/scanner.h:15, from yaml-cpp/scanscalar.cpp:2: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o In file included from yaml-cpp/scanner.h:15, from yaml-cpp/scantag.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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_vector.h:9, from yaml-cpp/scanner.h:15, from yaml-cpp/scantag.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o In file included from yaml-cpp/scanner.h:15, from yaml-cpp/scantoken.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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_vector.h:9, from yaml-cpp/scanner.h:15, from yaml-cpp/scantoken.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o In file included from yaml-cpp/scanner.h:15, from yaml-cpp/simplekey.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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_vector.h:9, from yaml-cpp/scanner.h:15, from yaml-cpp/simplekey.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/singledocparser.cpp -o yaml-cpp/singledocparser.o In file included from yaml-cpp/singledocparser.cpp:1: yaml-cpp/singledocparser.h:56:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr m_pCollectionStack; ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from yaml-cpp/singledocparser.h:13, from yaml-cpp/singledocparser.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/singledocparser.cpp:2: 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, from yaml-cpp/singledocparser.cpp:6: yaml-cpp/ptr_vector.h: At global scope: 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 C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from yaml-cpp/singledocparser.h:13, from yaml-cpp/singledocparser.cpp:1: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o 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-3.13-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-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/seqbias.buildbin-libdir/00LOCK-seqbias/00new/seqbias/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'seqbias' finding HTML links ... done count_reads html kmer_freq html random_intervals html seqbias-class html seqbias-package html seqbias_fit html seqbias_load html seqbias_predict html seqbias_save html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'seqbias' ... ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-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/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-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/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-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/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-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/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-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/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-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/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr m_pScanner; ^~~~~~~~ In file included from C:/rtools40/mingw64/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/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr m_pDirectives; ^~~~~~~~ In file included from C:/rtools40/mingw64/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/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] Iterator(std::auto_ptr pData); ^~~~~~~~ In file included from C:/rtools40/mingw64/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/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr m_pData; ^~~~~~~~ In file included from C:/rtools40/mingw64/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/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr Clone() const; ^~~~~~~~ In file included from C:/rtools40/mingw64/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/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr m_pOwnership; ^~~~~~~~ In file included from C:/rtools40/mingw64/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/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr m_pState; ^~~~~~~~ In file included from C:/rtools40/mingw64/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/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-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/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr m_pScanner; ^~~~~~~~ In file included from C:/rtools40/mingw64/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/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr m_pDirectives; ^~~~~~~~ In file included from C:/rtools40/mingw64/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/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] Iterator(std::auto_ptr pData); ^~~~~~~~ In file included from C:/rtools40/mingw64/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/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr m_pData; ^~~~~~~~ In file included from C:/rtools40/mingw64/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/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr Clone() const; ^~~~~~~~ In file included from C:/rtools40/mingw64/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/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr m_pOwnership; ^~~~~~~~ In file included from C:/rtools40/mingw64/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/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr m_pState; ^~~~~~~~ In file included from C:/rtools40/mingw64/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/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr m_pScanner; ^~~~~~~~ In file included from C:/rtools40/mingw64/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/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr m_pDirectives; ^~~~~~~~ In file included from C:/rtools40/mingw64/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/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] Iterator(std::auto_ptr pData); ^~~~~~~~ In file included from C:/rtools40/mingw64/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/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr m_pData; ^~~~~~~~ In file included from C:/rtools40/mingw64/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/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr Clone() const; ^~~~~~~~ In file included from C:/rtools40/mingw64/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/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr m_pOwnership; ^~~~~~~~ In file included from C:/rtools40/mingw64/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/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr m_pState; ^~~~~~~~ In file included from C:/rtools40/mingw64/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/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr m_pScanner; ^~~~~~~~ In file included from C:/rtools40/mingw64/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/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr m_pDirectives; ^~~~~~~~ In file included from C:/rtools40/mingw64/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/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] Iterator(std::auto_ptr pData); ^~~~~~~~ In file included from C:/rtools40/mingw64/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/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr m_pData; ^~~~~~~~ In file included from C:/rtools40/mingw64/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/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr Clone() const; ^~~~~~~~ In file included from C:/rtools40/mingw64/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/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr m_pOwnership; ^~~~~~~~ In file included from C:/rtools40/mingw64/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/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr m_pState; ^~~~~~~~ In file included from C:/rtools40/mingw64/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/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-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/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/aliasmanager.cpp -o yaml-cpp/aliasmanager.o In file included from ./yaml-cpp/node.h:12, 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/aliasmanager.cpp:2: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./yaml-cpp/node.h:12, 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/aliasmanager.cpp:2: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/aliasmanager.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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/aliasmanager.cpp:2: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/aliasmanager.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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/aliasmanager.cpp:2: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/directives.cpp -o yaml-cpp/directives.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/emitfromevents.cpp -o yaml-cpp/emitfromevents.o In file included from yaml-cpp/emitfromevents.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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/emitter.h:14, from yaml-cpp/emitfromevents.cpp:2: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o In file included from yaml-cpp/emitter.cpp:1: ./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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/emitter.h:14, from yaml-cpp/emitter.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:9, 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/emitter.h:14, from yaml-cpp/emitter.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:9, 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/emitter.h:14, from yaml-cpp/emitter.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:9, 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/emitter.h:14, from yaml-cpp/emitter.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:10, 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/emitter.h:14, from yaml-cpp/emitter.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:10, 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/emitter.h:14, from yaml-cpp/emitter.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:10, 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/emitter.h:14, from yaml-cpp/emitter.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:10, 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/emitter.h:14, from yaml-cpp/emitter.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o In file included from yaml-cpp/emitterstate.h:9, 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_stack.h:9, from yaml-cpp/emitterstate.h:9, from yaml-cpp/emitterstate.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:9, 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_stack.h:9, from yaml-cpp/emitterstate.h:9, from yaml-cpp/emitterstate.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:9, 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_stack.h:9, from yaml-cpp/emitterstate.h:9, from yaml-cpp/emitterstate.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:10, 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_stack.h:9, from yaml-cpp/emitterstate.h:9, from yaml-cpp/emitterstate.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:10, 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_stack.h:9, from yaml-cpp/emitterstate.h:9, from yaml-cpp/emitterstate.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:10, 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_stack.h:9, from yaml-cpp/emitterstate.h:9, from yaml-cpp/emitterstate.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:10, 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_stack.h:9, from yaml-cpp/emitterstate.h:9, from yaml-cpp/emitterstate.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_stack.h:9, from yaml-cpp/emitterstate.h:9, from yaml-cpp/emitterstate.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_stack.h:9, from yaml-cpp/emitterstate.h:9, from yaml-cpp/emitterstate.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o In file included from ./yaml-cpp/node.h:12, 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/iterator.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./yaml-cpp/node.h:12, 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/iterator.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/iterator.cpp:1: ./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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/iterator.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/iterator.cpp:1: ./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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/iterator.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/iterator.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/nodebuilder.cpp -o yaml-cpp/nodebuilder.o In file included from ./yaml-cpp/node.h:12, 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from yaml-cpp/nodebuilder.h:10, from yaml-cpp/nodebuilder.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./yaml-cpp/node.h:12, 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from yaml-cpp/nodebuilder.h:10, from yaml-cpp/nodebuilder.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/nodebuilder.cpp:3: ./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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from yaml-cpp/nodebuilder.h:10, from yaml-cpp/nodebuilder.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/nodebuilder.cpp:3: ./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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from yaml-cpp/nodebuilder.h:10, from yaml-cpp/nodebuilder.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/node.cpp -o yaml-cpp/node.o In file included from ./yaml-cpp/node.h:12, 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/node.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./yaml-cpp/node.h:12, 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/node.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/node.cpp:1: ./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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/node.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/node.cpp:1: ./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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/node.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/nodeownership.h:10, 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/node.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/node.cpp:10: ./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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/node.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/node.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/node.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/node.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/node.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/node.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/node.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/nodeownership.cpp -o yaml-cpp/nodeownership.o In file included from yaml-cpp/nodeownership.h:10, 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_vector.h:9, from yaml-cpp/nodeownership.h:10, from yaml-cpp/nodeownership.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./yaml-cpp/node.h:12, 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_vector.h:9, from yaml-cpp/nodeownership.h:10, from yaml-cpp/nodeownership.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./yaml-cpp/node.h:12, 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_vector.h:9, from yaml-cpp/nodeownership.h:10, from yaml-cpp/nodeownership.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/nodeownership.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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_vector.h:9, from yaml-cpp/nodeownership.h:10, from yaml-cpp/nodeownership.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/nodeownership.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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_vector.h:9, from yaml-cpp/nodeownership.h:10, from yaml-cpp/nodeownership.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_vector.h:9, from yaml-cpp/nodeownership.h:10, from yaml-cpp/nodeownership.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/null.cpp -o yaml-cpp/null.o In file included from ./yaml-cpp/node.h:12, 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/null.cpp:2: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./yaml-cpp/node.h:12, 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/null.cpp:2: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/null.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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/null.cpp:2: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/null.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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/iterator.h:9, from ./yaml-cpp/node.h:12, from yaml-cpp/null.cpp:2: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o In file included from yaml-cpp/parser.cpp:1: ./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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/parser.h:12, from yaml-cpp/parser.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/parser.cpp:1: ./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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/parser.h:12, from yaml-cpp/parser.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./yaml-cpp/node.h:12, from yaml-cpp/parser.cpp:5: ./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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/parser.h:12, from yaml-cpp/parser.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./yaml-cpp/node.h:12, from yaml-cpp/parser.cpp:5: ./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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/parser.h:12, from yaml-cpp/parser.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/parser.cpp:5: ./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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/parser.h:12, from yaml-cpp/parser.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/parser.cpp:5: ./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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/parser.h:12, from yaml-cpp/parser.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/scanner.h:15, from yaml-cpp/parser.cpp:7: 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/parser.h:12, from yaml-cpp/parser.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/parser.cpp:8: yaml-cpp/singledocparser.h:56:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr m_pCollectionStack; ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from ./yaml-cpp/parser.h:12, from yaml-cpp/parser.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o In file included from yaml-cpp/regex.cpp:1: yaml-cpp/regex.h: In constructor 'YAML::RegEx::RegEx(const string&, YAML::REGEX_OP)': yaml-cpp/regex.h:21:8: warning: '.YAML::RegEx::m_z' may be used uninitialized in this function [-Wmaybe-uninitialized] class RegEx ^~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o In file included from yaml-cpp/scanner.h:15, from yaml-cpp/scanner.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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_vector.h:9, from yaml-cpp/scanner.h:15, from yaml-cpp/scanner.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ yaml-cpp/scanner.cpp: In member function 'void YAML::Scanner::StartStream()': yaml-cpp/scanner.cpp:237:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr pIndent(new IndentMarker(-1, IndentMarker::NONE)); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_vector.h:9, from yaml-cpp/scanner.h:15, from yaml-cpp/scanner.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr pIndent(new IndentMarker(column, type)); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_vector.h:9, from yaml-cpp/scanner.h:15, from yaml-cpp/scanner.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o In file included from yaml-cpp/scanner.h:15, from yaml-cpp/scanscalar.cpp:2: 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_vector.h:9, from yaml-cpp/scanner.h:15, from yaml-cpp/scanscalar.cpp:2: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o In file included from yaml-cpp/scanner.h:15, from yaml-cpp/scantag.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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_vector.h:9, from yaml-cpp/scanner.h:15, from yaml-cpp/scantag.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o In file included from yaml-cpp/scanner.h:15, from yaml-cpp/scantoken.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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_vector.h:9, from yaml-cpp/scanner.h:15, from yaml-cpp/scantoken.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o In file included from yaml-cpp/scanner.h:15, from yaml-cpp/simplekey.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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from yaml-cpp/ptr_vector.h:9, from yaml-cpp/scanner.h:15, from yaml-cpp/simplekey.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/singledocparser.cpp -o yaml-cpp/singledocparser.o In file included from yaml-cpp/singledocparser.cpp:1: yaml-cpp/singledocparser.h:56:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr m_pCollectionStack; ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from yaml-cpp/singledocparser.h:13, from yaml-cpp/singledocparser.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from yaml-cpp/singledocparser.cpp:2: 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, from yaml-cpp/singledocparser.cpp:6: yaml-cpp/ptr_vector.h: At global scope: 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 C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from yaml-cpp/singledocparser.h:13, from yaml-cpp/singledocparser.cpp:1: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o C:/rtools40/mingw64/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-3.13-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/seqbias.buildbin-libdir/seqbias/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'seqbias' as seqbias_1.40.0.zip * DONE (seqbias) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'seqbias' successfully unpacked and MD5 sums checked