############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf seqbias.buildbin-libdir && mkdir seqbias.buildbin-libdir && F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=seqbias.buildbin-libdir seqbias_1.44.0.tar.gz ### ############################################################################## ############################################################################## * installing *source* package 'seqbias' ... ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sam.c -o sam.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bam_plbuf.c -o bam_plbuf.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bam_aux.c -o bam_aux.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c common.c -o common.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c miscmath.c -o miscmath.o gcc -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c pos_table.c -o pos_table.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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] 45 | std::auto_ptr m_pScanner; | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, from ./yaml-cpp/parser.h:12, from yaml-cpp/yaml.h:9, from kmer_matrix.hpp:13, from kmer_matrix.cpp:8: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | 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] 46 | std::auto_ptr m_pDirectives; | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, from ./yaml-cpp/parser.h:12, from yaml-cpp/yaml.h:9, from kmer_matrix.hpp:13, from kmer_matrix.cpp:8: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | 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] 20 | Iterator(std::auto_ptr pData); | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, from ./yaml-cpp/parser.h:12, from yaml-cpp/yaml.h:9, from kmer_matrix.hpp:13, from kmer_matrix.cpp:8: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | 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] 36 | std::auto_ptr m_pData; | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, from ./yaml-cpp/parser.h:12, from yaml-cpp/yaml.h:9, from kmer_matrix.hpp:13, from kmer_matrix.cpp:8: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | 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] 43 | std::auto_ptr Clone() const; | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, from ./yaml-cpp/parser.h:12, from yaml-cpp/yaml.h:9, from kmer_matrix.hpp:13, from kmer_matrix.cpp:8: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | 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] 115 | std::auto_ptr m_pOwnership; | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, from ./yaml-cpp/parser.h:12, from yaml-cpp/yaml.h:9, from kmer_matrix.hpp:13, from kmer_matrix.cpp:8: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | 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] 98 | std::auto_ptr m_pState; | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, from ./yaml-cpp/parser.h:12, from yaml-cpp/yaml.h:9, from kmer_matrix.hpp:13, from kmer_matrix.cpp:8: c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c logger.cpp -o logger.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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] 45 | std::auto_ptr m_pScanner; | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, 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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | 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] 46 | std::auto_ptr m_pDirectives; | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, 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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | 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] 20 | Iterator(std::auto_ptr pData); | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, 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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | 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] 36 | std::auto_ptr m_pData; | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, 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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | 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] 43 | std::auto_ptr Clone() const; | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, 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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | 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] 115 | std::auto_ptr m_pOwnership; | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, 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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | 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] 98 | std::auto_ptr m_pState; | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, 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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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] 45 | std::auto_ptr m_pScanner; | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, 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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | 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] 46 | std::auto_ptr m_pDirectives; | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, 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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | 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] 20 | Iterator(std::auto_ptr pData); | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, 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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | 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] 36 | std::auto_ptr m_pData; | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, 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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | 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] 43 | std::auto_ptr Clone() const; | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, 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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | 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] 115 | std::auto_ptr m_pOwnership; | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, 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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | 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] 98 | std::auto_ptr m_pState; | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, 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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ seqbias.cpp: In function 'void R_init_seqbias(DllInfo*)': seqbias.cpp:493:34: 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] 493 | { "seqbias_fit", (DL_FUNC) &seqbias_fit, 5 }, | ^~~~~~~~~~~~~~~~~~~~~~ seqbias.cpp:494:34: 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] 494 | { "seqbias_predict", (DL_FUNC) &seqbias_predict, 5 }, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ seqbias.cpp:495:34: warning: cast between incompatible function types from 'SEXPREC* (*)(SEXP, SEXP)' {aka 'SEXPREC* (*)(SEXPREC*, SEXPREC*)'} to 'DL_FUNC' {aka 'void* (*)()'} [-Wcast-function-type] 495 | { "seqbias_load", (DL_FUNC) &seqbias_load, 2 }, | ^~~~~~~~~~~~~~~~~~~~~~~ seqbias.cpp:496:34: warning: cast between incompatible function types from 'SEXPREC* (*)(SEXP, SEXP)' {aka 'SEXPREC* (*)(SEXPREC*, SEXPREC*)'} to 'DL_FUNC' {aka 'void* (*)()'} [-Wcast-function-type] 496 | { "seqbias_save", (DL_FUNC) &seqbias_save, 2 }, | ^~~~~~~~~~~~~~~~~~~~~~~ seqbias.cpp:497:37: warning: cast between incompatible function types from 'SEXPREC* (*)(SEXP)' {aka 'SEXPREC* (*)(SEXPREC*)'} to 'DL_FUNC' {aka 'void* (*)()'} [-Wcast-function-type] 497 | { "seqbias_open_bam", (DL_FUNC) &seqbias_open_bam, 1 }, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ seqbias.cpp:498:37: 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] 498 | { "seqbias_count_reads", (DL_FUNC) &seqbias_count_reads, 7 }, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ seqbias.cpp:499:49: warning: cast between incompatible function types from 'SEXPREC* (*)(SEXP, SEXP)' {aka 'SEXPREC* (*)(SEXPREC*, SEXPREC*)'} to 'DL_FUNC' {aka 'void* (*)()'} [-Wcast-function-type] 499 | { "seqbias_alloc_kmer_matrix", (DL_FUNC) &seqbias_alloc_kmer_matrix, 2 }, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ seqbias.cpp:500:49: 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] 500 | { "seqbias_tally_kmers", (DL_FUNC) &seqbias_tally_kmers, 4 }, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ seqbias.cpp:501:49: warning: cast between incompatible function types from 'SEXPREC* (*)(SEXP, SEXP)' {aka 'SEXPREC* (*)(SEXPREC*, SEXPREC*)'} to 'DL_FUNC' {aka 'void* (*)()'} [-Wcast-function-type] 501 | { "sebqias_dataframe_from_kmer_matrix", (DL_FUNC) &seqbias_dataframe_from_kmer_matrix, 2 }, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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] 45 | std::auto_ptr m_pScanner; | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, 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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | 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] 46 | std::auto_ptr m_pDirectives; | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, 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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | 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] 20 | Iterator(std::auto_ptr pData); | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, 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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | 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] 36 | std::auto_ptr m_pData; | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, 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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | 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] 43 | std::auto_ptr Clone() const; | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, 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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | 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] 115 | std::auto_ptr m_pOwnership; | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, 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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | 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] 98 | std::auto_ptr m_pState; | ^~~~~~~~ In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83, 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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c twobitseq.cpp -o twobitseq.o 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 F:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -lsbml-static -lwinmm -lwldap32 -lgdi32 -lbz2 -lcurl -lrtmp -lssl -lssh2 -lidn2 -lunistring -lcharset -lintl -liconv -lgcrypt -lcrypto -lgpg-error -lws2_32 -llzma -lz -lzstd -lmincore -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.15-bioc/meat/seqbias.buildbin-libdir/00LOCK-seqbias/00new/seqbias/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * MD5 sums packaged installation of 'seqbias' as seqbias_1.44.0.zip * DONE (seqbias)