##############################################################################
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###
### Running command:
###
### rm -rf seqbias.buildbin-libdir && mkdir seqbias.buildbin-libdir && F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL --build --library=seqbias.buildbin-libdir seqbias_1.47.0.tar.gz
###
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* installing *source* package 'seqbias' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
$SEQBIAS_OBJ is [common.o miscmath.o pos_table.o kmer_matrix.o logger.o motif.o seqbias.o sequencing_bias.o twobitseq.o]
$YAML_CPP_OBJ is [aliasmanager.o conversion.o directives.o emitfromevents.o emitter.o emitterstate.o emitterutils.o exp.o iterator.o nodebuilder.o node.o nodeownership.o null.o ostream.o parser.o regex.o scanner.o scanscalar.o scantag.o scantoken.o simplekey.o singledocparser.o stream.o tag.o]
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/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:45:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
45 | std::auto_ptr<Scanner> m_pScanner;
| ^~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
from ./yaml-cpp/parser.h:12:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./yaml-cpp/parser.h:46:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
46 | std::auto_ptr<Directives> m_pDirectives;
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/yaml.h:10:
./yaml-cpp/iterator.h:20:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
20 | Iterator(std::auto_ptr<IterPriv> pData);
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./yaml-cpp/iterator.h:36:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
36 | std::auto_ptr<IterPriv> m_pData;
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./yaml-cpp/node.h:43:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
43 | std::auto_ptr<Node> Clone() const;
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./yaml-cpp/node.h:115:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
115 | std::auto_ptr<NodeOwnership> m_pOwnership;
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:13:
./yaml-cpp/emitter.h:98:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
98 | std::auto_ptr <EmitterState> m_pState;
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/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:45:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
45 | std::auto_ptr<Scanner> m_pScanner;
| ^~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
from ./yaml-cpp/parser.h:12:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./yaml-cpp/parser.h:46:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
46 | std::auto_ptr<Directives> m_pDirectives;
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/yaml.h:10:
./yaml-cpp/iterator.h:20:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
20 | Iterator(std::auto_ptr<IterPriv> pData);
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./yaml-cpp/iterator.h:36:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
36 | std::auto_ptr<IterPriv> m_pData;
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./yaml-cpp/node.h:43:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
43 | std::auto_ptr<Node> Clone() const;
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./yaml-cpp/node.h:115:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
115 | std::auto_ptr<NodeOwnership> m_pOwnership;
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:13:
./yaml-cpp/emitter.h:98:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
98 | std::auto_ptr <EmitterState> m_pState;
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/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:45:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
45 | std::auto_ptr<Scanner> m_pScanner;
| ^~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
from ./yaml-cpp/parser.h:12:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./yaml-cpp/parser.h:46:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
46 | std::auto_ptr<Directives> m_pDirectives;
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/yaml.h:10:
./yaml-cpp/iterator.h:20:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
20 | Iterator(std::auto_ptr<IterPriv> pData);
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./yaml-cpp/iterator.h:36:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
36 | std::auto_ptr<IterPriv> m_pData;
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./yaml-cpp/node.h:43:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
43 | std::auto_ptr<Node> Clone() const;
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./yaml-cpp/node.h:115:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
115 | std::auto_ptr<NodeOwnership> m_pOwnership;
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:13:
./yaml-cpp/emitter.h:98:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
98 | std::auto_ptr <EmitterState> m_pState;
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> 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-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/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:45:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
45 | std::auto_ptr<Scanner> m_pScanner;
| ^~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
from ./yaml-cpp/parser.h:12:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./yaml-cpp/parser.h:46:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
46 | std::auto_ptr<Directives> m_pDirectives;
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/yaml.h:10:
./yaml-cpp/iterator.h:20:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
20 | Iterator(std::auto_ptr<IterPriv> pData);
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./yaml-cpp/iterator.h:36:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
36 | std::auto_ptr<IterPriv> m_pData;
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./yaml-cpp/node.h:43:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
43 | std::auto_ptr<Node> Clone() const;
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
./yaml-cpp/node.h:115:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
115 | std::auto_ptr<NodeOwnership> m_pOwnership;
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:13:
./yaml-cpp/emitter.h:98:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
98 | std::auto_ptr <EmitterState> m_pState;
| ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
64 | template<typename> class auto_ptr;
| ^~~~~~~~
sequencing_bias.cpp: In member function 'void sequencing_bias::build(const char*, pos_table*, size_t, pos_t, pos_t, double)':
sequencing_bias.cpp:398:9: warning: 'void free(void*)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
398 | free(local_seq);
| ~~~~^~~~~~~~~~~
sequencing_bias.cpp:301:37: note: returned from 'void* operator new [](std::size_t)'
301 | local_seq = new char[ L + R + 2 ];
| ^
sequencing_bias.cpp: In function 'kmer_matrix tabulate_bias(double*, pos_t, pos_t, int, const char*, const char*, const char*)':
sequencing_bias.cpp:628:9: warning: 'void free(void*)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
628 | free(local_seq);
| ~~~~^~~~~~~~~~~
sequencing_bias.cpp:541:51: note: returned from 'void* operator new [](std::size_t)'
541 | local_seq = new char[ (k - 1) + L + 1 + R + 1 ];
| ^
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/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 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-3.17-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lz -lm -lbz2 -llzma -lcurl -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc-rtools43/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_1.47.0.zip
* DONE (seqbias)