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###
### Running command:
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### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL seqbias
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘seqbias’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
$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"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c common.c -o common.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c miscmath.c -o miscmath.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c pos_table.c -o pos_table.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c kmer_matrix.cpp -o kmer_matrix.o
In file included from yaml-cpp/yaml.h:9,
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 /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
./yaml-cpp/parser.h:46:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
46 | std::auto_ptr<Directives> m_pDirectives;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
./yaml-cpp/iterator.h:20:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
20 | Iterator(std::auto_ptr<IterPriv> pData);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
./yaml-cpp/iterator.h:36:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
36 | std::auto_ptr<IterPriv> m_pData;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
./yaml-cpp/node.h:43:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
43 | std::auto_ptr<Node> Clone() const;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
./yaml-cpp/node.h:115:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
115 | std::auto_ptr<NodeOwnership> m_pOwnership;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:13,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
./yaml-cpp/emitter.h:98:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
98 | std::auto_ptr <EmitterState> m_pState;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c logger.cpp -o logger.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c motif.cpp -o motif.o
In file included from yaml-cpp/yaml.h:9,
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 /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
./yaml-cpp/parser.h:46:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
46 | std::auto_ptr<Directives> m_pDirectives;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
./yaml-cpp/iterator.h:20:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
20 | Iterator(std::auto_ptr<IterPriv> pData);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
./yaml-cpp/iterator.h:36:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
36 | std::auto_ptr<IterPriv> m_pData;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
./yaml-cpp/node.h:43:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
43 | std::auto_ptr<Node> Clone() const;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
./yaml-cpp/node.h:115:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
115 | std::auto_ptr<NodeOwnership> m_pOwnership;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:13,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
./yaml-cpp/emitter.h:98:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
98 | std::auto_ptr <EmitterState> m_pState;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c seqbias.cpp -o seqbias.o
In file included from yaml-cpp/yaml.h:9,
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 /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
./yaml-cpp/parser.h:46:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
46 | std::auto_ptr<Directives> m_pDirectives;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
./yaml-cpp/iterator.h:20:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
20 | Iterator(std::auto_ptr<IterPriv> pData);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
./yaml-cpp/iterator.h:36:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
36 | std::auto_ptr<IterPriv> m_pData;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
./yaml-cpp/node.h:43:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
43 | std::auto_ptr<Node> Clone() const;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
./yaml-cpp/node.h:115:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
115 | std::auto_ptr<NodeOwnership> m_pOwnership;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:13,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
./yaml-cpp/emitter.h:98:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
98 | std::auto_ptr <EmitterState> m_pState;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | 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++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c sequencing_bias.cpp -o sequencing_bias.o
In file included from yaml-cpp/yaml.h:9,
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 /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
./yaml-cpp/parser.h:46:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
46 | std::auto_ptr<Directives> m_pDirectives;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
./yaml-cpp/iterator.h:20:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
20 | Iterator(std::auto_ptr<IterPriv> pData);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
./yaml-cpp/iterator.h:36:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
36 | std::auto_ptr<IterPriv> m_pData;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
./yaml-cpp/node.h:43:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
43 | std::auto_ptr<Node> Clone() const;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
./yaml-cpp/node.h:115:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
115 | std::auto_ptr<NodeOwnership> m_pOwnership;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:13,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
./yaml-cpp/emitter.h:98:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
98 | std::auto_ptr <EmitterState> m_pState;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | 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++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c twobitseq.cpp -o twobitseq.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/aliasmanager.cpp -o yaml-cpp/aliasmanager.o
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/aliasmanager.cpp:2:
./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);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/aliasmanager.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/aliasmanager.cpp:2:
./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;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/aliasmanager.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/aliasmanager.cpp:2:
./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;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/aliasmanager.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/aliasmanager.cpp:2:
./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;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/aliasmanager.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/directives.cpp -o yaml-cpp/directives.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/emitfromevents.cpp -o yaml-cpp/emitfromevents.o
In file included from yaml-cpp/emitfromevents.cpp:2:
./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;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitfromevents.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
In file included from yaml-cpp/emitter.cpp:1:
./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;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitter.cpp:2:
yaml-cpp/ptr_stack.h:29:24: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
29 | void push(std::auto_ptr<T> t) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitter.cpp:2:
yaml-cpp/ptr_stack.h:33:14: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
33 | std::auto_ptr<T> pop() {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> 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<T>::pop()’:
yaml-cpp/ptr_stack.h:34:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
34 | std::auto_ptr<T> t(m_data.back());
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> 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:24:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
24 | std::auto_ptr <SettingChangeBase> set(const T& value);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:10,
from yaml-cpp/emitter.cpp:2:
yaml-cpp/setting.h:59:21: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
59 | inline std::auto_ptr <SettingChangeBase> Setting<T>::set(const T& value) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> 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::SettingChangeBase> YAML::Setting<T>::set(const T&)’:
yaml-cpp/setting.h:60:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
60 | std::auto_ptr <SettingChangeBase> pChange(new SettingChange<T> (this));
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> 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:84:32: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
84 | void push(std::auto_ptr <SettingChangeBase> pSettingChange) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
In file included from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/ptr_stack.h:29:24: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
29 | void push(std::auto_ptr<T> t) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/ptr_stack.h:33:14: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
33 | std::auto_ptr<T> pop() {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> 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<T> ptr_stack<T>::pop()’:
yaml-cpp/ptr_stack.h:34:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
34 | std::auto_ptr<T> t(m_data.back());
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> 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:24:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
24 | std::auto_ptr <SettingChangeBase> set(const T& value);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:10,
from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/setting.h:59:21: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
59 | inline std::auto_ptr <SettingChangeBase> Setting<T>::set(const T& value) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> 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::SettingChangeBase> YAML::Setting<T>::set(const T&)’:
yaml-cpp/setting.h:60:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
60 | std::auto_ptr <SettingChangeBase> pChange(new SettingChange<T> (this));
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> 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:84:32: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
84 | void push(std::auto_ptr <SettingChangeBase> pSettingChange) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
yaml-cpp/emitterstate.cpp: In member function ‘void YAML::EmitterState::BeginGroup(YAML::GROUP_TYPE)’:
yaml-cpp/emitterstate.cpp:51:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
51 | std::auto_ptr<Group> pGroup(new Group(type));
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
yaml-cpp/emitterstate.cpp: In member function ‘void YAML::EmitterState::EndGroup(YAML::GROUP_TYPE)’:
yaml-cpp/emitterstate.cpp:71:30: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
71 | std::auto_ptr<Group> pFinishedGroup = m_groups.pop();
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/iterator.cpp:1:
./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);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/iterator.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/iterator.cpp:1:
./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;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/iterator.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/iterator.cpp:1:
./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;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/iterator.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/iterator.cpp:1:
./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;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/iterator.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
yaml-cpp/iterator.cpp:11:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
11 | Iterator::Iterator(std::auto_ptr<IterPriv> pData): m_pData(pData)
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/iterator.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/nodebuilder.cpp -o yaml-cpp/nodebuilder.o
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/nodebuilder.cpp:3:
./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);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/nodebuilder.h:10,
from yaml-cpp/nodebuilder.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/nodebuilder.cpp:3:
./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;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/nodebuilder.h:10,
from yaml-cpp/nodebuilder.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/nodebuilder.cpp:3:
./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;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/nodebuilder.h:10,
from yaml-cpp/nodebuilder.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/nodebuilder.cpp:3:
./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;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/nodebuilder.h:10,
from yaml-cpp/nodebuilder.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/node.cpp -o yaml-cpp/node.o
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
./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);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
./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;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/node.cpp:1:
./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;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/node.cpp:1:
./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;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/nodeownership.h:10,
from yaml-cpp/node.cpp:4:
yaml-cpp/ptr_vector.h:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
31 | void push_back(std::auto_ptr<T> t) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/node.cpp:10:
./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;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
yaml-cpp/node.cpp:54:14: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
54 | std::auto_ptr<Node> Node::Clone() const
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
yaml-cpp/node.cpp: In member function ‘std::auto_ptr<YAML::Node> YAML::Node::Clone() const’:
yaml-cpp/node.cpp:56:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
56 | std::auto_ptr<Node> pNode(new Node);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
yaml-cpp/node.cpp: In member function ‘YAML::Iterator YAML::Node::begin() const’:
yaml-cpp/node.cpp:148:54: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
148 | return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_seqData.begin())));
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
yaml-cpp/node.cpp:150:54: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
150 | return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_mapData.begin())));
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
yaml-cpp/node.cpp: In member function ‘YAML::Iterator YAML::Node::end() const’:
yaml-cpp/node.cpp:166:54: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
166 | return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_seqData.end())));
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
yaml-cpp/node.cpp:168:54: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
168 | return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_mapData.end())));
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/nodeownership.cpp -o yaml-cpp/nodeownership.o
In file included from yaml-cpp/nodeownership.h:10,
from yaml-cpp/nodeownership.cpp:1:
yaml-cpp/ptr_vector.h:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
31 | void push_back(std::auto_ptr<T> t) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/nodeownership.h:10,
from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/nodeownership.cpp:2:
./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);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/nodeownership.h:10,
from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/nodeownership.cpp:2:
./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;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/nodeownership.h:10,
from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/nodeownership.cpp:2:
./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;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/nodeownership.h:10,
from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/nodeownership.cpp:2:
./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;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/nodeownership.h:10,
from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
yaml-cpp/nodeownership.cpp: In member function ‘YAML::Node& YAML::NodeOwnership::_Create()’:
yaml-cpp/nodeownership.cpp:18:40: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
18 | m_nodes.push_back(std::auto_ptr<Node>(new Node));
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/nodeownership.h:10,
from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/null.cpp -o yaml-cpp/null.o
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/null.cpp:2:
./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);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/null.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/null.cpp:2:
./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;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/null.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/null.cpp:2:
./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;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/null.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/null.cpp:2:
./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;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/null.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
In file included from yaml-cpp/parser.cpp:1:
./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 /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/parser.cpp:1:
./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;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/parser.cpp:5:
./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);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/parser.cpp:5:
./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;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/parser.cpp:5:
./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;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/parser.cpp:5:
./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;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/scanner.h:15,
from yaml-cpp/parser.cpp:7:
yaml-cpp/ptr_vector.h:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
31 | void push_back(std::auto_ptr<T> t) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/parser.cpp:8:
yaml-cpp/singledocparser.h:56:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
56 | std::auto_ptr<CollectionStack> m_pCollectionStack;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -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:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
31 | void push_back(std::auto_ptr<T> t) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/scanner.h:15,
from yaml-cpp/scanner.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
yaml-cpp/scanner.cpp: In member function ‘void YAML::Scanner::StartStream()’:
yaml-cpp/scanner.cpp:237:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
237 | std::auto_ptr<IndentMarker> pIndent(new IndentMarker(-1, IndentMarker::NONE));
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/scanner.h:15,
from yaml-cpp/scanner.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> 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:284:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
284 | std::auto_ptr<IndentMarker> pIndent(new IndentMarker(column, type));
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/scanner.h:15,
from yaml-cpp/scanner.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -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:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
31 | void push_back(std::auto_ptr<T> t) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/scanner.h:15,
from yaml-cpp/scanscalar.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -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:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
31 | void push_back(std::auto_ptr<T> t) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/scanner.h:15,
from yaml-cpp/scantag.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -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:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
31 | void push_back(std::auto_ptr<T> t) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/scanner.h:15,
from yaml-cpp/scantoken.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -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:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
31 | void push_back(std::auto_ptr<T> t) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/scanner.h:15,
from yaml-cpp/simplekey.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/singledocparser.cpp -o yaml-cpp/singledocparser.o
In file included from yaml-cpp/singledocparser.cpp:1:
yaml-cpp/singledocparser.h:56:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
56 | std::auto_ptr<CollectionStack> m_pCollectionStack;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/singledocparser.h:13,
from yaml-cpp/singledocparser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> 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:28:62: warning: unused parameter ‘type’ [-Wunused-parameter]
28 | 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:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
31 | void push_back(std::auto_ptr<T> t) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/singledocparser.h:13,
from yaml-cpp/singledocparser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fpic -g -O2 -Wall -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o seqbias.so 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 /home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc/R/site-library/00LOCK-seqbias/00new/seqbias/libs
** 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
Warning: Package 'seqbias' is deprecated and will be removed from Bioconductor
version 3.19
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'seqbias' is deprecated and will be removed from Bioconductor
version 3.19
** testing if installed package keeps a record of temporary installation path
* DONE (seqbias)
