############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL seqbias ### ############################################################################## ############################################################################## * 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 45 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 46 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 20 | Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 36 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 43 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 115 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 98 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 45 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 46 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 20 | Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 36 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 43 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 115 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 98 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 45 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 46 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 20 | Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 36 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 43 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 115 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 98 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 45 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 46 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 20 | Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 36 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 43 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 115 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 98 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 20 | Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 36 | std::auto_ptr 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 class auto_ptr; | ^~~~~~~~ In file included from yaml-cpp/aliasmanager.cpp:2: ./yaml-cpp/node.h:43:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 43 | std::auto_ptr 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 class auto_ptr; | ^~~~~~~~ In file included from yaml-cpp/aliasmanager.cpp:2: ./yaml-cpp/node.h:115:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 115 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 98 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 98 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 29 | void push(std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 33 | std::auto_ptr 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 class auto_ptr; | ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:9, from yaml-cpp/emitter.cpp:2: yaml-cpp/ptr_stack.h: In member function ‘std::auto_ptr<_Up> ptr_stack::pop()’: yaml-cpp/ptr_stack.h:34:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 34 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 24 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 59 | inline std::auto_ptr Setting::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 class auto_ptr; | ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:10, from yaml-cpp/emitter.cpp:2: yaml-cpp/setting.h: In member function ‘std::auto_ptr YAML::Setting::set(const T&)’: yaml-cpp/setting.h:60:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 60 | std::auto_ptr pChange(new SettingChange (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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 84 | void push(std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 29 | void push(std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 33 | std::auto_ptr 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 class auto_ptr; | ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:9, from yaml-cpp/emitterstate.cpp:1: yaml-cpp/ptr_stack.h: In member function ‘std::auto_ptr ptr_stack::pop()’: yaml-cpp/ptr_stack.h:34:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 34 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 24 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 59 | inline std::auto_ptr Setting::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 class auto_ptr; | ^~~~~~~~ In file included from yaml-cpp/emitterstate.h:10, from yaml-cpp/emitterstate.cpp:1: yaml-cpp/setting.h: In member function ‘std::auto_ptr YAML::Setting::set(const T&)’: yaml-cpp/setting.h:60:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 60 | std::auto_ptr pChange(new SettingChange (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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 84 | void push(std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 51 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 71 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 20 | Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 36 | std::auto_ptr 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 class auto_ptr; | ^~~~~~~~ In file included from yaml-cpp/iterator.cpp:1: ./yaml-cpp/node.h:43:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 43 | std::auto_ptr 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 class auto_ptr; | ^~~~~~~~ In file included from yaml-cpp/iterator.cpp:1: ./yaml-cpp/node.h:115:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 115 | std::auto_ptr 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 class auto_ptr; | ^~~~~~~~ yaml-cpp/iterator.cpp:11:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 11 | Iterator::Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 20 | Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 36 | std::auto_ptr 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 class auto_ptr; | ^~~~~~~~ In file included from yaml-cpp/nodebuilder.cpp:3: ./yaml-cpp/node.h:43:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 43 | std::auto_ptr 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 class auto_ptr; | ^~~~~~~~ In file included from yaml-cpp/nodebuilder.cpp:3: ./yaml-cpp/node.h:115:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 115 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 20 | Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 36 | std::auto_ptr 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 class auto_ptr; | ^~~~~~~~ In file included from yaml-cpp/node.cpp:1: ./yaml-cpp/node.h:43:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 43 | std::auto_ptr 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 class auto_ptr; | ^~~~~~~~ In file included from yaml-cpp/node.cpp:1: ./yaml-cpp/node.h:115:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 115 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 31 | void push_back(std::auto_ptr 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 class auto_ptr; | ^~~~~~~~ In file included from yaml-cpp/node.cpp:10: ./yaml-cpp/emitter.h:98:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 98 | std::auto_ptr 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 class auto_ptr; | ^~~~~~~~ yaml-cpp/node.cpp:54:14: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 54 | 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 class auto_ptr; | ^~~~~~~~ yaml-cpp/node.cpp: In member function ‘std::auto_ptr YAML::Node::Clone() const’: yaml-cpp/node.cpp:56:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 56 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 148 | return Iterator(std::auto_ptr(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 class auto_ptr; | ^~~~~~~~ yaml-cpp/node.cpp:150:54: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 150 | return Iterator(std::auto_ptr(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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 166 | return Iterator(std::auto_ptr(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 class auto_ptr; | ^~~~~~~~ yaml-cpp/node.cpp:168:54: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 168 | return Iterator(std::auto_ptr(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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 31 | void push_back(std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 20 | Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 36 | std::auto_ptr 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 class auto_ptr; | ^~~~~~~~ In file included from yaml-cpp/nodeownership.cpp:2: ./yaml-cpp/node.h:43:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 43 | std::auto_ptr 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 class auto_ptr; | ^~~~~~~~ In file included from yaml-cpp/nodeownership.cpp:2: ./yaml-cpp/node.h:115:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 115 | std::auto_ptr 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 class auto_ptr; | ^~~~~~~~ yaml-cpp/nodeownership.cpp: In member function ‘YAML::Node& YAML::NodeOwnership::_Create()’: yaml-cpp/nodeownership.cpp:18:40: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 18 | m_nodes.push_back(std::auto_ptr(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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 20 | Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 36 | std::auto_ptr 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 class auto_ptr; | ^~~~~~~~ In file included from yaml-cpp/null.cpp:2: ./yaml-cpp/node.h:43:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 43 | std::auto_ptr 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 class auto_ptr; | ^~~~~~~~ In file included from yaml-cpp/null.cpp:2: ./yaml-cpp/node.h:115:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 115 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 45 | std::auto_ptr 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 class auto_ptr; | ^~~~~~~~ In file included from yaml-cpp/parser.cpp:1: ./yaml-cpp/parser.h:46:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 46 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 20 | Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 36 | std::auto_ptr 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 class auto_ptr; | ^~~~~~~~ In file included from yaml-cpp/parser.cpp:5: ./yaml-cpp/node.h:43:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 43 | std::auto_ptr 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 class auto_ptr; | ^~~~~~~~ In file included from yaml-cpp/parser.cpp:5: ./yaml-cpp/node.h:115:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 115 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 31 | void push_back(std::auto_ptr 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 class auto_ptr; | ^~~~~~~~ In file included from yaml-cpp/parser.cpp:8: yaml-cpp/singledocparser.h:56:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 56 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 31 | void push_back(std::auto_ptr 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 class auto_ptr; | ^~~~~~~~ yaml-cpp/scanner.cpp: In member function ‘void YAML::Scanner::StartStream()’: yaml-cpp/scanner.cpp:237:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 237 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 284 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 31 | void push_back(std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 31 | void push_back(std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 31 | void push_back(std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 31 | void push_back(std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 56 | std::auto_ptr 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 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 std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 31 | void push_back(std::auto_ptr 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 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)