=> Bootstrap dependency digest>=20211023: found digest-20220214 ===> Skipping vulnerability checks. WARNING: No /usr/pkg/pkgdb/pkg-vulnerabilities file found. WARNING: To fix run: `/usr/sbin/pkg_admin -K /usr/pkg/pkgdb fetch-pkg-vulnerabilities'. ===> Building for hisat2-2.2.1nb2 c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include/python3.10 -DCOMPILER_OPTIONS="\"-O2 -fPIC -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include/python3.10 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat HISAT2_VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \ -I. -I third_party \ -o hisat2-build-s hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include/python3.10 -DCOMPILER_OPTIONS="\"-O2 -fPIC -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include/python3.10 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat HISAT2_VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-build-l hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include/python3.10 -DCOMPILER_OPTIONS="\"-O2 -fPIC -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include/python3.10 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat HISAT2_VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-align-s hisat2.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include/python3.10 -DCOMPILER_OPTIONS="\"-O2 -fPIC -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include/python3.10 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat HISAT2_VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-align-l hisat2.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread In file included from hisat2_build.cpp:35:0: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hisat2_build.cpp:35:0: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hgfm.h:24:0, from hisat2.cpp:33: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hgfm.h:24:0, from hisat2.cpp:33: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hisat2_build.cpp:35:0: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hisat2_build.cpp:35:0: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hgfm.h:24:0, from hisat2.cpp:33: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hgfm.h:24:0, from hisat2.cpp:33: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hisat2_build.cpp:35:0: gfm.h: In instantiation of 'void GFM::initFromVector(TStr&, const string&, const string&, const string&, const string&, const string&, const string&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, bool, index_t, index_t, index_t, int, EList*, EList >*, uint32_t, bool) [with TStr = SString; index_t = long unsigned int; std::__cxx11::string = std::__cxx11::basic_string; std::ofstream = std::basic_ofstream; uint32_t = unsigned int]': gfm.h:1039:23: required from 'GFM::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, index_t, index_t, index_t, int, EList&, EList&, index_t, const RefReadInParams&, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; int32_t = int; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' hgfm.h:1989:14: required from 'HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; local_index_t = short unsigned int; int32_t = int; std::__cxx11::string = std::__cxx11::basic_string; TIndexOffU = long unsigned int; uint32_t = unsigned int]' hisat2_build.cpp:535:15: required from 'void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int, bool, EList*, EList >*, EList*, EList >*) [with TStr = SString; std::__cxx11::string = std::__cxx11::basic_string]' hisat2_build.cpp:801:56: required from here gfm.h:2167:33: warning: variable 'template_len' set but not used [-Wunused-but-set-variable] index_t template_len = 0; ^~~~~~~~~~~~ In file included from hisat2_build.cpp:35:0: gfm.h: In instantiation of 'void GFM::initFromVector(TStr&, const string&, const string&, const string&, const string&, const string&, const string&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, bool, index_t, index_t, index_t, int, EList*, EList >*, uint32_t, bool) [with TStr = SString; index_t = unsigned int; std::__cxx11::string = std::__cxx11::basic_string; std::ofstream = std::basic_ofstream; uint32_t = unsigned int]': gfm.h:1039:23: required from 'GFM::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, index_t, index_t, index_t, int, EList&, EList&, index_t, const RefReadInParams&, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; int32_t = int; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' hgfm.h:1989:14: required from 'HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int; int32_t = int; std::__cxx11::string = std::__cxx11::basic_string; TIndexOffU = unsigned int; uint32_t = unsigned int]' hisat2_build.cpp:535:15: required from 'void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int, bool, EList*, EList >*, EList*, EList >*) [with TStr = SString; std::__cxx11::string = std::__cxx11::basic_string]' hisat2_build.cpp:801:56: required from here gfm.h:2167:33: warning: variable 'template_len' set but not used [-Wunused-but-set-variable] index_t template_len = 0; ^~~~~~~~~~~~ hisat2.cpp: In function 'void parseOptions(int, const char**)': hisat2.cpp:1823:2: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr presets(new PresetsV0()); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ hisat2.cpp: In function 'void multiseedSearchWorker_hisat2(void*)': hisat2.cpp:3167:2: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ hisat2.cpp:3168:2: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ps(patsrcFact->create()); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ hisat2.cpp:3189:2: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ hisat2.cpp: In function 'void driver(const char*, const string&, const string&)': hisat2.cpp:4035:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr refs( ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ hisat2.cpp: In function 'void parseOptions(int, const char**)': hisat2.cpp:1823:2: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr presets(new PresetsV0()); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from spliced_aligner.h:23:0, from hisat2.cpp:46: hi_aligner.h: In instantiation of 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]': hisat2.cpp:3556:58: required from here hi_aligner.h:4385:84: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) hi_aligner.h:4404:55: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(positions[p].first.tid != res.refid()) continue; ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:4405:63: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(positions[p].first.toff + 1000 < res.refoff() || ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:4406:52: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] res.refoff() + 1000 < positions[p].first.toff) continue; ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:4407:88: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) hi_aligner.h:4489:92: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) hi_aligner.h:4578:69: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] align2repeat = (numBestPair == 0 || numBestPair > rp.khits); ~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:4584:83: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] align2repeat = (rs->size() == 0 || sink.numBestUnp(rdi).first > rp.khits); hi_aligner.h:4614:55: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(sink.numBestUnp(rdi).first > rp.khits) { hi_aligner.h: In instantiation of 'bool HI_Aligner::pairReads(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, WalkMetrics&, PerReadMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]': hi_aligner.h:4088:26: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]' hisat2.cpp:3556:58: required from here hi_aligner.h:5990:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(_repeatConcordant[r].first == left.off() && ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:5991:52: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] _repeatConcordant[r].second == left2.off()) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]': hi_aligner.h:4107:48: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]' hisat2.cpp:3556:58: required from here hi_aligner.h:5661:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(nelt > 0 && nelt <= rp.kseeds && hitlen > max_hitlen) { ~~~~~^~~~~~~~~~~~ hi_aligner.h:5688:105: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(coord.off() + pepol.maxFragLen() * 2 < toff || toff + pepol.maxFragLen() * 2 < coord.off()) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ In file included from hgfm.h:24:0, from hisat2.cpp:33: gfm.h: In instantiation of 'void GFM::checkOrigs(const EList >&, bool) const [with index_t = long unsigned int]': hisat2.cpp:3815:17: required from 'void driver(const char*, const string&, const string&) [with TStr = SString; std::__cxx11::string = std::__cxx11::basic_string]' hisat2.cpp:4351:51: required from here gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^~~~~~~~ hisat2.cpp: In function 'void multiseedSearchWorker_hisat2(void*)': hisat2.cpp:3167:2: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from spliced_aligner.h:23:0, from hisat2.cpp:46: hi_aligner.h: In instantiation of 'index_t HI_Aligner::getAnchorHits(const GFM&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB&, const RepeatDB&, const BitPairReference&, RandomSource&, index_t, bool, EList >&, index_t, SharedTempVars&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool) [with index_t = long unsigned int; local_index_t = short unsigned int]': hi_aligner.h:5525:36: required from 'bool HI_Aligner::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]' hi_aligner.h:4080:36: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]' hisat2.cpp:3556:58: required from here hi_aligner.h:5150:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(coord.ref() == numeric_limits::max()) ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hisat2.cpp:3168:2: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ps(patsrcFact->create()); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ hisat2.cpp:3189:2: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ hi_aligner.h: In instantiation of 'static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long unsigned int]': hi_aligner.h:5692:54: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]' hi_aligner.h:4107:48: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]' hisat2.cpp:3556:58: required from here hi_aligner.h:2267:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] findSSOffs(gfm, altdb, (coord.joinedOff() >= width ? (index_t)(coord.joinedOff() - width) : 0), (index_t)(coord.joinedOff() + width), ssOffs); ~~~~~~~~~~~~~~~~~~^~~~~~~~ hisat2.cpp: In function 'void driver(const char*, const string&, const string&)': hisat2.cpp:4035:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr refs( ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from aligner_seed2.h:109:0, from aligner_driver.h:78, from hi_aligner.h:41, from spliced_aligner.h:23, from hisat2.cpp:46: group_walk.h: In instantiation of 'std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]': group_walk.h:1517:4: required from 'bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]' hi_aligner.h:5901:9: required from 'bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = long unsigned int; local_index_t = short unsigned int]' hi_aligner.h:5664:38: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]' hi_aligner.h:4107:48: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]' hisat2.cpp:3556:58: required from here group_walk.h:1147:60: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(new_node_bot - new_node_top < gws.map.size()) { group_walk.h:1158:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(index_t j = 0; j + 1 < gws.map.size(); j++) { group_walk.h:1213:69: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(node_range.second - node_range.first < st.back().map_.size()) { group_walk.h:1224:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { In file included from spliced_aligner.h:23:0, from hisat2.cpp:46: hi_aligner.h: In instantiation of 'static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]': hi_aligner.h:717:28: required from 'static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]' hi_aligner.h:2337:47: required from 'static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long unsigned int]' hi_aligner.h:5692:54: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]' hi_aligner.h:4107:48: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]' hisat2.cpp:3556:58: required from here hi_aligner.h:2801:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(rfoff >= contig_len) return 0; ~~~~~~^~~~~~~~~~~~~ hi_aligner.h:2879:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(alt_range.first >= alts.size()) { hi_aligner.h:3044:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i = 0; i < alt.len; i++) { ~~^~~~~~~~~ hi_aligner.h:3085:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { ~~~~~^~~~~~~~ hi_aligner.h:3161:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(alignedLen == next_rdlen) return rdlen; ~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3197:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(mm_max_rd_i + rdoff > best_rdoff) { ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:3202:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] } else if(mm_max_rd_i + rdoff == best_rdoff) { ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3454:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(best_rdoff < rdoff + rd_i) { ~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from spliced_aligner.h:23:0, from hisat2.cpp:46: hi_aligner.h: In instantiation of 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]': hi_aligner.h:4107:48: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]' hisat2.cpp:3556:58: required from here hi_aligner.h:5688:105: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(coord.off() + pepol.maxFragLen() * 2 < toff || toff + pepol.maxFragLen() * 2 < coord.off()) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ In file included from aligner_seed2.h:109:0, from aligner_driver.h:78, from hi_aligner.h:41, from spliced_aligner.h:23, from hisat2.cpp:46: group_walk.h: In instantiation of 'std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]': group_walk.h:494:14: required from 'std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]' group_walk.h:1453:3: required from 'void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]' hi_aligner.h:5896:5: required from 'bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = long unsigned int; local_index_t = short unsigned int]' hi_aligner.h:5664:38: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]' hi_aligner.h:4107:48: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]' hisat2.cpp:3556:58: required from here group_walk.h:785:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(i + 1 < tmp_zOffs.size() && new_top == tmp_zOffs[i+1]) { group_walk.h:789:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(new_top - top == tmp_gbwt_to_node.size()) { group_walk.h:795:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(i + 1 < tmp_zOffs.size()) { group_walk.h:801:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(new_bot - top < tmp_gbwt_to_node.size()) { In file included from spliced_aligner.h:23:0, from hisat2.cpp:46: hi_aligner.h: In instantiation of 'void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = long unsigned int]': hi_aligner.h:2915:39: required from 'static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]' hi_aligner.h:717:28: required from 'static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]' hi_aligner.h:2337:47: required from 'static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long unsigned int]' hi_aligner.h:5692:54: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]' hi_aligner.h:4107:48: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]' hisat2.cpp:3556:58: required from here hi_aligner.h:2660:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(ht_range.first >= haplotypes.size()) hi_aligner.h:2675:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(ht_list[h].first == ht_range.first) { ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2713:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(ht_list[h].first == ht_range.first) { ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2737:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(; ht_range.second < haplotypes.size(); ht_range.second++) { hi_aligner.h:2744:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(ht_list[h].first == ht_range.second) { ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from hgfm.h:24:0, from hisat2.cpp:33: gfm.h: In instantiation of 'void GFM::checkOrigs(const EList >&, bool) const [with index_t = unsigned int]': hisat2.cpp:3815:17: required from 'void driver(const char*, const string&, const string&) [with TStr = SString; std::__cxx11::string = std::__cxx11::basic_string]' hisat2.cpp:4351:51: required from here gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^~~~~~~~ In file included from hisat2.cpp:46:0: spliced_aligner.h: In instantiation of 'int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int; int64_t = long int]': hisat2.cpp:4370:1: required from here spliced_aligner.h:408:18: warning: variable 'another_spliced' set but not used [-Wunused-but-set-variable] bool another_spliced = false; ^~~~~~~~~~~~~~~ spliced_aligner.h:782:65: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] tempHit.score() + sc.sc(0) * hit.rdoff() >= hit.score()) { spliced_aligner.h:1465:105: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] combinedHit.score() + sc.sc(0) * (rdlen - hit.rdoff() - hit.len() - hit.trim5()) >= hit.score()) { In file included from spliced_aligner.h:23:0, from hisat2.cpp:46: hi_aligner.h: In instantiation of 'bool GenomeHit::combineWith(const GenomeHit&, const Read&, const GFM&, const BitPairReference&, const ALTDB&, const RepeatDB&, SpliceSiteDB&, SwAligner&, SwMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, index_t, index_t, index_t, index_t, index_t, const SpliceSite*, bool) [with index_t = long unsigned int; TAlScore = long int]': spliced_aligner.h:494:30: required from 'int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int; int64_t = long int]' hisat2.cpp:4370:1: required from here hi_aligner.h:1926:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(alt.seq == rdc) { ~~~~~~~~^~~~~~ hi_aligner.h: In instantiation of 'index_t HI_Aligner::globalGFMSearch(const GFM&, const Read&, const Scoring&, const ReportingParams&, bool, index_t, index_t&, index_t&, index_t&, index_t&, index_t&, EList >&, RandomSource&, bool&, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]': spliced_aligner.h:1086:25: required from 'int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int; int64_t = long int]' hisat2.cpp:4370:1: required from here hi_aligner.h:6719:85: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(node_range.first < node_range.second && node_range.second - node_range.first <= rp.kseeds) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from aligner_seed2.h:109:0, from aligner_driver.h:78, from hi_aligner.h:41, from spliced_aligner.h:23, from hisat2.cpp:46: group_walk.h: In instantiation of 'std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]': group_walk.h:1517:4: required from 'bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]' hi_aligner.h:5901:9: required from 'bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]' hi_aligner.h:5664:38: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]' hi_aligner.h:4107:48: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]' hisat2.cpp:3556:58: required from here group_walk.h:1147:60: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(new_node_bot - new_node_top < gws.map.size()) { group_walk.h:1158:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(index_t j = 0; j + 1 < gws.map.size(); j++) { group_walk.h:1213:69: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(node_range.second - node_range.first < st.back().map_.size()) { group_walk.h:1224:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { In file included from spliced_aligner.h:23:0, from hisat2.cpp:46: hi_aligner.h: In instantiation of 'static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]': hi_aligner.h:717:28: required from 'static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]' hi_aligner.h:2337:47: required from 'static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]' hi_aligner.h:5692:54: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]' hi_aligner.h:4107:48: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]' hisat2.cpp:3556:58: required from here hi_aligner.h:2801:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(rfoff >= contig_len) return 0; ~~~~~~^~~~~~~~~~~~~ hi_aligner.h:2879:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(alt_range.first >= alts.size()) { hi_aligner.h:3044:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i = 0; i < alt.len; i++) { ~~^~~~~~~~~ hi_aligner.h:3085:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { ~~~~~^~~~~~~~ hi_aligner.h:3161:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(alignedLen == next_rdlen) return rdlen; ~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3197:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(mm_max_rd_i + rdoff > best_rdoff) { ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:3202:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] } else if(mm_max_rd_i + rdoff == best_rdoff) { ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3454:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(best_rdoff < rdoff + rd_i) { ~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from aligner_seed2.h:109:0, from aligner_driver.h:78, from hi_aligner.h:41, from spliced_aligner.h:23, from hisat2.cpp:46: group_walk.h: In instantiation of 'std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]': group_walk.h:494:14: required from 'std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]' group_walk.h:1453:3: required from 'void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]' hi_aligner.h:5896:5: required from 'bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]' hi_aligner.h:5664:38: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]' hi_aligner.h:4107:48: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]' hisat2.cpp:3556:58: required from here group_walk.h:785:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(i + 1 < tmp_zOffs.size() && new_top == tmp_zOffs[i+1]) { group_walk.h:789:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(new_top - top == tmp_gbwt_to_node.size()) { group_walk.h:795:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(i + 1 < tmp_zOffs.size()) { group_walk.h:801:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(new_bot - top < tmp_gbwt_to_node.size()) { In file included from spliced_aligner.h:23:0, from hisat2.cpp:46: hi_aligner.h: In instantiation of 'void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = unsigned int]': hi_aligner.h:2915:39: required from 'static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]' hi_aligner.h:717:28: required from 'static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]' hi_aligner.h:2337:47: required from 'static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]' hi_aligner.h:5692:54: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]' hi_aligner.h:4107:48: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]' hisat2.cpp:3556:58: required from here hi_aligner.h:2660:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(ht_range.first >= haplotypes.size()) hi_aligner.h:2675:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(ht_list[h].first == ht_range.first) { ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2713:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(ht_list[h].first == ht_range.first) { ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2737:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(; ht_range.second < haplotypes.size(); ht_range.second++) { hi_aligner.h:2744:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(ht_list[h].first == ht_range.second) { ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from hisat2.cpp:46:0: spliced_aligner.h: In instantiation of 'int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long int]': hisat2.cpp:4370:1: required from here spliced_aligner.h:408:18: warning: variable 'another_spliced' set but not used [-Wunused-but-set-variable] bool another_spliced = false; ^~~~~~~~~~~~~~~ In file included from spliced_aligner.h:23:0, from hisat2.cpp:46: hi_aligner.h: In instantiation of 'bool GenomeHit::combineWith(const GenomeHit&, const Read&, const GFM&, const BitPairReference&, const ALTDB&, const RepeatDB&, SpliceSiteDB&, SwAligner&, SwMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, index_t, index_t, index_t, index_t, index_t, const SpliceSite*, bool) [with index_t = unsigned int; TAlScore = long int]': spliced_aligner.h:494:30: required from 'int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long int]' hisat2.cpp:4370:1: required from here hi_aligner.h:1926:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(alt.seq == rdc) { ~~~~~~~~^~~~~~ ref_read.cpp: In function 'std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)': ref_read.cpp:367:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(i + 1 >= recs.size() || recs[i+1].first) { ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function 'std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)': ref_read.cpp:440:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(i + 1 >= recs.size() || recs[i+1].first) { ~~~~~~^~~~~~~~~~~~~~ In file included from gfm.h:59:0, from hgfm.h:24, from hisat2.cpp:33: repeat.h: In member function 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]': repeat.h:41:20: warning: 'cmp.RepeatCoord::fw' may be used uninitialized in this function [-Wmaybe-uninitialized] if(fw != o.fw) ~~^~ repeat.h:43:26: warning: 'cmp.RepeatCoord::alleleID' may be used uninitialized in this function [-Wmaybe-uninitialized] if(alleleID != o.alleleID) ~~^~~~~~~~ In file included from gfm.h:59:0, from hgfm.h:24, from hisat2.cpp:33: repeat.h: In member function 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]': repeat.h:41:20: warning: 'cmp.RepeatCoord::fw' may be used uninitialized in this function [-Wmaybe-uninitialized] if(fw != o.fw) ~~^~ repeat.h:43:26: warning: 'cmp.RepeatCoord::alleleID' may be used uninitialized in this function [-Wmaybe-uninitialized] if(alleleID != o.alleleID) ~~^~~~~~~~ ref_read.cpp: In function 'std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)': ref_read.cpp:367:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(i + 1 >= recs.size() || recs[i+1].first) { ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function 'std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)': ref_read.cpp:440:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(i + 1 >= recs.size() || recs[i+1].first) { ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from edit.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from edit.cpp:21: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from edit.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from edit.cpp:21: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21:0: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from gfm.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21:0: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from gfm.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ reference.cpp: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': reference.cpp:522:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^~~~~~~~~~ reference.cpp:516:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] bool binarySearched = false; ^~~~~~~~~~~~~~ In file included from gfm.cpp:21:0: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from gfm.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21:0: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from gfm.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ reference.cpp: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': reference.cpp:522:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^~~~~~~~~~ reference.cpp:516:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] bool binarySearched = false; ^~~~~~~~~~~~~~ ref_read.cpp: In function 'std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)': ref_read.cpp:367:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(i + 1 >= recs.size() || recs[i+1].first) { ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function 'std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)': ref_read.cpp:440:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(i + 1 >= recs.size() || recs[i+1].first) { ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function 'std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)': ref_read.cpp:367:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(i + 1 >= recs.size() || recs[i+1].first) { ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function 'std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)': ref_read.cpp:440:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(i + 1 >= recs.size() || recs[i+1].first) { ~~~~~~^~~~~~~~~~~~~~ c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include/python3.10 \ -DCOMPILER_OPTIONS="\"-O2 -fPIC -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include/python3.10 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat HISAT2_VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DHISAT2_INSPECT_MAIN -Wall \ -I. -I third_party -I . \ -o hisat2-inspect-s hisat2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread In file included from splice_site.h:34:0, from edit.h:30, from edit.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from edit.cpp:21: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from edit.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from edit.cpp:21: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include/python3.10 \ -DCOMPILER_OPTIONS="\"-O2 -fPIC -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include/python3.10 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat HISAT2_VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN -Wall \ -I. -I third_party -I . \ -o hisat2-inspect-l hisat2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread In file included from hisat2_inspect.cpp:25:0: alt.h: In member function 'bool ALT::repOk() const': assert_helpers.h:227:11: warning: comparison of constant '1' with boolean expression is always true [-Wbool-compare] if(!((a) <= (b))) { \ ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro 'assert_leq' assert_leq(fw, 1); ^~~~~~~~~~ In file included from hgfm.h:24:0, from hisat2_inspect.cpp:27: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from hgfm.h:24, from hisat2_inspect.cpp:27: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hgfm.h:24:0, from hisat2_inspect.cpp:27: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from hgfm.h:24, from hisat2_inspect.cpp:27: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21:0: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from gfm.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21:0: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from gfm.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21:0: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from gfm.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21:0: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from gfm.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hisat2_inspect.cpp:25:0: alt.h: In member function 'bool ALT::repOk() const': assert_helpers.h:227:11: warning: comparison of constant '1' with boolean expression is always true [-Wbool-compare] if(!((a) <= (b))) { \ ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro 'assert_leq' assert_leq(fw, 1); ^~~~~~~~~~ reference.cpp: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': reference.cpp:522:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^~~~~~~~~~ reference.cpp:516:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] bool binarySearched = false; ^~~~~~~~~~~~~~ In file included from hgfm.h:24:0, from hisat2_inspect.cpp:27: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from hgfm.h:24, from hisat2_inspect.cpp:27: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hgfm.h:24:0, from hisat2_inspect.cpp:27: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from hgfm.h:24, from hisat2_inspect.cpp:27: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ reference.cpp: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': reference.cpp:522:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^~~~~~~~~~ reference.cpp:516:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] bool binarySearched = false; ^~~~~~~~~~~~~~ ref_read.cpp: In function 'std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)': ref_read.cpp:367:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(i + 1 >= recs.size() || recs[i+1].first) { ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function 'std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)': ref_read.cpp:440:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(i + 1 >= recs.size() || recs[i+1].first) { ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function 'std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)': ref_read.cpp:367:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(i + 1 >= recs.size() || recs[i+1].first) { ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function 'std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)': ref_read.cpp:440:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(i + 1 >= recs.size() || recs[i+1].first) { ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from edit.h:26:0, from edit.cpp:21: alt.h: In member function 'bool ALT::repOk() const': assert_helpers.h:227:11: warning: comparison of constant '1' with boolean expression is always true [-Wbool-compare] if(!((a) <= (b))) { \ ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro 'assert_leq' assert_leq(fw, 1); ^~~~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from edit.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from edit.cpp:21: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from edit.h:26:0, from edit.cpp:21: alt.h: In member function 'bool ALT::repOk() const': assert_helpers.h:227:11: warning: comparison of constant '1' with boolean expression is always true [-Wbool-compare] if(!((a) <= (b))) { \ ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro 'assert_leq' assert_leq(fw, 1); ^~~~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from edit.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from edit.cpp:21: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from alphabet.h:27:0, from gfm.h:40, from gfm.cpp:21: alt.h: In member function 'bool ALT::repOk() const': assert_helpers.h:227:11: warning: comparison of constant '1' with boolean expression is always true [-Wbool-compare] if(!((a) <= (b))) { \ ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro 'assert_leq' assert_leq(fw, 1); ^~~~~~~~~~ In file included from gfm.cpp:21:0: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from gfm.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21:0: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from gfm.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from alphabet.h:27:0, from gfm.h:40, from gfm.cpp:21: alt.h: In member function 'bool ALT::repOk() const': assert_helpers.h:227:11: warning: comparison of constant '1' with boolean expression is always true [-Wbool-compare] if(!((a) <= (b))) { \ ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro 'assert_leq' assert_leq(fw, 1); ^~~~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21:0: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from gfm.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21:0: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from gfm.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from aln_sink.cpp:20: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from aln_sink.cpp:20: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from aln_sink.cpp:20: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from aln_sink.cpp:20: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ c++ -O2 -fPIC -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include/python3.10 -DCOMPILER_OPTIONS="\"-O2 -fPIC -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include/python3.10 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat HISAT2_VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-repeat hisat2_repeat.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp mask.cpp qual.cpp aligner_bt.cpp scoring.cpp simple_func.cpp dp_framer.cpp aligner_result.cpp aligner_sw_driver.cpp aligner_sw.cpp aligner_swsse_ee_i16.cpp aligner_swsse_ee_u8.cpp aligner_swsse_loc_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse.cpp bit_packed_array.cpp repeat_builder.cpp diff_sample.cpp hisat2_repeat_main.cpp \ -lpthread In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hisat2_repeat.cpp:36:0: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from hisat2_repeat.cpp:31: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hisat2_repeat.cpp:36:0: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from hisat2_repeat.cpp:31: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ ref_read.cpp: In function 'std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)': ref_read.cpp:367:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(i + 1 >= recs.size() || recs[i+1].first) { ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function 'std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)': ref_read.cpp:440:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(i + 1 >= recs.size() || recs[i+1].first) { ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from edit.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from edit.cpp:21: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21:0: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from gfm.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21:0: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/memory:80:0, from gfm.h:28, from gfm.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ reference.cpp: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': reference.cpp:522:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^~~~~~~~~~ reference.cpp:516:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] bool binarySearched = false; ^~~~~~~~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from splice_site.cpp:20: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from splice_site.cpp:20: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from splice_site.cpp:20: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from splice_site.cpp:20: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from splice_site.cpp:20: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from splice_site.cpp:20: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from splice_site.cpp:20: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from splice_site.cpp:20: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ splice_site.cpp: In member function 'void SpliceSiteDB::read(const GFM&, const EList >&)': splice_site.cpp:717:59: warning: ?: using integer constants in boolean context, the expression will always evaluate to 'true' [-Wint-in-bool-context] exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC); ~~~~~~~~~~^~~~~~~~~~~~~~~~~ splice_site.cpp: In member function 'void SpliceSiteDB::read(const GFM&, const EList >&)': splice_site.cpp:717:59: warning: ?: using integer constants in boolean context, the expression will always evaluate to 'true' [-Wint-in-bool-context] exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC); ~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from bit_packed_array.cpp:24: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from bit_packed_array.cpp:23: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from bit_packed_array.cpp:24: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from bit_packed_array.cpp:23: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from repeat_builder.cpp:26: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from repeat_builder.cpp:25: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from repeat_builder.cpp:26: gfm.h:1189:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/g++/bits/locale_conv.h:41:0, from /usr/include/g++/locale:43, from /usr/include/g++/iomanip:43, from timer.h:26, from repeat_builder.cpp:25: /usr/include/g++/bits/unique_ptr.h:51:28: note: declared here template class auto_ptr; ^~~~~~~~ repeat_builder.cpp: In function 'std::__cxx11::string reverse_complement(const string&)': repeat_builder.cpp:88:32: warning: array subscript has type 'char' [-Wchar-subscripts] rev[i] = asc2dnacomp[nt]; ^ repeat_builder.cpp: In function 'std::__cxx11::string reverseComplement(const string&)': repeat_builder.cpp:200:39: warning: array subscript has type 'char' [-Wchar-subscripts] rc.push_back(asc2dnacomp[str[si - 1]]); ^ repeat_builder.cpp: In member function 'int CoordHelper::mapJoinedOffToSeq(TIndexOffU)': repeat_builder.cpp:403:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(size_t i = 0; i < num_cached_; i++) { ~~^~~~~~~~~~~~~ repeat_builder.cpp: In function 'size_t extract_kmer(const string&, size_t, size_t)': repeat_builder.cpp:1217:53: warning: array subscript has type 'char' [-Wchar-subscripts] kmer = (kmer << 2) | asc2dna[seq[offset + i]]; ^ repeat_builder.cpp: In function 'size_t next_kmer(size_t, char, size_t)': repeat_builder.cpp:1225:38: warning: array subscript has type 'char' [-Wchar-subscripts] kmer = (kmer << 2) | asc2dna[base]; ^ repeat_builder.cpp: In function 'void find_gap_pos(const string&, const string&, EList&, EList&, bool, size_t, size_t, size_t&, size_t&, bool)': repeat_builder.cpp:1275:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int i = seq_len - 1; i >= gap_len; i--) { ~~^~~~~~~~~~ repeat_builder.cpp:1277:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(i == seq_len - 1) ed2[i] = add; ~~^~~~~~~~~~~~~~ repeat_builder.cpp: In member function 'void RB_SWAligner::makePadString(const string&, const string&, std::__cxx11::string&, size_t)': repeat_builder.cpp:2915:39: warning: array subscript has type 'char' [-Wchar-subscripts] pad[i] = "CGTA"[asc2dna[ref[i]]]; ^ repeat_builder.cpp:2919:43: warning: array subscript has type 'char' [-Wchar-subscripts] pad[i] = "CGTA"[asc2dna[pad[i]]]; ^ repeat_builder.cpp:2926:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(size_t i = 0; i < head_len; i++) { ~~^~~~~~~~~~ repeat_builder.cpp:2929:67: warning: array subscript has type 'char' [-Wchar-subscripts] pad[pad_start + i] = "CGTA"[asc2dna[pad[pad_start + i]]]; ^ repeat_builder.cpp: In member function 'int RB_SWAligner::alignStrings(const string&, const string&, EList&, Coord&)': repeat_builder.cpp:3065:13: warning: variable 'max_match_len' set but not used [-Wunused-but-set-variable] int max_match_len = 0; ^~~~~~~~~~~~~ In file included from repeat_builder.cpp:31:0: repeat_builder.cpp: In instantiation of 'RepeatBuilder::RepeatBuilder(TStr&, const EList&, const EList >&, bool, const string&) [with TStr = SString; std::__cxx11::string = std::__cxx11::basic_string]': repeat_builder.cpp:4753:16: required from here repeat_builder.h:947:17: warning: 'RepeatBuilder >::coordHelper_' will be initialized after [-Wreorder] CoordHelper coordHelper_; ^~~~~~~~~~~~ repeat_builder.h:940:10: warning: 'bool RepeatBuilder >::forward_only_' [-Wreorder] bool forward_only_; ^~~~~~~~~~~~~ repeat_builder.cpp:3167:1: warning: when initialized here [-Wreorder] RepeatBuilder::RepeatBuilder(TStr& s, ^~~~~~~~~~~~~~~~~~~ repeat_builder.cpp: In instantiation of 'void RepeatBuilder::build(const RepeatParameter&) [with TStr = SString]': repeat_builder.cpp:4753:16: required from here repeat_builder.cpp:3396:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(spos != string::npos) { ~~~~~^~~~~~~~~ repeat_builder.cpp:3426:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(spos != string::npos) { ~~~~~^~~~~~~~~ repeat_builder.cpp:3553:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ repeat_builder.cpp:3563:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ repeat_builder.cpp: In instantiation of 'void RepeatBuilder::saveConsensus(const RepeatParameter&, const string&) [with TStr = SString; std::__cxx11::string = std::__cxx11::basic_string]': repeat_builder.cpp:4753:16: required from here repeat_builder.cpp:4114:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if((oskip + out_len) == output_width) { ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp: In instantiation of 'void dump_tstr(const TStr&) [with TStr = SString]': repeat_builder.cpp:4754:46: required from here repeat_builder.cpp:309:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(size_t j = 0; (j < print_width) && (i + j < s_len); j++) { ~~~^~~~~~~~~~~~~~ repeat_builder.cpp:310:25: warning: array subscript has type 'char' [-Wchar-subscripts] buf.push_back("ACGTN"[s[i + j]]); ~~~~~~~^ repeat_builder.cpp: In instantiation of 'std::__cxx11::string getString(const TStr&, TIndexOffU, size_t) [with TStr = SString; std::__cxx11::string = std::__cxx11::basic_string; TIndexOffU = long unsigned int; size_t = long unsigned int]': repeat_builder.cpp:3312:30: required from 'void RepeatBuilder::build(const RepeatParameter&) [with TStr = SString]' repeat_builder.cpp:4753:16: required from here repeat_builder.cpp:272:19: warning: array subscript has type 'char' [-Wchar-subscripts] char nt = "ACGT"[ref[start + i]]; ~~~~~~^ repeat_builder.cpp: In instantiation of 'void getString(const TStr&, TIndexOffU, size_t, std::__cxx11::string&) [with TStr = SString; TIndexOffU = long unsigned int; size_t = long unsigned int; std::__cxx11::string = std::__cxx11::basic_string]': repeat_builder.cpp:3545:22: required from 'void RepeatBuilder::build(const RepeatParameter&) [with TStr = SString]' repeat_builder.cpp:4753:16: required from here repeat_builder.cpp:286:25: warning: array subscript has type 'char' [-Wchar-subscripts] char nt = "ACGT"[ref[start + i]]; ~~~~~~^