=> Bootstrap dependency digest>=20211023: found digest-20220214 ===> _pkgformat-check-vulnerable [hisat2-2.2.1nb4] ===> 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'. ===> build-message [hisat2-2.2.1nb4] ===> Building for hisat2-2.2.1nb4 c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -DCOMPILER_OPTIONS="\"-O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -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 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -DCOMPILER_OPTIONS="\"-O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -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 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -DCOMPILER_OPTIONS="\"-O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -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 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -DCOMPILER_OPTIONS="\"-O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -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 c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 \ -DCOMPILER_OPTIONS="\"-O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -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 c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 \ -DCOMPILER_OPTIONS="\"-O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -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 c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -DCOMPILER_OPTIONS="\"-O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -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 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 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 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 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; ^~~~~~~~~~~~ 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 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 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 /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 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 /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; ^~~~~~~~ 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) { 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; ^~~~~~~~ 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()) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 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 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; ^~~~~~~~ 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()) ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); ~~~~~~~~~~~~~~~~~~^~~~~~~~ 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 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 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 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 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

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