+ case "${usergroup_phase}" in + local run_cmd + run_cmd=run_su + shift + run_su /opt/local/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=39 WRKLOG=/tmp/bulklog/hisat2-2.1.0.23nb5/work.log + su pbulk -c '"$@"' make /opt/local/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=39 WRKLOG=/tmp/bulklog/hisat2-2.1.0.23nb5/work.log => Bootstrap dependency digest>=20211023: found digest-20211023 ===> Building for hisat2-2.1.0.23nb5 g++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/opt/local/include/python3.9 -I/opt/local/include -DCOMPILER_OPTIONS="\"-pipe -O2 -msave-args -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/opt/local/include/python3.9 -I/opt/local/include \"" \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -DMASSIVE_DATA_RLCSA \ -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 \ -L/opt/local/gcc10/lib/gcc/x86_64-sun-solaris2.11/10.3.0 -Wl,-R/opt/local/gcc10/lib/gcc/x86_64-sun-solaris2.11/10.3.0 -pthread -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 -L/opt/local/lib -Wl,-R/opt/local/lib In file included from hisat2_build.cpp:35: 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:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1099 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from hisat2_build.cpp:35: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1103 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, 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:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1099 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1103 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.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:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1099 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/memory:83, from gfm.h:28, from gfm.cpp:21: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1103 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/memory:83, from gfm.h:28, from gfm.cpp:21: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ g++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/opt/local/include/python3.9 -I/opt/local/include -DCOMPILER_OPTIONS="\"-pipe -O2 -msave-args -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/opt/local/include/python3.9 -I/opt/local/include \"" \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG \ -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 \ -L/opt/local/gcc10/lib/gcc/x86_64-sun-solaris2.11/10.3.0 -Wl,-R/opt/local/gcc10/lib/gcc/x86_64-sun-solaris2.11/10.3.0 -pthread -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 -L/opt/local/lib -Wl,-R/opt/local/lib In file included from hisat2_build.cpp:35: 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:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1099 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from hisat2_build.cpp:35: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1103 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, 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:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1099 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1103 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.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:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1099 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/memory:83, from gfm.h:28, from gfm.cpp:21: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1103 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/memory:83, from gfm.h:28, from gfm.cpp:21: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ g++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/opt/local/include/python3.9 -I/opt/local/include -DCOMPILER_OPTIONS="\"-pipe -O2 -msave-args -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/opt/local/include/python3.9 -I/opt/local/include \"" \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG \ -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 \ -L/opt/local/gcc10/lib/gcc/x86_64-sun-solaris2.11/10.3.0 -Wl,-R/opt/local/gcc10/lib/gcc/x86_64-sun-solaris2.11/10.3.0 -pthread -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 -L/opt/local/lib -Wl,-R/opt/local/lib In file included from hgfm.h:24, 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:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1099 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/memory:83, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1103 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/memory:83, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function 'void parseOptions(int, const char**)': hisat2.cpp:1753:2: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1753 | auto_ptr presets(new PresetsV0()); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/memory:83, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: At global scope: hisat2.cpp:1910:20: error: conflicting declaration 'typedef TIndexOffU index_t' 1910 | typedef TIndexOffU index_t; | ^~~~~~~ In file included from /usr/include/sys/wait.h:37, from /usr/include/stdlib.h:45, from /opt/local/gcc10/include/c++/10.3.0/cstdlib:75, from /opt/local/gcc10/include/c++/10.3.0/stdlib.h:36, from hisat2.cpp:20: /usr/include/sys/types.h:128:16: note: previous declaration as 'typedef short int index_t' 128 | typedef short index_t; | ^~~~~~~ hisat2.cpp: In function 'void multiseedSearchWorker_hisat2(void*)': hisat2.cpp:3068:2: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 3068 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/memory:83, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3069:2: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 3069 | auto_ptr ps(patsrcFact->create()); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/memory:83, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3085:2: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 3085 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/memory:83, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function 'void driver(const char*, const string&, const string&)': hisat2.cpp:3826:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 3826 | auto_ptr refs( | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/memory:83, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3868:38: error: no matching function for call to 'SpliceSiteDB::read(HGFM&, EList, 128>&)' 3868 | ssdb->read(gfm, altdb->alts()); | ^ In file included from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from hisat2.cpp:37: splice_site.h:547:10: note: candidate: 'bool SpliceSiteDB::read() const' 547 | bool read() const { return _read; } | ^~~~ splice_site.h:547:10: note: candidate expects 0 arguments, 2 provided splice_site.h:556:10: note: candidate: 'void SpliceSiteDB::read(const GFM&, const EList >&)' 556 | void read(const GFM& gfm, const EList >& alts); | ^~~~ splice_site.h:556:38: note: no known conversion for argument 1 from 'HGFM' to 'const GFM&' 556 | void read(const GFM& gfm, const EList >& alts); | ~~~~~~~~~~~~~~~~~~~~~~~^~~ splice_site.h:557:10: note: candidate: 'void SpliceSiteDB::read(std::ifstream&, bool)' 557 | void read(ifstream& in, bool known = false); | ^~~~ splice_site.h:557:25: note: no known conversion for argument 1 from 'HGFM' to 'std::ifstream&' {aka 'std::basic_ifstream&'} 557 | void read(ifstream& in, bool known = false); | ~~~~~~~~~~^~ In file included from ds.h:32, from sequence_io.h:28, from multikey_qsort.h:24, from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from hgfm.h:24, from hisat2.cpp:33: hi_aligner.h: In instantiation of 'index_t HI_Aligner::partialSearch(const GFM&, const Read&, const Scoring&, const ReportingParams&, bool, std::size_t, std::size_t&, std::size_t&, ReadBWTHit&, RandomSource&, bool&, bool&) [with index_t = short int; local_index_t = short unsigned int; std::size_t = long unsigned int]': hi_aligner.h:4041:13: required from 'bool HI_Aligner::nextBWT(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, index_t&, bool&, WalkMetrics&, PerReadMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' hi_aligner.h:3897:15: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' hisat2.cpp:3435:151: required from here btypes.h:39:19: warning: overflow in conversion from 'unsigned int' to 'short int' changes value from '4294967295' to '-1' [-Woverflow] 39 | #define INDEX_MAX 0xffffffff | ^~~~~~~~~~ hi_aligner.h:5654:37: note: in expansion of macro 'INDEX_MAX' 5654 | partialHits.back().init(INDEX_MAX, | ^~~~~~~~~ btypes.h:39:19: warning: overflow in conversion from 'unsigned int' to 'short int' changes value from '4294967295' to '-1' [-Woverflow] 39 | #define INDEX_MAX 0xffffffff | ^~~~~~~~~~ hi_aligner.h:5655:37: note: in expansion of macro 'INDEX_MAX' 5655 | INDEX_MAX, | ^~~~~~~~~ btypes.h:39:19: warning: overflow in conversion from 'unsigned int' to 'short int' changes value from '4294967295' to '-1' [-Woverflow] 39 | #define INDEX_MAX 0xffffffff | ^~~~~~~~~~ hi_aligner.h:5656:37: note: in expansion of macro 'INDEX_MAX' 5656 | INDEX_MAX, | ^~~~~~~~~ btypes.h:39:19: warning: overflow in conversion from 'unsigned int' to 'short int' changes value from '4294967295' to '-1' [-Woverflow] 39 | #define INDEX_MAX 0xffffffff | ^~~~~~~~~~ hi_aligner.h:5657:37: note: in expansion of macro 'INDEX_MAX' 5657 | INDEX_MAX, | ^~~~~~~~~ spliced_aligner.h: In instantiation of 'void SplicedAligner::hybridSearch(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]': spliced_aligner.h:113:6: required from here btypes.h:39:19: warning: overflow in conversion from 'unsigned int' to 'short int' changes value from '4294967295' to '-1' [-Woverflow] 39 | #define INDEX_MAX 0xffffffff | ^~~~~~~~~~ spliced_aligner.h:154:26: note: in expansion of macro 'INDEX_MAX' 154 | INDEX_MAX, | ^~~~~~~~~ sam.h: In instantiation of 'void SamConfig::printAlignedOptFlags(BTString&, bool, const Read&, AlnRes&, StackedAln&, const AlnFlags&, const AlnSetSumm&, const SeedAlSumm&, const PerReadMetrics&, const Scoring&, const char*, const ALTDB*) const [with index_t = short int; BTString = SStringExpandable]': aln_sink.h:3036:29: required from 'void AlnSinkSam::appendMate(BTString&, StackedAln&, const Read&, const Read*, TReadId, AlnRes*, AlnRes*, const AlnSetSumm&, const SeedAlSumm&, const SeedAlSumm&, const AlnFlags&, const PerReadMetrics&, const Mapq&, const Scoring&) [with index_t = short int; BTString = SStringExpandable; TReadId = long unsigned int]' aln_sink.h:1415:4: required from 'void AlnSinkSam::append(BTString&, StackedAln&, std::size_t, const Read*, const Read*, TReadId, AlnRes*, AlnRes*, const AlnSetSumm&, const SeedAlSumm&, const SeedAlSumm&, const AlnFlags*, const AlnFlags*, const PerReadMetrics&, const Mapq&, const Scoring&, bool) [with index_t = short int; BTString = SStringExpandable; std::size_t = long unsigned int; TReadId = long unsigned int]' aln_sink.h:1393:15: required from here btypes.h:39:19: warning: overflow in conversion from 'unsigned int' to 'short int' changes value from '4294967295' to '-1' [-Woverflow] 39 | #define INDEX_MAX 0xffffffff | ^~~~~~~~~~ sam.h:964:28: note: in expansion of macro 'INDEX_MAX' 964 | index_t prev_snp_idx = INDEX_MAX; | ^~~~~~~~~ In file included from splice_site.h:34, 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:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1099 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1103 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.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:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1099 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/memory:83, from gfm.h:28, from gfm.cpp:21: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1103 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/memory:83, from gfm.h:28, from gfm.cpp:21: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, 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:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1099 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/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: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1103 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/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: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, 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:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1099 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/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: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1103 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/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: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, 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:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1099 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/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: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, 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:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1103 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/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: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, 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:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1099 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1103 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, 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:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1099 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/iomanip:43, from aln_sink.cpp:20: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, 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:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1103 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/iomanip:43, from aln_sink.cpp:20: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, 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:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1099 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/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: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1103 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/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: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, 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:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1099 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/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: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, 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:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1103 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/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: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, 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:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1099 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/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: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1103 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/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: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, 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:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1099 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/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: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, 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:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1103 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/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: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, 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:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1099 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/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: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, 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:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1103 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/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: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, 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:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1099 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/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: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, 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:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1103 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/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: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, 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:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1099 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/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: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, 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:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1103 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/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: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, 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:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1099 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/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: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, 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:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1103 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/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: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, 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:1099:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1099 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from splice_site.cpp:20: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h:1103:3: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 1103 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/locale_conv.h:41, from /opt/local/gcc10/include/c++/10.3.0/locale:43, from /opt/local/gcc10/include/c++/10.3.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from splice_site.cpp:20: /opt/local/gcc10/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ gmake: *** [/data/jenkins/workspace/pkgsrc-2021Q4-x86_64/biology/hisat2/files/Makefile.pkg:282: hisat2-align-s] Error 1 *** Error code 2 Stop. bmake[1]: stopped in /data/jenkins/workspace/pkgsrc-2021Q4-x86_64/biology/hisat2 *** Error code 1 Stop. bmake: stopped in /data/jenkins/workspace/pkgsrc-2021Q4-x86_64/biology/hisat2