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This page was generated on 2021-10-15 15:06:19 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the Rhisat2 package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rhisat2.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1577/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Rhisat2 1.8.0 (landing page) Charlotte Soneson
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: Rhisat2 |
Version: 1.8.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch Rhisat2 |
StartedAt: 2021-10-14 10:32:21 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 10:37:54 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 332.7 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch Rhisat2 ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' * installing *source* package 'Rhisat2' ... ** using staged installation ** libs running 'src/Makefile.win' ... c:/rtools40/mingw64/bin/g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`c:/rtools40/mingw64/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -Wall -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 \ In file included from hisat2_build.cpp:35: gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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:1098:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<stringstream> ss(new stringstream()); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ In file included from hisat2_build.cpp:35: gfm.h:1102:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<FileBuf> fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ ref_read.cpp: In function 'std::pair<long long unsigned int, long long unsigned int> fastaRefReadSizes(EList<FileBuf*>&, EList<RefRecord>&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)': ref_read.cpp:327:22: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long long int'} and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] if(i + 1 >= recs.size() || recs[i+1].first) { ~~~~~~^~~~~~~~~~~~~~ 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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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:1098:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<stringstream> ss(new stringstream()); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1102:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<FileBuf> fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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:1098:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<stringstream> ss(new stringstream()); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from gfm.h:28, from gfm.cpp:21: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1102:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<FileBuf> fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from gfm.h:28, from gfm.cpp:21: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ reference.cpp: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': reference.cpp:456:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^~~~~~~~~~ reference.cpp:450:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] bool binarySearched = false; ^~~~~~~~~~~~~~ c:/rtools40/mingw64/bin/g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`c:/rtools40/mingw64/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -Wall \ -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 \ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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:1098:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<stringstream> ss(new stringstream()); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h:1102:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<FileBuf> fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ hisat2.cpp: In function 'void parseOptions(int, const char**)': hisat2.cpp:1753:2: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<Presets> presets(new PresetsV0()); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ hisat2.cpp: In function 'void multiseedSearchWorker_hisat2(void*)': hisat2.cpp:3068:2: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<PatternSourcePerThreadFactory> patsrcFact(createPatsrcFactory(patsrc, tid)); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ hisat2.cpp:3069:2: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<PatternSourcePerThread> ps(patsrcFact->create()); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ hisat2.cpp:3085:2: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<Mapq> bmapq(new_mapq(mapqv, scoreMin, sc)); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ hisat2.cpp: In function 'void driver(const char*, const string&, const string&)': hisat2.cpp:3826:9: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<BitPairReference> refs( ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In instantiation of 'void GFM<index_t>::checkOrigs(const EList<SString<char> >&, bool) const [with index_t = unsigned int]': hisat2.cpp:3686:17: required from 'void driver(const char*, const string&, const string&) [with TStr = SString<char>; std::__cxx11::string = std::__cxx11::basic_string<char>]' hisat2.cpp:4115:51: required from here gfm.h:6451:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41, from spliced_aligner.h:23, from hisat2.cpp:45: group_walk.h: In instantiation of 'std::pair<int, int> GWState<index_t, T>::advance(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, EList<GWState<index_t, T>, S>&, GroupWalkState<index_t>&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice<short unsigned int, 16>]': group_walk.h:1542:4: required from 'bool GroupWalk2S<index_t, T, S>::advanceElement(index_t, const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, GroupWalkState<index_t>&, WalkResult<index_t>&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice<short unsigned int, 16>; int S = 16]' hi_aligner.h:5003:9: required from 'bool HI_Aligner<index_t, local_index_t>::getGenomeCoords_local(const GFM<local_index_t>&, const ALTDB<index_t>&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList<std::pair<index_t, index_t> >&, bool, index_t, index_t, EList<Coord>&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]' hi_aligner.h:4773:17: required from 'bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]' hi_aligner.h:3926:39: required from 'int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = unsigned int; local_index_t = short unsigned int]' hisat2.cpp:3435:151: required from here group_walk.h:1172:60: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] if(new_node_bot - new_node_top < gws.map.size()) { group_walk.h:1183:58: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] for(index_t j = 0; j + 1 < gws.map.size(); j++) { group_walk.h:1238:69: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] if(node_range.second - node_range.first < st.back().map_.size()) { group_walk.h:1249:58: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { In file included from spliced_aligner.h:23, from hisat2.cpp:45: hi_aligner.h: In instantiation of 'static index_t GenomeHit<index_t>::alignWithALTs_recur(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList<SStringExpandable<char, 1024, 2> >&, EList<Edit>&, int&, const char*, index_t, int, index_t, bool, EList<Edit>&, index_t, ELList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]': hi_aligner.h:706:28: required from 'static index_t GenomeHit<index_t>::alignWithALTs(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars<index_t>&, index_t, int, index_t, bool, const GraphPolicy&, EList<Edit>&, ELList<std::pair<_FIter, _FIter> >&, EList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]' hi_aligner.h:2194:47: required from 'static bool GenomeHit<index_t>::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars<index_t>&, EList<GenomeHit<index_t> >&, const Read&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]' hi_aligner.h:4796:54: required from 'bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]' hi_aligner.h:3926:39: required from 'int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = unsigned int; local_index_t = short unsigned int]' hisat2.cpp:3435:151: required from here hi_aligner.h:2625:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] if(rfoff >= contig_len) return 0; ~~~~~~^~~~~~~~~~~~~ hi_aligner.h:2703:32: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] if(alt_range.first >= alts.size()) { hi_aligner.h:2868:42: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for(int i = 0; i < alt.len; i++) { ~~^~~~~~~~~ hi_aligner.h:2909:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { ~~~~~^~~~~~~~ hi_aligner.h:2985:31: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if(alignedLen == next_rdlen) return rdlen; ~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3021:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if(mm_max_rd_i + rdoff > best_rdoff) { ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:3026:39: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] } else if(mm_max_rd_i + rdoff == best_rdoff) { ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3278:35: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] if(best_rdoff < rdoff + rd_i) { ~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41, from spliced_aligner.h:23, from hisat2.cpp:45: group_walk.h: In instantiation of 'std::pair<int, int> GWState<index_t, T>::init(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, EList<GWState<index_t, T>, S>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice<short unsigned int, 16>]': group_walk.h:492:66: required from 'std::pair<int, int> GWState<index_t, T>::init(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, EList<GWState<index_t, T>, S>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, index_t, index_t, index_t, index_t, const EList<std::pair<_FIter, _FIter> >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice<short unsigned int, 16>]' group_walk.h:1478:3: required from 'void GroupWalk2S<index_t, T, S>::init(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice<short unsigned int, 16>; int S = 16]' hi_aligner.h:4998:5: required from 'bool HI_Aligner<index_t, local_index_t>::getGenomeCoords_local(const GFM<local_index_t>&, const ALTDB<index_t>&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList<std::pair<index_t, index_t> >&, bool, index_t, index_t, EList<Coord>&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]' hi_aligner.h:4773:17: required from 'bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]' hi_aligner.h:3926:39: required from 'int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = unsigned int; local_index_t = short unsigned int]' hisat2.cpp:3435:151: required from here group_walk.h:794:37: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] while(new_top - top < tmp_gbwt_to_node.size()) { group_walk.h:801:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] if(new_top - top == tmp_gbwt_to_node.size()) { group_walk.h:817:26: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] if(i + 1 < tmp_zOffs.size()) { group_walk.h:823:38: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] while(new_bot2 - top < tmp_gbwt_to_node.size()) { group_walk.h:830:35: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] if(new_bot2 - top < tmp_gbwt_to_node.size()) { In file included from spliced_aligner.h:23, from hisat2.cpp:45: hi_aligner.h: In instantiation of 'void add_haplotypes(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, Haplotype<index_t>&, EList<std::pair<_FIter, _FIter> >&, index_t, bool, bool) [with index_t = unsigned int]': hi_aligner.h:2739:39: required from 'static index_t GenomeHit<index_t>::alignWithALTs_recur(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList<SStringExpandable<char, 1024, 2> >&, EList<Edit>&, int&, const char*, index_t, int, index_t, bool, EList<Edit>&, index_t, ELList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]' hi_aligner.h:706:28: required from 'static index_t GenomeHit<index_t>::alignWithALTs(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars<index_t>&, index_t, int, index_t, bool, const GraphPolicy&, EList<Edit>&, ELList<std::pair<_FIter, _FIter> >&, EList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]' hi_aligner.h:2194:47: required from 'static bool GenomeHit<index_t>::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars<index_t>&, EList<GenomeHit<index_t> >&, const Read&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]' hi_aligner.h:4796:54: required from 'bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]' hi_aligner.h:3926:39: required from 'int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = unsigned int; local_index_t = short unsigned int]' hisat2.cpp:3435:151: required from here hi_aligner.h:2484:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] if(ht_range.first >= haplotypes.size()) hi_aligner.h:2499:37: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if(ht_list[h].first == ht_range.first) { ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2537:41: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if(ht_list[h].first == ht_range.first) { ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2561:31: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] for(; ht_range.second < haplotypes.size(); ht_range.second++) { hi_aligner.h:2568:41: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if(ht_list[h].first == ht_range.second) { ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from hisat2.cpp:45: spliced_aligner.h: In instantiation of 'int64_t SplicedAligner<index_t, local_index_t>::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit<index_t>&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long long int]': spliced_aligner.h:214:9: required from here spliced_aligner.h:282:18: warning: variable 'another_spliced' set but not used [-Wunused-but-set-variable] bool another_spliced = false; ^~~~~~~~~~~~~~~ In file included from spliced_aligner.h:23, from hisat2.cpp:45: hi_aligner.h: In instantiation of 'bool GenomeHit<index_t>::combineWith(const GenomeHit<index_t>&, const Read&, const GFM<index_t>&, const BitPairReference&, const ALTDB<index_t>&, SpliceSiteDB&, SwAligner&, SwMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, index_t, index_t, index_t, index_t, index_t, const SpliceSite*, bool) [with index_t = unsigned int; TAlScore = long long int]': spliced_aligner.h:365:30: required from 'int64_t SplicedAligner<index_t, local_index_t>::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit<index_t>&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long long int]' spliced_aligner.h:214:9: required from here hi_aligner.h:1790:32: warning: comparison of integer expressions of different signedness: 'const uint64_t' {aka 'const long long unsigned int'} and 'char' [-Wsign-compare] if(alt.seq == rdc) { ~~~~~~~~^~~~~~ ref_read.cpp: In function 'std::pair<long long unsigned int, long long unsigned int> fastaRefReadSizes(EList<FileBuf*>&, EList<RefRecord>&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)': ref_read.cpp:327:22: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long long int'} and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] if(i + 1 >= recs.size() || recs[i+1].first) { ~~~~~~^~~~~~~~~~~~~~ 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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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:1098:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<stringstream> ss(new stringstream()); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1102:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<FileBuf> fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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:1098:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<stringstream> ss(new stringstream()); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from gfm.h:28, from gfm.cpp:21: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1102:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<FileBuf> fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from gfm.h:28, from gfm.cpp:21: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ reference.cpp: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': reference.cpp:456:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^~~~~~~~~~ reference.cpp:450:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] bool binarySearched = false; ^~~~~~~~~~~~~~ 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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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:1098:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<stringstream> ss(new stringstream()); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/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: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> 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:1102:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<FileBuf> fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/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: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> 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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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:1098:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<stringstream> ss(new stringstream()); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/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: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> 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:1102:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<FileBuf> fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/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: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> 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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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:1098:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<stringstream> ss(new stringstream()); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/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: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> 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:1102:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<FileBuf> fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/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: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> 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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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:1098:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<stringstream> ss(new stringstream()); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> 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:1102:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<FileBuf> fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> 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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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:1098:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<stringstream> ss(new stringstream()); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from aln_sink.cpp:20: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> 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:1102:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<FileBuf> fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from aln_sink.cpp:20: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> 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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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:1098:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<stringstream> ss(new stringstream()); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/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: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> 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:1102:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<FileBuf> fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/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: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> 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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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:1098:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<stringstream> ss(new stringstream()); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/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: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> 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:1102:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<FileBuf> fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/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: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> 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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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:1098:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<stringstream> ss(new stringstream()); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/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: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> 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:1102:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<FileBuf> fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/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: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> 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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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:1098:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<stringstream> ss(new stringstream()); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/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: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> 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:1102:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<FileBuf> fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/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: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> 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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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:1098:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<stringstream> ss(new stringstream()); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/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: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> 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:1102:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<FileBuf> fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/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: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> 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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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:1098:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<stringstream> ss(new stringstream()); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/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: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> 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:1102:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<FileBuf> fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/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: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> 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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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:1098:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<stringstream> ss(new stringstream()); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/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: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> 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:1102:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<FileBuf> fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/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: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> 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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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:1098:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<stringstream> ss(new stringstream()); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/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: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> 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:1102:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<FileBuf> fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/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: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> 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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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:1098:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<stringstream> ss(new stringstream()); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from splice_site.cpp:20: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h:1102:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr<FileBuf> fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw64/include/c++/8.3.0/locale:43, from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from splice_site.cpp:20: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ splice_site.cpp: In member function 'void SpliceSiteDB::read(const GFM<unsigned int>&, const EList<ALT<unsigned int> >&)': splice_site.cpp:717:59: warning: ?: using integer constants in boolean context, the expression will always evaluate to 'true' [-Wint-in-bool-context] exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC); ~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from edit.h:29, from splice_site.cpp:20: ds.h: In instantiation of 'void EList<T, S>::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = long long unsigned int]': splice_site.cpp:722:59: required from here ds.h:663:14: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'class Exon'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] std::memcpy(list_ + cur_, l, bytes); ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from edit.h:30, from splice_site.cpp:20: splice_site.h:377:7: note: 'class Exon' declared here class Exon { ^~~~ echo "@echo off" > hisat2.bat echo "perl %~dp0/hisat2 %*" >> hisat2.bat echo "@echo off" > hisat2-build.bat echo "python %~dp0/hisat2-build %*" >> hisat2-build.bat echo "@echo off" > hisat2-inspect.bat echo "python %~dp0/hisat2-inspect %*" >> hisat2-inspect.bat mkdir -p ../inst cp hisat2-align-s ../inst/hisat2 cp hisat2-build-s ../inst/hisat2-build ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'Rhisat2' finding HTML links ... done Rhisat2-package html dot-createFlags html dot-hisat2Bin html extract_splice_sites html hisat2 html hisat2_build html hisat2_build_usage html hisat2_usage html hisat2_version html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Rhisat2) Making 'packages.html' ... done