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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 check --no-multiarch --install=check:Rhisat2.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings Rhisat2_1.8.0.tar.gz |
StartedAt: 2021-10-15 04:33:13 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 04:37:18 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 245.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: Rhisat2.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:Rhisat2.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings Rhisat2_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/Rhisat2.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'Rhisat2/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'Rhisat2' version '1.8.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'Rhisat2' can be installed ... WARNING Found the following significant warnings: gfm.h:1098:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] gfm.h:1102:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] hisat2.cpp:1753:2: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] hisat2.cpp:3068:2: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] hisat2.cpp:3069:2: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] hisat2.cpp:3085:2: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] hisat2.cpp:3826:9: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] 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] See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/Rhisat2.Rcheck/00install.out' for details. * checking installed package size ... NOTE installed size is 58.7Mb * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking include directives in Makefiles ... OK * checking compiled code ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/Rhisat2.Rcheck/00check.log' for details.
Rhisat2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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
Rhisat2.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(Rhisat2) > > test_check("Rhisat2") *** Warning *** 'hisat2-build-s' was run directly. It is recommended that you run the wrapper script 'hisat2-build' instead. [1] "HISAT2 version 2.1.0 by Daehwan Kim (infphilo@gmail.com, http://www.ccb.jhu.edu/people/infphilo)" [2] "Usage: hisat2-build [options]* <reference_in> <ht2_index_base>" [3] " reference_in comma-separated list of files with ref sequences" [4] " hisat2_index_base write ht2 data to files with this dir/basename" [5] "Options:" [6] " -c reference sequences given on cmd line (as" [7] " <reference_in>)" [8] " -a/--noauto disable automatic -p/--bmax/--dcv memory-fitting" [9] " -p number of threads" [10] " --bmax <int> max bucket sz for blockwise suffix-array builder" [11] " --bmaxdivn <int> max bucket sz as divisor of ref len (default: 4)" [12] " --dcv <int> diff-cover period for blockwise (default: 1024)" [13] " --nodc disable diff-cover (algorithm becomes quadratic)" [14] " -r/--noref don't build .3/.4.ht2 (packed reference) portion" [15] " -3/--justref just build .3/.4.ht2 (packed reference) portion" [16] " -o/--offrate <int> SA is sampled every 2^offRate BWT chars (default: 5)" [17] " -t/--ftabchars <int> # of chars consumed in initial lookup (default: 10)" [18] " --localoffrate <int> SA (local) is sampled every 2^offRate BWT chars (default: 3)" [19] " --localftabchars <int> # of chars consumed in initial lookup in a local index (default: 6)" [20] " --snp <path> SNP file name" [21] " --haplotype <path> haplotype file name" [22] " --ss <path> Splice site file name" [23] " --exon <path> Exon file name" [24] " --seed <int> seed for random number generator" [25] " -q/--quiet verbose output (for debugging)" [26] " -h/--help print detailed description of tool and its options" [27] " --usage print this usage message" [28] " --version print version information and quit" *** Warning *** 'hisat2-align' was run directly. It is recommended that you run the wrapper script 'hisat2' instead. [1] "HISAT2 version 2.1.0 by Daehwan Kim (infphilo@gmail.com, www.ccb.jhu.edu/people/infphilo)" [2] "Usage: " [3] " hisat2-align [options]* -x <ht2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]" [4] "" [5] " <ht2-idx> Index filename prefix (minus trailing .X.ht2)." [6] " <m1> Files with #1 mates, paired with files in <m2>." [7] " <m2> Files with #2 mates, paired with files in <m1>." [8] " <r> Files with unpaired reads." [9] " <sam> File for SAM output (default: stdout)" [10] "" [11] " <m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be" [12] " specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'." [13] "" [14] "Options (defaults in parentheses):" [15] "" [16] " Input:" [17] " -q query input files are FASTQ .fq/.fastq (default)" [18] " --qseq query input files are in Illumina's qseq format" [19] " -f query input files are (multi-)FASTA .fa/.mfa" [20] " -r query input files are raw one-sequence-per-line" [21] " -c <m1>, <m2>, <r> are sequences themselves, not files" [22] " -s/--skip <int> skip the first <int> reads/pairs in the input (none)" [23] " -u/--upto <int> stop after first <int> reads/pairs (no limit)" [24] " -5/--trim5 <int> trim <int> bases from 5'/left end of reads (0)" [25] " -3/--trim3 <int> trim <int> bases from 3'/right end of reads (0)" [26] " --phred33 qualities are Phred+33 (default)" [27] " --phred64 qualities are Phred+64" [28] " --int-quals qualities encoded as space-delimited integers" [29] "" [30] " Alignment:" [31] " --n-ceil <func> func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)" [32] " --ignore-quals treat all quality values as 30 on Phred scale (off)" [33] " --nofw do not align forward (original) version of read (off)" [34] " --norc do not align reverse-complement version of read (off)" [35] "" [36] " Spliced Alignment:" [37] " --pen-cansplice <int> penalty for a canonical splice site (0)" [38] " --pen-noncansplice <int> penalty for a non-canonical splice site (12)" [39] " --pen-canintronlen <func> penalty for long introns (G,-8,1) with canonical splice sites" [40] " --pen-noncanintronlen <func> penalty for long introns (G,-8,1) with noncanonical splice sites" [41] " --min-intronlen <int> minimum intron length (20)" [42] " --max-intronlen <int> maximum intron length (500000)" [43] " --known-splicesite-infile <path> provide a list of known splice sites" [44] " --novel-splicesite-outfile <path> report a list of splice sites" [45] " --novel-splicesite-infile <path> provide a list of novel splice sites" [46] " --no-temp-splicesite disable the use of splice sites found" [47] " --no-spliced-alignment disable spliced alignment" [48] " --rna-strandness <string> specify strand-specific information (unstranded)" [49] " --tmo reports only those alignments within known transcriptome" [50] " --dta reports alignments tailored for transcript assemblers" [51] " --dta-cufflinks reports alignments tailored specifically for cufflinks" [52] " --avoid-pseudogene tries to avoid aligning reads to pseudogenes (experimental option)\023" [53] " --no-templatelen-adjustment disables template length adjustment for RNA-seq reads" [54] "" [55] " Scoring:" [56] " --mp <int>,<int> max and min penalties for mismatch; lower qual = lower penalty <6,2>" [57] " --sp <int>,<int> max and min penalties for soft-clipping; lower qual = lower penalty <2,1>" [58] " --no-softclip no soft-clipping" [59] " --np <int> penalty for non-A/C/G/Ts in read/ref (1)" [60] " --rdg <int>,<int> read gap open, extend penalties (5,3)" [61] " --rfg <int>,<int> reference gap open, extend penalties (5,3)" [62] " --score-min <func> min acceptable alignment score w/r/t read length" [63] " (L,0.0,-0.2)" [64] "" [65] " Reporting:" [66] " -k <int> (default: 5) report up to <int> alns per read" [67] "" [68] " Paired-end:" [69] " -I/--minins <int> minimum fragment length (0), only valid with --no-spliced-alignment" [70] " -X/--maxins <int> maximum fragment length (500), only valid with --no-spliced-alignment" [71] " --fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)" [72] " --no-mixed suppress unpaired alignments for paired reads" [73] " --no-discordant suppress discordant alignments for paired reads" [74] "" [75] " Output:" [76] " -t/--time print wall-clock time taken by search phases" [77] " --summary-file print alignment summary to this file." [78] " --new-summary print alignment summary in a new style, which is more machine-friendly." [79] " --quiet print nothing to stderr except serious errors" [80] " --met-file <path> send metrics to file at <path> (off)" [81] " --met-stderr send metrics to stderr (off)" [82] " --met <int> report internal counters & metrics every <int> secs (1)" [83] " --no-head supppress header lines, i.e. lines starting with @" [84] " --no-sq supppress @SQ header lines" [85] " --rg-id <text> set read group id, reflected in @RG line and RG:Z: opt field" [86] " --rg <text> add <text> (\"lab:value\") to @RG line of SAM header." [87] " Note: @RG line only printed when --rg-id is set." [88] " --omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments." [89] "" [90] " Performance:" [91] " -o/--offrate <int> override offrate of index; must be >= index's offrate" [92] " -p/--threads <int> number of alignment threads to launch (1)" [93] " --reorder force SAM output order to match order of input reads" [94] "" [95] " Other:" [96] " --qc-filter filter out reads that are bad according to QSEQ filter" [97] " --seed <int> seed for random number generator (0)" [98] " --non-deterministic seed rand. gen. arbitrarily instead of using read attributes" [99] " --remove-chrname remove 'chr' from reference names in alignment" [100] " --add-chrname add 'chr' to reference names in alignment " [101] " --version print version information and quit" [102] " -h/--help print this usage message" [1] "C:\\Users\\BIOCBU~1\\BBS-3~1.13-\\R\\library\\Rhisat2\\hisat2.exe version 2.1.0" [2] "64-bit" [3] "Built on TOKAY2" [4] "Thu Oct 14 10:34:09 EDT 2021" [5] "Compiler: gcc version 8.3.0 (Built by Jeroen for the R-project) " [6] "Options: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY" [7] "Sizeof {int, long, long long, void*, size_t, off_t}: {4, 4, 8, 8, 8, 8}" Settings: Output files: "C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp4U9Juu/hisat2indexdir/index.*.ht2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Local offset rate: 3 (one in 8) Local fTable chars: 6 Local sequence length: 57344 Local sequence overlap between two consecutive indexes: 1024 Endianness: little Actual local endianness: little Sanity checking: disabled Assertions: disabled Random seed: 0 Sizeofs: void*:8, int:4, long:4, size_t:8 Input files DNA, FASTA: C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhisat2/extdata/refs/chr1.fa Reading reference sizes Time reading reference sizes: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:00 Time to read SNPs and splice sites: 00:00:00 Using parameters --bmax 18650 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 18650 --dcv 1024 Constructing suffix-array element generator Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering GFM loop Exited GFM loop fchr[A]: 0 fchr[C]: 26955 fchr[G]: 49554 fchr[T]: 72459 fchr[$]: 99465 Exiting GFM::buildToDisk() Returning from initFromVector Wrote 4227718 bytes to primary GFM file: C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp4U9Juu/hisat2indexdir/index.1.ht2 Wrote 24872 bytes to secondary GFM file: C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp4U9Juu/hisat2indexdir/index.2.ht2 Re-opening _in1 and _in2 as input streams Returning from GFM constructor Returning from initFromVector Wrote 45363 bytes to primary GFM file: C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp4U9Juu/hisat2indexdir/index.5.ht2 Wrote 25130 bytes to secondary GFM file: C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp4U9Juu/hisat2indexdir/index.6.ht2 Re-opening _in5 and _in5 as input streams Returning from HierEbwt constructor Headers: len: 99465 gbwtLen: 99466 nodes: 99466 sz: 24867 gbwtSz: 24867 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 0 eftabSz: 0 ftabLen: 1048577 ftabSz: 4194308 offsLen: 6217 offsSz: 24868 lineSz: 64 sideSz: 64 sideGbwtSz: 48 sideGbwtLen: 192 numSides: 519 numLines: 519 gbwtTotLen: 33216 gbwtTotSz: 33216 reverse: 0 linearFM: Yes Total time for call to driver() for forward index: 00:00:00 Settings: Output files: "C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp4U9Juu/hisat2indexdir/index.*.ht2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Local offset rate: 3 (one in 8) Local fTable chars: 6 Local sequence length: 57344 Local sequence overlap between two consecutive indexes: 1024 Endianness: little Actual local endianness: little Sanity checking: disabled Assertions: disabled Random seed: 0 Sizeofs: void*:8, int:4, long:4, size_t:8 Input files DNA, FASTA: C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhisat2/extdata/refs/chr1.fa Reading reference sizes Time reading reference sizes: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:00 Time to read SNPs and splice sites: 00:00:00 Using parameters --bmax 18650 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 18650 --dcv 1024 Constructing suffix-array element generator Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering GFM loop Exited GFM loop fchr[A]: 0 fchr[C]: 26955 fchr[G]: 49554 fchr[T]: 72459 fchr[$]: 99465 Exiting GFM::buildToDisk() Returning from initFromVector Wrote 4227718 bytes to primary GFM file: C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp4U9Juu/hisat2indexdir/index.1.ht2 Wrote 24872 bytes to secondary GFM file: C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp4U9Juu/hisat2indexdir/index.2.ht2 Re-opening _in1 and _in2 as input streams Returning from GFM constructor Returning from initFromVector Wrote 45363 bytes to primary GFM file: C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp4U9Juu/hisat2indexdir/index.5.ht2 Wrote 25130 bytes to secondary GFM file: C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp4U9Juu/hisat2indexdir/index.6.ht2 Re-opening _in5 and _in5 as input streams Returning from HierEbwt constructor Headers: len: 99465 gbwtLen: 99466 nodes: 99466 sz: 24867 gbwtSz: 24867 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 0 eftabSz: 0 ftabLen: 1048577 ftabSz: 4194308 offsLen: 6217 offsSz: 24868 lineSz: 64 sideSz: 64 sideGbwtSz: 48 sideGbwtLen: 192 numSides: 519 numLines: 519 gbwtTotLen: 33216 gbwtTotSz: 33216 reverse: 0 linearFM: Yes Total time for call to driver() for forward index: 00:00:01 4 reads; of these: 4 (100.00%) were unpaired; of these: 2 (50.00%) aligned 0 times 2 (50.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 50.00% overall alignment rate [ FAIL 0 | WARN 1 | SKIP 0 | PASS 32 ] > > proc.time() user system elapsed 16.95 0.51 19.14
Rhisat2.Rcheck/Rhisat2-Ex.timings
name | user | system | elapsed | |
extract_splice_sites | 2.52 | 0.10 | 2.68 | |
hisat2 | 0.01 | 0.00 | 1.03 | |
hisat2_build | 0.00 | 0.01 | 0.47 | |
hisat2_build_usage | 0.00 | 0.00 | 0.22 | |
hisat2_usage | 0.00 | 0.02 | 0.23 | |
hisat2_version | 0.00 | 0.00 | 0.22 | |