############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rhisat2 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘Rhisat2’ ... ** using staged installation ** libs /usr/bin/g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"2.2.1\"" -DBUILD_HOST="\"kjohnson3\"" -DBUILD_TIME="\"Mon Dec 2 15:14:16 EST 2024\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DUSESIMDE -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \ -I. -I third_party \ -o hisat2-build-s hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread In file included from hisat2_build.cpp:28: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from hisat2_build.cpp:35: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from hisat2_build.cpp:35: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] size_t est_count = 0; ^ In file included from hisat2_build.cpp:35: ./gfm.h:1185:3: warning: 'auto_ptr>' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr>' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from hisat2_build.cpp:35: ./gfm.h:1189:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from hisat2_build.cpp:35: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ 8 warnings generated. In file included from ref_read.cpp:20: In file included from ./ref_read.h:33: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from edit.cpp:21: In file included from ./edit.h:29: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] size_t est_count = 0; ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1185:3: warning: 'auto_ptr>' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr>' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1189:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:31: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 9 warnings generated. In file included from gfm.cpp:21: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from gfm.cpp:21: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from gfm.cpp:21: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] size_t est_count = 0; ^ In file included from gfm.cpp:21: ./gfm.h:1185:3: warning: 'auto_ptr>' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr>' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from gfm.cpp:21: ./gfm.h:1189:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from gfm.cpp:21: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ 8 warnings generated. In file included from reference.cpp:22: In file included from ./reference.h:32: In file included from ./ref_read.h:33: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ reference.cpp:133:16: warning: variable 'skips' set but not used [-Wunused-but-set-variable] TIndexOffU skips = 0; ^ reference.cpp:522:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^ reference.cpp:516:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] bool binarySearched = false; ^ 4 warnings generated. In file included from ds.cpp:20: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:27: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ 4 warnings generated. In file included from random_source.cpp:21: In file included from ./random_util.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from diff_sample.cpp:20: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from diff_sample.cpp:20: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ 4 warnings generated. In file included from hisat2_build_main.cpp:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. /usr/bin/g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"2.2.1\"" -DBUILD_HOST="\"kjohnson3\"" -DBUILD_TIME="\"Mon Dec 2 15:14:26 EST 2024\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DUSESIMDE -DBOWTIE2 -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-align-s hisat2.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread In file included from hisat2.cpp:33: In file included from ./hgfm.h:24: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from hisat2.cpp:33: In file included from ./hgfm.h:24: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from hisat2.cpp:33: In file included from ./hgfm.h:24: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] size_t est_count = 0; ^ In file included from hisat2.cpp:33: In file included from ./hgfm.h:24: ./gfm.h:1185:3: warning: 'auto_ptr>' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr>' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from hisat2.cpp:33: In file included from ./hgfm.h:24: ./gfm.h:1189:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from hisat2.cpp:33: In file included from ./hgfm.h:24: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ In file included from hisat2.cpp:46: In file included from ./spliced_aligner.h:23: In file included from ./hi_aligner.h:41: In file included from ./aligner_driver.h:78: ./aligner_seed2.h:1226:10: warning: variable 'nuninited' set but not used [-Wunused-but-set-variable] size_t nuninited = 0; ^ ./aligner_seed2.h:2446:10: warning: variable 'ns' set but not used [-Wunused-but-set-variable] size_t ns = 0, ngap = 0, nrefn = 0; ^ ./aligner_seed2.h:2446:18: warning: variable 'ngap' set but not used [-Wunused-but-set-variable] size_t ns = 0, ngap = 0, nrefn = 0; ^ ./aligner_seed2.h:2446:28: warning: variable 'nrefn' set but not used [-Wunused-but-set-variable] size_t ns = 0, ngap = 0, nrefn = 0; ^ ./aligner_seed2.h:4132:11: warning: variable 'nopts' set but not used [-Wunused-but-set-variable] size_t nopts = 0; ^ ./aligner_seed2.h:3869:9: warning: variable 'off3p' set but not used [-Wunused-but-set-variable] size_t off3p = q.length() - off5p - 1; ^ ./aligner_seed2.h:3876:9: warning: variable 'nalloc' set but not used [-Wunused-but-set-variable] size_t nalloc = 0; ^ In file included from hisat2.cpp:46: In file included from ./spliced_aligner.h:23: In file included from ./hi_aligner.h:42: ./aligner_sw_driver.h:1597:13: warning: variable 'pastedRefoff' set but not used [-Wunused-but-set-variable] int64_t pastedRefoff = (int64_t)wr.toff - rdoff; ^ ./aligner_sw_driver.h:2295:13: warning: variable 'pastedRefoff' set but not used [-Wunused-but-set-variable] int64_t pastedRefoff = (int64_t)wr.toff - rdoff; ^ In file included from hisat2.cpp:46: In file included from ./spliced_aligner.h:23: ./hi_aligner.h:3730:13: warning: variable 'toff_base' set but not used [-Wunused-but-set-variable] int64_t toff_base = _toff; ^ In file included from hisat2.cpp:46: ./spliced_aligner.h:408:18: warning: variable 'another_spliced' set but not used [-Wunused-but-set-variable] bool another_spliced = false; ^ hisat2.cpp:1823:2: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr presets(new PresetsV0()); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ hisat2.cpp:3167:2: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ hisat2.cpp:3168:2: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ps(patsrcFact->create()); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ hisat2.cpp:3189:2: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ hisat2.cpp:4035:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr refs( ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from hisat2.cpp:38: In file included from ./aln_sink.h:24: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ In file included from hisat2.cpp:38: In file included from ./aln_sink.h:24: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./pat.h:1298:6: note: in instantiation of function template specialization 'itoa10' requested here itoa10(readCnt_ - subReadCnt_, cbuf); ^ In file included from hisat2.cpp:38: In file included from ./aln_sink.h:24: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./sam.h:705:9: note: in instantiation of function template specialization 'itoa10' requested here itoa10(rd.seed, buf); ^ ./aln_sink.h:3225:9: note: in instantiation of member function 'SamConfig::printAlignedOptFlags' requested here samc_.printAlignedOptFlags( ^ ./aln_sink.h:1569:4: note: in instantiation of member function 'AlnSinkSam::appendMate' requested here appendMate(o, staln, *rd1, rd2, rdid, rs1, rs2, summ, ssm1, ssm2, ^ ./aln_sink.h:1521:2: note: in instantiation of member function 'AlnSinkSam::append' requested here AlnSinkSam( ^ hisat2.cpp:4116:18: note: in instantiation of member function 'AlnSinkSam::AlnSinkSam' requested here mssink = new AlnSinkSam( ^ hisat2.cpp:4351:4: note: in instantiation of function template specialization 'driver>' requested here driver >("DNA", bt2index, outfile); ^ 27 warnings generated. In file included from ref_read.cpp:20: In file included from ./ref_read.h:33: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from edit.cpp:21: In file included from ./edit.h:29: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] size_t est_count = 0; ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1185:3: warning: 'auto_ptr>' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr>' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1189:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:31: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 9 warnings generated. In file included from gfm.cpp:21: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from gfm.cpp:21: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from gfm.cpp:21: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] size_t est_count = 0; ^ In file included from gfm.cpp:21: ./gfm.h:1185:3: warning: 'auto_ptr>' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr>' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from gfm.cpp:21: ./gfm.h:1189:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from gfm.cpp:21: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ 8 warnings generated. In file included from reference.cpp:22: In file included from ./reference.h:32: In file included from ./ref_read.h:33: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ reference.cpp:133:16: warning: variable 'skips' set but not used [-Wunused-but-set-variable] TIndexOffU skips = 0; ^ reference.cpp:522:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^ reference.cpp:516:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] bool binarySearched = false; ^ 4 warnings generated. In file included from ds.cpp:20: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:27: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ 4 warnings generated. In file included from random_source.cpp:21: In file included from ./random_util.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from pat.cpp:26: In file included from ./pat.h:40: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from pat.cpp:26: In file included from ./pat.h:41: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ In file included from pat.cpp:26: In file included from ./pat.h:41: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./pat.h:1298:6: note: in instantiation of function template specialization 'itoa10' requested here itoa10(readCnt_ - subReadCnt_, cbuf); ^ 3 warnings generated. In file included from read_qseq.cpp:20: In file included from ./pat.h:40: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from read_qseq.cpp:20: In file included from ./pat.h:41: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ In file included from read_qseq.cpp:20: In file included from ./pat.h:41: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./pat.h:1298:6: note: in instantiation of function template specialization 'itoa10' requested here itoa10(readCnt_ - subReadCnt_, cbuf); ^ 3 warnings generated. In file included from aligner_seed_policy.cpp:24: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from aligner_seed.cpp:20: In file included from ./aligner_cache.h:59: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from aligner_seed.cpp:21: In file included from ./aligner_seed.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from aligner_seed.cpp:21: In file included from ./aligner_seed.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] size_t est_count = 0; ^ In file included from aligner_seed.cpp:21: In file included from ./aligner_seed.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1185:3: warning: 'auto_ptr>' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr>' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from aligner_seed.cpp:21: In file included from ./aligner_seed.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1189:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from aligner_seed.cpp:21: In file included from ./aligner_seed.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ In file included from aligner_seed.cpp:20: In file included from ./aligner_cache.h:60: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 9 warnings generated. In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:101: In file included from ./random_util.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] size_t est_count = 0; ^ In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1185:3: warning: 'auto_ptr>' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr>' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1189:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ In file included from aligner_seed2.cpp:22: ./aligner_seed2.h:1226:10: warning: variable 'nuninited' set but not used [-Wunused-but-set-variable] size_t nuninited = 0; ^ ./aligner_seed2.h:2446:10: warning: variable 'ns' set but not used [-Wunused-but-set-variable] size_t ns = 0, ngap = 0, nrefn = 0; ^ ./aligner_seed2.h:2446:18: warning: variable 'ngap' set but not used [-Wunused-but-set-variable] size_t ns = 0, ngap = 0, nrefn = 0; ^ ./aligner_seed2.h:2446:28: warning: variable 'nrefn' set but not used [-Wunused-but-set-variable] size_t ns = 0, ngap = 0, nrefn = 0; ^ ./aligner_seed2.h:4132:11: warning: variable 'nopts' set but not used [-Wunused-but-set-variable] size_t nopts = 0; ^ ./aligner_seed2.h:3869:9: warning: variable 'off3p' set but not used [-Wunused-but-set-variable] size_t off3p = q.length() - off5p - 1; ^ ./aligner_seed2.h:3876:9: warning: variable 'nalloc' set but not used [-Wunused-but-set-variable] size_t nalloc = 0; ^ In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 16 warnings generated. In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] size_t est_count = 0; ^ In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1185:3: warning: 'auto_ptr>' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr>' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1189:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 9 warnings generated. In file included from aligner_cache.cpp:20: In file included from ./aligner_cache.h:59: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from aligner_cache.cpp:20: In file included from ./aligner_cache.h:60: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 warnings generated. In file included from aligner_result.cpp:21: In file included from ./reference.h:32: In file included from ./ref_read.h:33: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from aligner_result.cpp:22: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from aligner_result.cpp:22: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] size_t est_count = 0; ^ In file included from aligner_result.cpp:22: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1185:3: warning: 'auto_ptr>' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr>' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from aligner_result.cpp:22: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1189:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from aligner_result.cpp:22: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ In file included from aligner_result.cpp:22: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 9 warnings generated. In file included from aln_sink.cpp:22: In file included from ./aln_sink.h:24: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from aln_sink.cpp:22: In file included from ./aln_sink.h:25: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from aln_sink.cpp:22: In file included from ./aln_sink.h:25: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] size_t est_count = 0; ^ In file included from aln_sink.cpp:22: In file included from ./aln_sink.h:25: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1185:3: warning: 'auto_ptr>' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr>' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from aln_sink.cpp:22: In file included from ./aln_sink.h:25: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1189:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from aln_sink.cpp:22: In file included from ./aln_sink.h:25: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ In file included from aln_sink.cpp:22: In file included from ./aln_sink.h:24: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 9 warnings generated. In file included from dp_framer.cpp:20: In file included from ./dp_framer.h:51: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from presets.cpp:21: In file included from ./presets.h:32: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from unique.cpp:20: In file included from ./unique.h:38: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from unique.cpp:20: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from unique.cpp:20: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] size_t est_count = 0; ^ In file included from unique.cpp:20: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1185:3: warning: 'auto_ptr>' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr>' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from unique.cpp:20: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1189:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from unique.cpp:20: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ In file included from unique.cpp:20: In file included from ./unique.h:38: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 9 warnings generated. In file included from simple_func.cpp:22: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from random_util.cpp:20: In file included from ./random_util.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:25: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:25: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:25: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] size_t est_count = 0; ^ In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:25: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1185:3: warning: 'auto_ptr>' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr>' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:25: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1189:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:25: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ aligner_bt.cpp:125:10: warning: variable 'neval' set but not used [-Wunused-but-set-variable] size_t neval = 0; // # cells evaluated in this diag ^ aligner_bt.cpp:1170:9: warning: variable 'iters' set but not used [-Wunused-but-set-variable] size_t iters = 0; ^ In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:25: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 11 warnings generated. In file included from sse_util.cpp:20: In file included from ./sse_util.h:29: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from aligner_swsse.cpp:21: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from aligner_swsse.cpp:21: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from aligner_swsse.cpp:21: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] size_t est_count = 0; ^ In file included from aligner_swsse.cpp:21: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1185:3: warning: 'auto_ptr>' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr>' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from aligner_swsse.cpp:21: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1189:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from aligner_swsse.cpp:21: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ In file included from aligner_swsse.cpp:21: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 9 warnings generated. In file included from outq.cpp:20: In file included from ./outq.h:24: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from outq.cpp:20: In file included from ./outq.h:26: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 warnings generated. In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] size_t est_count = 0; ^ In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1185:3: warning: 'auto_ptr>' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr>' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1189:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 9 warnings generated. In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] size_t est_count = 0; ^ In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1185:3: warning: 'auto_ptr>' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr>' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1189:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 9 warnings generated. In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] size_t est_count = 0; ^ In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1185:3: warning: 'auto_ptr>' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr>' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1189:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 9 warnings generated. In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] size_t est_count = 0; ^ In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1185:3: warning: 'auto_ptr>' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr>' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1189:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:80: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 9 warnings generated. In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: In file included from ./aligner_seed2.h:101: In file included from ./random_util.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] size_t est_count = 0; ^ In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1185:3: warning: 'auto_ptr>' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr>' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1189:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: ./aligner_seed2.h:1226:10: warning: variable 'nuninited' set but not used [-Wunused-but-set-variable] size_t nuninited = 0; ^ ./aligner_seed2.h:2446:10: warning: variable 'ns' set but not used [-Wunused-but-set-variable] size_t ns = 0, ngap = 0, nrefn = 0; ^ ./aligner_seed2.h:2446:18: warning: variable 'ngap' set but not used [-Wunused-but-set-variable] size_t ns = 0, ngap = 0, nrefn = 0; ^ ./aligner_seed2.h:2446:28: warning: variable 'nrefn' set but not used [-Wunused-but-set-variable] size_t ns = 0, ngap = 0, nrefn = 0; ^ ./aligner_seed2.h:4132:11: warning: variable 'nopts' set but not used [-Wunused-but-set-variable] size_t nopts = 0; ^ ./aligner_seed2.h:3869:9: warning: variable 'off3p' set but not used [-Wunused-but-set-variable] size_t off3p = q.length() - off5p - 1; ^ ./aligner_seed2.h:3876:9: warning: variable 'nalloc' set but not used [-Wunused-but-set-variable] size_t nalloc = 0; ^ In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 16 warnings generated. In file included from splice_site.cpp:20: In file included from ./edit.h:29: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from splice_site.cpp:20: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from splice_site.cpp:20: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] size_t est_count = 0; ^ In file included from splice_site.cpp:20: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1185:3: warning: 'auto_ptr>' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr>' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from splice_site.cpp:20: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1189:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from splice_site.cpp:20: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ In file included from splice_site.cpp:20: In file included from ./edit.h:30: In file included from ./splice_site.h:31: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 9 warnings generated. In file included from hisat2_main.cpp:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. mkdir -p ../inst cp hisat2-align-s ../inst/hisat2 cp hisat2-build-s ../inst/hisat2-build /usr/bin/g++ -shared -fPIC -o Rhisat2.so get_info.cpp installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-Rhisat2/00new/Rhisat2/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Rhisat2)