############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf Rhisat2.buildbin-libdir && mkdir Rhisat2.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rhisat2_1.14.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rhisat2.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rhisat2.buildbin-libdir Rhisat2_1.14.0.tar.gz' >>>>>>> * installing *source* package ‘Rhisat2’ ... ** using staged installation rm -f hisat2-build-s hisat2-align-s \ hisat2-build-s.exe hisat2-align-s.exe \ hisat2-src.zip hisat2-bin.zip rm -f core.* .tmp.head rm -rf *.dSYM rm -rf .ht2lib-obj* rm -f libhisat2lib*.a libhisat2lib*.so rm -f *.so rm -f ../inst/hisat2 ../inst/hisat2-build ** libs ** arch - /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="\"kjohnson\"" -DBUILD_TIME="\"Tue Apr 18 18:49:53 EDT 2023\"" -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:35: ./gfm.h:1185:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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; ^ 3 warnings generated. 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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); ^ 4 warnings generated. 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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; ^ 3 warnings generated. 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; ^ 2 warnings 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="\"kjohnson\"" -DBUILD_TIME="\"Tue Apr 18 18:51:03 EDT 2023\"" -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: ./gfm.h:1185:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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: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: ./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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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); ^ 14 warnings generated. 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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); ^ 4 warnings generated. 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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; ^ 3 warnings generated. 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; ^ 2 warnings generated. 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); ^ 2 warnings generated. 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); ^ 2 warnings generated. 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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); ^ 4 warnings generated. 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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: 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); ^ 4 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: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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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); ^ 4 warnings generated. 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); ^ 1 warning generated. 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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); ^ 4 warnings generated. 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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); ^ 4 warnings generated. 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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); ^ 4 warnings 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: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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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; ^ 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); ^ 4 warnings 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: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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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); ^ 4 warnings generated. 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); ^ 1 warning 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: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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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); ^ 4 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: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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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); ^ 4 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: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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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); ^ 4 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: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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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); ^ 4 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: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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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: 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); ^ 4 warnings generated. 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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/MacOSX.sdk/usr/include/c++/v1/__memory/auto_ptr.h:32:28: note: 'auto_ptr' has been explicitly marked deprecated here class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: 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); ^ 4 warnings 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 /Volumes/External/bbs-3.16-bioc-m1/meat/Rhisat2.buildbin-libdir/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) >>>>>>> >>>>>>> FIXING LINKS FOR Rhisat2.buildbin-libdir/Rhisat2/libs/Rhisat2.so >>>>>>> install_name_tool -change "/opt/R/arm64/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgcc_s.1.1.dylib" "Rhisat2.buildbin-libdir/Rhisat2/libs/Rhisat2.so" install_name_tool -change "/opt/R/arm64/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgfortran.5.dylib" "Rhisat2.buildbin-libdir/Rhisat2/libs/Rhisat2.so" install_name_tool -change "/opt/R/arm64/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libquadmath.0.dylib" "Rhisat2.buildbin-libdir/Rhisat2/libs/Rhisat2.so"