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This page was generated on 2024-06-11 14:42 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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Package 1764/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rhisat2 1.20.0  (landing page)
Charlotte Soneson
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/Rhisat2
git_branch: RELEASE_3_19
git_last_commit: 5205ee6
git_last_commit_date: 2024-04-30 11:11:59 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


BUILD BIN results for Rhisat2 on lconway

To the developers/maintainers of the Rhisat2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rhisat2.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: Rhisat2
Version: 1.20.0
Command: rm -rf Rhisat2.buildbin-libdir && mkdir Rhisat2.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rhisat2_1.20.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rhisat2.buildbin-libdir
StartedAt: 2024-06-10 00:35:28 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 00:38:29 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 181.3 seconds
RetCode: 0
Status:   OK  
PackageFile: Rhisat2_1.20.0.tgz
PackageFileSize: 1.2 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Rhisat2.buildbin-libdir && mkdir Rhisat2.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rhisat2_1.20.0.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_1.20.0.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
/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="\"lconway\"" -DBUILD_TIME="\"Mon Jun 10 00:35:32 EDT 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:35:
./gfm.h:1185:3: warning: 'auto_ptr<std::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' 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<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' 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;
            ^
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<std::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' 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<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' 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<unsigned long>' 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<std::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' 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<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' 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;
            ^
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="\"lconway\"" -DBUILD_TIME="\"Mon Jun 10 00:36:12 EDT 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:
./gfm.h:1185:3: warning: 'auto_ptr<std::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' 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<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' 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: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<Presets>' is deprecated [-Wdeprecated-declarations]
        auto_ptr<Presets> presets(new PresetsV0());
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<Presets>' 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<PatternSourcePerThreadFactory>' is deprecated [-Wdeprecated-declarations]
        auto_ptr<PatternSourcePerThreadFactory> patsrcFact(createPatsrcFactory(patsrc, tid));
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<PatternSourcePerThreadFactory>' 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<PatternSourcePerThread>' is deprecated [-Wdeprecated-declarations]
        auto_ptr<PatternSourcePerThread> ps(patsrcFact->create());
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<PatternSourcePerThread>' 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<Mapq>' is deprecated [-Wdeprecated-declarations]
        auto_ptr<Mapq> bmapq(new_mapq(mapqv, scoreMin, sc));
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<Mapq>' 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<BitPairReference>' is deprecated [-Wdeprecated-declarations]
        auto_ptr<BitPairReference> refs(
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<BitPairReference>' 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<unsigned long>' 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<unsigned long long>' requested here
                                        itoa10<TReadId>(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<unsigned int>' requested here
        itoa10<uint32_t>(rd.seed, buf);
        ^
./aln_sink.h:3225:9: note: in instantiation of member function 'SamConfig<unsigned int>::printAlignedOptFlags' requested here
                samc_.printAlignedOptFlags(
                      ^
./aln_sink.h:1569:4: note: in instantiation of member function 'AlnSinkSam<unsigned int>::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<unsigned int>::append' requested here
        AlnSinkSam(
        ^
hisat2.cpp:4116:18: note: in instantiation of member function 'AlnSinkSam<unsigned int>::AlnSinkSam' requested here
                                mssink = new AlnSinkSam<index_t>(
                                             ^
hisat2.cpp:4351:4: note: in instantiation of function template specialization 'driver<SString<char>>' requested here
                        driver<SString<char> >("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<std::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' 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<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' 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<unsigned long>' 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<std::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' 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<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' 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;
            ^
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<unsigned long>' 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<unsigned long long>' requested here
                                        itoa10<TReadId>(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<unsigned long>' 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<unsigned long long>' requested here
                                        itoa10<TReadId>(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<std::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' 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<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' 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<unsigned long>' 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<std::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' 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<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' 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:
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<unsigned long>' 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<std::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' 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<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' 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<unsigned long>' 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<unsigned long>' 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<std::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' 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<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' 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<unsigned long>' 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<std::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' 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<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' 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<unsigned long>' 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<std::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' 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<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' 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<unsigned long>' 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<std::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' 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<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' 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;
            ^
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<unsigned long>' 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<std::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' 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<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' 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<unsigned long>' 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<unsigned long>' 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<std::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' 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<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' 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<unsigned long>' 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<std::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' 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<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' 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<unsigned long>' 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<std::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' 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<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' 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<unsigned long>' 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<std::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' 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<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' 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<unsigned long>' 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<std::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' 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<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' 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:
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<unsigned long>' 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<std::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' 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<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' 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<unsigned long>' 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 /Users/biocbuild/bbs-3.19-bioc/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 PATHS TO DYNAMIC LIBRARIES FOR Rhisat2.buildbin-libdir/Rhisat2/libs/Rhisat2.so
>>>>>>> 

>>>>>>> Paths before fix:
Rhisat2.buildbin-libdir/Rhisat2/libs/Rhisat2.so:
	Rhisat2.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgcc_s.1.1.dylib" "Rhisat2.buildbin-libdir/Rhisat2/libs/Rhisat2.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "Rhisat2.buildbin-libdir/Rhisat2/libs/Rhisat2.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "Rhisat2.buildbin-libdir/Rhisat2/libs/Rhisat2.so"

>>>>>>> Paths after fix:
Rhisat2.buildbin-libdir/Rhisat2/libs/Rhisat2.so:
	Rhisat2.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)