Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2024-07-12 17:42 -0400 (Fri, 12 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4741
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4461
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1764/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rhisat2 1.20.0  (landing page)
Charlotte Soneson
Snapshot Date: 2024-07-10 14:00 -0400 (Wed, 10 Jul 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
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


BUILD BIN results for Rhisat2 on kjohnson1

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: 2024-07-12 16:05:22 -0400 (Fri, 12 Jul 2024)
EndedAt: 2024-07-12 16:07:55 -0400 (Fri, 12 Jul 2024)
EllapsedTime: 152.8 seconds
RetCode: 0
Status:   OK  
PackageFile: Rhisat2_1.20.0.tgz
PackageFileSize: 1.09 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="\"kjohnson1\"" -DBUILD_TIME="\"Fri Jul 12 16:05:24 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:28:
In file included from ./sequence_io.h:28:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
In file included from hisat2_build.cpp:35:
In file included from ./gfm.h:43:
In file included from ./blockwise_sa.h:29:
./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
        size_t amapEnts = 1;
               ^
./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
In file included from hisat2_build.cpp:35:
In file included from ./gfm.h:60:
./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable]
        size_t est_count = 0;
               ^
In file included from hisat2_build.cpp:35:
./gfm.h:1185:3: warning: 'auto_ptr<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;
            ^
8 warnings generated.
In file included from ref_read.cpp:20:
In file included from ./ref_read.h:33:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
1 warning generated.
In file included from edit.cpp:21:
In file included from ./edit.h:29:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
In file included from edit.cpp:21:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:43:
In file included from ./blockwise_sa.h:29:
./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
        size_t amapEnts = 1;
               ^
./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
In file included from edit.cpp:21:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:60:
./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable]
        size_t est_count = 0;
               ^
In file included from edit.cpp:21:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<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);
                                ^
9 warnings generated.
In file included from gfm.cpp:21:
In file included from ./gfm.h:43:
In file included from ./blockwise_sa.h:29:
In file included from ./diff_sample.h:26:
In file included from ./multikey_qsort.h:24:
In file included from ./sequence_io.h:28:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
In file included from gfm.cpp:21:
In file included from ./gfm.h:43:
In file included from ./blockwise_sa.h:29:
./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
        size_t amapEnts = 1;
               ^
./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
In file included from gfm.cpp:21:
In file included from ./gfm.h:60:
./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable]
        size_t est_count = 0;
               ^
In file included from gfm.cpp:21:
./gfm.h:1185:3: warning: 'auto_ptr<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;
            ^
8 warnings generated.
In file included from reference.cpp:22:
In file included from ./reference.h:32:
In file included from ./ref_read.h:33:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
reference.cpp:133:16: warning: variable 'skips' set but not used [-Wunused-but-set-variable]
    TIndexOffU skips = 0;
               ^
reference.cpp:522:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable]
                uint64_t origBufOff = bufOff;
                         ^
reference.cpp:516:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable]
        bool binarySearched = false;
             ^
4 warnings generated.
In file included from ds.cpp:20:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
1 warning generated.
In file included from multikey_qsort.cpp:20:
In file included from ./multikey_qsort.h:24:
In file included from ./sequence_io.h:28:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
In file included from multikey_qsort.cpp:20:
In file included from ./multikey_qsort.h:27:
./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
        size_t amapEnts = 1;
               ^
./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
4 warnings generated.
In file included from random_source.cpp:21:
In file included from ./random_util.h:25:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
1 warning generated.
In file included from diff_sample.cpp:20:
In file included from ./diff_sample.h:26:
In file included from ./multikey_qsort.h:24:
In file included from ./sequence_io.h:28:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
In file included from diff_sample.cpp:20:
./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
        size_t amapEnts = 1;
               ^
./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
4 warnings generated.
In file included from hisat2_build_main.cpp:25:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
1 warning generated.
/usr/bin/g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -std=c++11\"" -std=c++11 \
	-fno-strict-aliasing -DHISAT2_VERSION="\"2.2.1\"" -DBUILD_HOST="\"kjohnson1\"" -DBUILD_TIME="\"Fri Jul 12 16:05:58 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:
In file included from ./gfm.h:43:
In file included from ./blockwise_sa.h:29:
In file included from ./diff_sample.h:26:
In file included from ./multikey_qsort.h:24:
In file included from ./sequence_io.h:28:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
In file included from hisat2.cpp:33:
In file included from ./hgfm.h:24:
In file included from ./gfm.h:43:
In file included from ./blockwise_sa.h:29:
./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
        size_t amapEnts = 1;
               ^
./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
In file included from hisat2.cpp:33:
In file included from ./hgfm.h:24:
In file included from ./gfm.h:60:
./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable]
        size_t est_count = 0;
               ^
In file included from hisat2.cpp:33:
In file included from ./hgfm.h:24:
./gfm.h:1185:3: warning: 'auto_ptr<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:41:
In file included from ./aligner_driver.h:78:
./aligner_seed2.h:1226:10: warning: variable 'nuninited' set but not used [-Wunused-but-set-variable]
                size_t nuninited = 0;
                       ^
./aligner_seed2.h:2446:10: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
                size_t ns = 0, ngap = 0, nrefn = 0;
                       ^
./aligner_seed2.h:2446:18: warning: variable 'ngap' set but not used [-Wunused-but-set-variable]
                size_t ns = 0, ngap = 0, nrefn = 0;
                               ^
./aligner_seed2.h:2446:28: warning: variable 'nrefn' set but not used [-Wunused-but-set-variable]
                size_t ns = 0, ngap = 0, nrefn = 0;
                                         ^
./aligner_seed2.h:4132:11: warning: variable 'nopts' set but not used [-Wunused-but-set-variable]
                        size_t nopts = 0;
                               ^
./aligner_seed2.h:3869:9: warning: variable 'off3p' set but not used [-Wunused-but-set-variable]
        size_t off3p = q.length() - off5p - 1;
               ^
./aligner_seed2.h:3876:9: warning: variable 'nalloc' set but not used [-Wunused-but-set-variable]
        size_t nalloc = 0;
               ^
In file included from hisat2.cpp:46:
In file included from ./spliced_aligner.h:23:
In file included from ./hi_aligner.h:42:
./aligner_sw_driver.h:1597:13: warning: variable 'pastedRefoff' set but not used [-Wunused-but-set-variable]
                                int64_t pastedRefoff = (int64_t)wr.toff - rdoff;
                                        ^
./aligner_sw_driver.h:2295:13: warning: variable 'pastedRefoff' set but not used [-Wunused-but-set-variable]
                                int64_t pastedRefoff = (int64_t)wr.toff - rdoff;
                                        ^
In file included from hisat2.cpp:46:
In file included from ./spliced_aligner.h:23:
./hi_aligner.h:3730:13: warning: variable 'toff_base' set but not used [-Wunused-but-set-variable]
    int64_t toff_base = _toff;
            ^
In file included from hisat2.cpp:46:
./spliced_aligner.h:408:18: warning: variable 'another_spliced' set but not used [-Wunused-but-set-variable]
            bool another_spliced = false;
                 ^
hisat2.cpp:1823:2: warning: 'auto_ptr<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);
                        ^
27 warnings generated.
In file included from ref_read.cpp:20:
In file included from ./ref_read.h:33:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
1 warning generated.
In file included from edit.cpp:21:
In file included from ./edit.h:29:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
In file included from edit.cpp:21:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:43:
In file included from ./blockwise_sa.h:29:
./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
        size_t amapEnts = 1;
               ^
./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
In file included from edit.cpp:21:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:60:
./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable]
        size_t est_count = 0;
               ^
In file included from edit.cpp:21:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<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);
                                ^
9 warnings generated.
In file included from gfm.cpp:21:
In file included from ./gfm.h:43:
In file included from ./blockwise_sa.h:29:
In file included from ./diff_sample.h:26:
In file included from ./multikey_qsort.h:24:
In file included from ./sequence_io.h:28:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
In file included from gfm.cpp:21:
In file included from ./gfm.h:43:
In file included from ./blockwise_sa.h:29:
./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
        size_t amapEnts = 1;
               ^
./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
In file included from gfm.cpp:21:
In file included from ./gfm.h:60:
./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable]
        size_t est_count = 0;
               ^
In file included from gfm.cpp:21:
./gfm.h:1185:3: warning: 'auto_ptr<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;
            ^
8 warnings generated.
In file included from reference.cpp:22:
In file included from ./reference.h:32:
In file included from ./ref_read.h:33:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
reference.cpp:133:16: warning: variable 'skips' set but not used [-Wunused-but-set-variable]
    TIndexOffU skips = 0;
               ^
reference.cpp:522:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable]
                uint64_t origBufOff = bufOff;
                         ^
reference.cpp:516:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable]
        bool binarySearched = false;
             ^
4 warnings generated.
In file included from ds.cpp:20:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
1 warning generated.
In file included from multikey_qsort.cpp:20:
In file included from ./multikey_qsort.h:24:
In file included from ./sequence_io.h:28:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
In file included from multikey_qsort.cpp:20:
In file included from ./multikey_qsort.h:27:
./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
        size_t amapEnts = 1;
               ^
./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
4 warnings generated.
In file included from random_source.cpp:21:
In file included from ./random_util.h:25:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
1 warning generated.
In file included from pat.cpp:26:
In file included from ./pat.h:40:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
In file included from pat.cpp:26:
In file included from ./pat.h:41:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
                if (value <= 0 && value != 0) *out++ = '-';
                    ~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:418:5: note: in instantiation of function template specialization 'itoa10<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);
                                        ^
3 warnings generated.
In file included from read_qseq.cpp:20:
In file included from ./pat.h:40:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
In file included from read_qseq.cpp:20:
In file included from ./pat.h:41:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
                if (value <= 0 && value != 0) *out++ = '-';
                    ~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:418:5: note: in instantiation of function template specialization 'itoa10<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);
                                        ^
3 warnings generated.
In file included from aligner_seed_policy.cpp:24:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
1 warning generated.
In file included from aligner_seed.cpp:20:
In file included from ./aligner_cache.h:59:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
In file included from aligner_seed.cpp:21:
In file included from ./aligner_seed.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:43:
In file included from ./blockwise_sa.h:29:
./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
        size_t amapEnts = 1;
               ^
./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
In file included from aligner_seed.cpp:21:
In file included from ./aligner_seed.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:60:
./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable]
        size_t est_count = 0;
               ^
In file included from aligner_seed.cpp:21:
In file included from ./aligner_seed.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<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);
                                ^
9 warnings generated.
In file included from aligner_seed2.cpp:22:
In file included from ./aligner_seed2.h:101:
In file included from ./random_util.h:25:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
In file included from aligner_seed2.cpp:22:
In file included from ./aligner_seed2.h:102:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:43:
In file included from ./blockwise_sa.h:29:
./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
        size_t amapEnts = 1;
               ^
./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
In file included from aligner_seed2.cpp:22:
In file included from ./aligner_seed2.h:102:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:60:
./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable]
        size_t est_count = 0;
               ^
In file included from aligner_seed2.cpp:22:
In file included from ./aligner_seed2.h:102:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<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:
./aligner_seed2.h:1226:10: warning: variable 'nuninited' set but not used [-Wunused-but-set-variable]
                size_t nuninited = 0;
                       ^
./aligner_seed2.h:2446:10: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
                size_t ns = 0, ngap = 0, nrefn = 0;
                       ^
./aligner_seed2.h:2446:18: warning: variable 'ngap' set but not used [-Wunused-but-set-variable]
                size_t ns = 0, ngap = 0, nrefn = 0;
                               ^
./aligner_seed2.h:2446:28: warning: variable 'nrefn' set but not used [-Wunused-but-set-variable]
                size_t ns = 0, ngap = 0, nrefn = 0;
                                         ^
./aligner_seed2.h:4132:11: warning: variable 'nopts' set but not used [-Wunused-but-set-variable]
                        size_t nopts = 0;
                               ^
./aligner_seed2.h:3869:9: warning: variable 'off3p' set but not used [-Wunused-but-set-variable]
        size_t off3p = q.length() - off5p - 1;
               ^
./aligner_seed2.h:3876:9: warning: variable 'nalloc' set but not used [-Wunused-but-set-variable]
        size_t nalloc = 0;
               ^
In file included from aligner_seed2.cpp:22:
In file included from ./aligner_seed2.h:102:
In file included from ./aligner_result.h:27:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
                if (value <= 0 && value != 0) *out++ = '-';
                    ~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:418:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
                                itoa10(ops[i].n, buf); o.append(buf);
                                ^
16 warnings generated.
In file included from aligner_sw.cpp:25:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:27:
In file included from ./read.h:25:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
In file included from aligner_sw.cpp:25:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:43:
In file included from ./blockwise_sa.h:29:
./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
        size_t amapEnts = 1;
               ^
./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
In file included from aligner_sw.cpp:25:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:60:
./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable]
        size_t est_count = 0;
               ^
In file included from aligner_sw.cpp:25:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<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);
                                ^
9 warnings generated.
In file included from aligner_cache.cpp:20:
In file included from ./aligner_cache.h:59:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
In file included from aligner_cache.cpp:20:
In file included from ./aligner_cache.h:60:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
                if (value <= 0 && value != 0) *out++ = '-';
                    ~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:418:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
                                itoa10(ops[i].n, buf); o.append(buf);
                                ^
2 warnings generated.
In file included from aligner_result.cpp:21:
In file included from ./reference.h:32:
In file included from ./ref_read.h:33:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
In file included from aligner_result.cpp:22:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:43:
In file included from ./blockwise_sa.h:29:
./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
        size_t amapEnts = 1;
               ^
./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
In file included from aligner_result.cpp:22:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:60:
./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable]
        size_t est_count = 0;
               ^
In file included from aligner_result.cpp:22:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<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);
                                ^
9 warnings generated.
In file included from aln_sink.cpp:22:
In file included from ./aln_sink.h:24:
In file included from ./read.h:25:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
In file included from aln_sink.cpp:22:
In file included from ./aln_sink.h:25:
In file included from ./unique.h:38:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:43:
In file included from ./blockwise_sa.h:29:
./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
        size_t amapEnts = 1;
               ^
./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
In file included from aln_sink.cpp:22:
In file included from ./aln_sink.h:25:
In file included from ./unique.h:38:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:60:
./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable]
        size_t est_count = 0;
               ^
In file included from aln_sink.cpp:22:
In file included from ./aln_sink.h:25:
In file included from ./unique.h:38:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<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);
                                ^
9 warnings generated.
In file included from dp_framer.cpp:20:
In file included from ./dp_framer.h:51:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
1 warning generated.
In file included from presets.cpp:21:
In file included from ./presets.h:32:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
1 warning generated.
In file included from unique.cpp:20:
In file included from ./unique.h:38:
In file included from ./aligner_result.h:27:
In file included from ./read.h:25:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
In file included from unique.cpp:20:
In file included from ./unique.h:38:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:43:
In file included from ./blockwise_sa.h:29:
./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
        size_t amapEnts = 1;
               ^
./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
In file included from unique.cpp:20:
In file included from ./unique.h:38:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:60:
./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable]
        size_t est_count = 0;
               ^
In file included from unique.cpp:20:
In file included from ./unique.h:38:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<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);
                                ^
9 warnings generated.
In file included from simple_func.cpp:22:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
1 warning generated.
In file included from random_util.cpp:20:
In file included from ./random_util.h:25:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
1 warning generated.
In file included from aligner_bt.cpp:20:
In file included from ./aligner_bt.h:25:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:27:
In file included from ./read.h:25:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
In file included from aligner_bt.cpp:20:
In file included from ./aligner_bt.h:25:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:43:
In file included from ./blockwise_sa.h:29:
./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
        size_t amapEnts = 1;
               ^
./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
In file included from aligner_bt.cpp:20:
In file included from ./aligner_bt.h:25:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:60:
./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable]
        size_t est_count = 0;
               ^
In file included from aligner_bt.cpp:20:
In file included from ./aligner_bt.h:25:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<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;
            ^
aligner_bt.cpp:125:10: warning: variable 'neval' set but not used [-Wunused-but-set-variable]
                size_t neval = 0; // # cells evaluated in this diag
                       ^
aligner_bt.cpp:1170:9: warning: variable 'iters' set but not used [-Wunused-but-set-variable]
        size_t iters = 0;
               ^
In file included from aligner_bt.cpp:20:
In file included from ./aligner_bt.h:25:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:27:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
                if (value <= 0 && value != 0) *out++ = '-';
                    ~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:418:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
                                itoa10(ops[i].n, buf); o.append(buf);
                                ^
11 warnings generated.
In file included from sse_util.cpp:20:
In file included from ./sse_util.h:29:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
1 warning generated.
In file included from aligner_swsse.cpp:21:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:27:
In file included from ./read.h:25:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
In file included from aligner_swsse.cpp:21:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:43:
In file included from ./blockwise_sa.h:29:
./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
        size_t amapEnts = 1;
               ^
./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
In file included from aligner_swsse.cpp:21:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:60:
./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable]
        size_t est_count = 0;
               ^
In file included from aligner_swsse.cpp:21:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<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);
                                ^
9 warnings generated.
In file included from outq.cpp:20:
In file included from ./outq.h:24:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
In file included from outq.cpp:20:
In file included from ./outq.h:26:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
                if (value <= 0 && value != 0) *out++ = '-';
                    ~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:418:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
                                itoa10(ops[i].n, buf); o.append(buf);
                                ^
2 warnings generated.
In file included from aligner_swsse_loc_i16.cpp:56:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:27:
In file included from ./read.h:25:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
In file included from aligner_swsse_loc_i16.cpp:56:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:43:
In file included from ./blockwise_sa.h:29:
./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
        size_t amapEnts = 1;
               ^
./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
In file included from aligner_swsse_loc_i16.cpp:56:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:60:
./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable]
        size_t est_count = 0;
               ^
In file included from aligner_swsse_loc_i16.cpp:56:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<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);
                                ^
9 warnings generated.
In file included from aligner_swsse_ee_i16.cpp:56:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:27:
In file included from ./read.h:25:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
In file included from aligner_swsse_ee_i16.cpp:56:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:43:
In file included from ./blockwise_sa.h:29:
./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
        size_t amapEnts = 1;
               ^
./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
In file included from aligner_swsse_ee_i16.cpp:56:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:60:
./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable]
        size_t est_count = 0;
               ^
In file included from aligner_swsse_ee_i16.cpp:56:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<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);
                                ^
9 warnings generated.
In file included from aligner_swsse_loc_u8.cpp:56:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:27:
In file included from ./read.h:25:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
In file included from aligner_swsse_loc_u8.cpp:56:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:43:
In file included from ./blockwise_sa.h:29:
./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
        size_t amapEnts = 1;
               ^
./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
In file included from aligner_swsse_loc_u8.cpp:56:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:60:
./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable]
        size_t est_count = 0;
               ^
In file included from aligner_swsse_loc_u8.cpp:56:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<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);
                                ^
9 warnings generated.
In file included from aligner_swsse_ee_u8.cpp:56:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:27:
In file included from ./read.h:25:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
In file included from aligner_swsse_ee_u8.cpp:56:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:43:
In file included from ./blockwise_sa.h:29:
./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
        size_t amapEnts = 1;
               ^
./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
In file included from aligner_swsse_ee_u8.cpp:56:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:60:
./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable]
        size_t est_count = 0;
               ^
In file included from aligner_swsse_ee_u8.cpp:56:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<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);
                                ^
9 warnings generated.
In file included from aligner_driver.cpp:20:
In file included from ./aligner_driver.h:78:
In file included from ./aligner_seed2.h:101:
In file included from ./random_util.h:25:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
In file included from aligner_driver.cpp:20:
In file included from ./aligner_driver.h:78:
In file included from ./aligner_seed2.h:102:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:43:
In file included from ./blockwise_sa.h:29:
./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
        size_t amapEnts = 1;
               ^
./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
In file included from aligner_driver.cpp:20:
In file included from ./aligner_driver.h:78:
In file included from ./aligner_seed2.h:102:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:60:
./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable]
        size_t est_count = 0;
               ^
In file included from aligner_driver.cpp:20:
In file included from ./aligner_driver.h:78:
In file included from ./aligner_seed2.h:102:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<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:
./aligner_seed2.h:1226:10: warning: variable 'nuninited' set but not used [-Wunused-but-set-variable]
                size_t nuninited = 0;
                       ^
./aligner_seed2.h:2446:10: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
                size_t ns = 0, ngap = 0, nrefn = 0;
                       ^
./aligner_seed2.h:2446:18: warning: variable 'ngap' set but not used [-Wunused-but-set-variable]
                size_t ns = 0, ngap = 0, nrefn = 0;
                               ^
./aligner_seed2.h:2446:28: warning: variable 'nrefn' set but not used [-Wunused-but-set-variable]
                size_t ns = 0, ngap = 0, nrefn = 0;
                                         ^
./aligner_seed2.h:4132:11: warning: variable 'nopts' set but not used [-Wunused-but-set-variable]
                        size_t nopts = 0;
                               ^
./aligner_seed2.h:3869:9: warning: variable 'off3p' set but not used [-Wunused-but-set-variable]
        size_t off3p = q.length() - off5p - 1;
               ^
./aligner_seed2.h:3876:9: warning: variable 'nalloc' set but not used [-Wunused-but-set-variable]
        size_t nalloc = 0;
               ^
In file included from aligner_driver.cpp:20:
In file included from ./aligner_driver.h:78:
In file included from ./aligner_seed2.h:102:
In file included from ./aligner_result.h:27:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
                if (value <= 0 && value != 0) *out++ = '-';
                    ~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:418:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
                                itoa10(ops[i].n, buf); o.append(buf);
                                ^
16 warnings generated.
In file included from splice_site.cpp:20:
In file included from ./edit.h:29:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
In file included from splice_site.cpp:20:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:43:
In file included from ./blockwise_sa.h:29:
./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
        size_t amapEnts = 1;
               ^
./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
In file included from splice_site.cpp:20:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
In file included from ./gfm.h:60:
./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable]
        size_t est_count = 0;
               ^
In file included from splice_site.cpp:20:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<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);
                                ^
9 warnings generated.
In file included from hisat2_main.cpp:25:
./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        int thru = 0;
                            ^
1 warning generated.
mkdir -p ../inst
cp hisat2-align-s ../inst/hisat2
cp hisat2-build-s ../inst/hisat2-build
/usr/bin/g++ -shared -fPIC -o Rhisat2.so get_info.cpp
installing to /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-arm64/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-arm64/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-arm64/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)