Mock Version: 1.4.2 Mock Version: 1.4.2 Mock Version: 1.4.2 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/hisat2.spec'], chrootPath='/var/lib/mock/583334-epel-7-x86_64/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--private-network']printOutput=True) ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/hisat2.spec'], chrootPath='/var/lib/mock/583334-epel-7-x86_64/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--private-network']printOutput=True) Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '5dae918ca1b74cd5a3e90fa707d57694', '-D', '/var/lib/mock/583334-epel-7-x86_64/root', '-a', '--private-network', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=en_US.UTF-8', '-u', 'mockbuild', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/hisat2.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '5dae918ca1b74cd5a3e90fa707d57694', '-D', '/var/lib/mock/583334-epel-7-x86_64/root', '-a', '--private-network', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=en_US.UTF-8', '-u', 'mockbuild', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/hisat2.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False warning: Could not canonicalize hostname: 5dae918ca1b74cd5a3e90fa707d57694 warning: Could not canonicalize hostname: 5dae918ca1b74cd5a3e90fa707d57694 Building target platforms: x86_64 Building target platforms: x86_64 Building for target x86_64 Building for target x86_64 Wrote: /builddir/build/SRPMS/hisat2-2.1.0-1.el7.centos.src.rpm Wrote: /builddir/build/SRPMS/hisat2-2.1.0-1.el7.centos.src.rpm Child return code was: 0 Child return code was: 0 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/hisat2.spec'], chrootPath='/var/lib/mock/583334-epel-7-x86_64/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--private-network', '--private-network']printOutput=True) ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/hisat2.spec'], chrootPath='/var/lib/mock/583334-epel-7-x86_64/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--private-network', '--private-network']printOutput=True) Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '940d58bf5f874018ae20f7b321696e94', '-D', '/var/lib/mock/583334-epel-7-x86_64/root', '-a', '--private-network', '--private-network', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=en_US.UTF-8', '-u', 'mockbuild', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/hisat2.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '940d58bf5f874018ae20f7b321696e94', '-D', '/var/lib/mock/583334-epel-7-x86_64/root', '-a', '--private-network', '--private-network', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=en_US.UTF-8', '-u', 'mockbuild', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/hisat2.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False Building target platforms: x86_64 Building target platforms: x86_64 Building for target x86_64 Building for target x86_64 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.SF8ZSn Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.SF8ZSn + umask 022 + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf hisat2-2.1.0 + rm -rf hisat2-2.1.0 + /usr/bin/unzip -qq /builddir/build/SOURCES/hisat2-2.1.0-source.zip + /usr/bin/unzip -qq /builddir/build/SOURCES/hisat2-2.1.0-source.zip + STATUS=0 + STATUS=0 + '[' 0 -ne 0 ']' + '[' 0 -ne 0 ']' + cd hisat2-2.1.0 + cd hisat2-2.1.0 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + exit 0 + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.qmqCo1 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.qmqCo1 + umask 022 + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + cd hisat2-2.1.0 + cd hisat2-2.1.0 + make -j2 BITS=64 SSE_FLAG= + make -j2 BITS=64 SSE_FLAG= /usr/bin/g++ -O3 -m64 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ /usr/bin/g++ -O3 -m64 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \ -I third_party \ -I third_party \ -o hisat2-build-s hisat2_build.cpp \ -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 \ 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 -lpthread /bin/sh: hostname: command not found /bin/sh: hostname: command not found /usr/bin/g++ -O3 -m64 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ /usr/bin/g++ -O3 -m64 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I third_party \ -I third_party \ -o hisat2-build-l hisat2_build.cpp \ -o hisat2-build-l 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 \ 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 -lpthread /bin/sh: hostname: command not found /bin/sh: hostname: command not found In file included from gfm.h:64:0, In file included from gfm.h:64:0, from hisat2_build.cpp:35: from hisat2_build.cpp:35: gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] RefGraph::RefGraph(const SString& s, RefGraph::RefGraph(const SString& s, ^ ^ gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from hisat2_build.cpp:35: from hisat2_build.cpp:35: gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from hisat2_build.cpp:35: from hisat2_build.cpp:35: gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] const SString& s = *(threadParam->s); const SString& s = *(threadParam->s); ^ ^ gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from hisat2_build.cpp:35: from hisat2_build.cpp:35: gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] RefGraph::RefGraph(const SString& s, RefGraph::RefGraph(const SString& s, ^ ^ gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from hisat2_build.cpp:35: from hisat2_build.cpp:35: gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from hisat2_build.cpp:35: from hisat2_build.cpp:35: gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] const SString& s = *(threadParam->s); const SString& s = *(threadParam->s); ^ ^ gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ ref_read.cpp: In function 'std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)': ref_read.cpp: In function 'std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)': ref_read.cpp:327:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] ref_read.cpp:327:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(i + 1 >= recs.size() || recs[i+1].first) { if(i + 1 >= recs.size() || recs[i+1].first) { ^ ^ ref_read.cpp: In function 'std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)': ref_read.cpp: In function 'std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)': ref_read.cpp:327:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] ref_read.cpp:327:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(i + 1 >= recs.size() || recs[i+1].first) { if(i + 1 >= recs.size() || recs[i+1].first) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from splice_site.h:34, from splice_site.h:34, from edit.h:30, from edit.h:30, from edit.cpp:21: from edit.cpp:21: gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] RefGraph::RefGraph(const SString& s, RefGraph::RefGraph(const SString& s, ^ ^ gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from splice_site.h:34, from splice_site.h:34, from edit.h:30, from edit.h:30, from edit.cpp:21: from edit.cpp:21: gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from splice_site.h:34, from splice_site.h:34, from edit.h:30, from edit.h:30, from edit.cpp:21: from edit.cpp:21: gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] const SString& s = *(threadParam->s); const SString& s = *(threadParam->s); ^ ^ gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from splice_site.h:34, from splice_site.h:34, from edit.h:30, from edit.h:30, from edit.cpp:21: from edit.cpp:21: gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] RefGraph::RefGraph(const SString& s, RefGraph::RefGraph(const SString& s, ^ ^ gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from splice_site.h:34, from splice_site.h:34, from edit.h:30, from edit.h:30, from edit.cpp:21: from edit.cpp:21: gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from splice_site.h:34, from splice_site.h:34, from edit.h:30, from edit.h:30, from edit.cpp:21: from edit.cpp:21: gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] const SString& s = *(threadParam->s); const SString& s = *(threadParam->s); ^ ^ gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from gfm.cpp:21: from gfm.cpp:21: gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] RefGraph::RefGraph(const SString& s, RefGraph::RefGraph(const SString& s, ^ ^ gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from gfm.cpp:21: from gfm.cpp:21: gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from gfm.cpp:21: from gfm.cpp:21: gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] const SString& s = *(threadParam->s); const SString& s = *(threadParam->s); ^ ^ gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from gfm.cpp:21: from gfm.cpp:21: gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] RefGraph::RefGraph(const SString& s, RefGraph::RefGraph(const SString& s, ^ ^ gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from gfm.cpp:21: from gfm.cpp:21: gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from gfm.cpp:21: from gfm.cpp:21: gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] const SString& s = *(threadParam->s); const SString& s = *(threadParam->s); ^ ^ gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ reference.cpp: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': reference.cpp: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': reference.cpp:456:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] reference.cpp:456:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; uint64_t origBufOff = bufOff; ^ ^ reference.cpp:450:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] reference.cpp:450:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] bool binarySearched = false; bool binarySearched = false; ^ ^ reference.cpp: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': reference.cpp: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': reference.cpp:456:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] reference.cpp:456:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; uint64_t origBufOff = bufOff; ^ ^ reference.cpp:450:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] reference.cpp:450:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] bool binarySearched = false; bool binarySearched = false; ^ ^ /usr/bin/g++ -O3 -m64 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ /usr/bin/g++ -O3 -m64 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ -I third_party \ -I third_party \ -o hisat2-align-s hisat2.cpp \ -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 \ 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 -lpthread /bin/sh: hostname: command not found /bin/sh: hostname: command not found /usr/bin/g++ -O3 -m64 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ /usr/bin/g++ -O3 -m64 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I third_party \ -I third_party \ -o hisat2-align-l hisat2.cpp \ -o hisat2-align-l 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 \ 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 -lpthread /bin/sh: hostname: command not found /bin/sh: hostname: command not found In file included from gfm.h:64:0, In file included from gfm.h:64:0, from hgfm.h:24, from hgfm.h:24, from hisat2.cpp:33: from hisat2.cpp:33: gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] RefGraph::RefGraph(const SString& s, RefGraph::RefGraph(const SString& s, ^ ^ gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from hgfm.h:24, from hgfm.h:24, from hisat2.cpp:33: from hisat2.cpp:33: gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from hgfm.h:24, from hgfm.h:24, from hisat2.cpp:33: from hisat2.cpp:33: gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] const SString& s = *(threadParam->s); const SString& s = *(threadParam->s); ^ ^ gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from hgfm.h:24, from hgfm.h:24, from hisat2.cpp:33: from hisat2.cpp:33: gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] RefGraph::RefGraph(const SString& s, RefGraph::RefGraph(const SString& s, ^ ^ gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from hgfm.h:24, from hgfm.h:24, from hisat2.cpp:33: from hisat2.cpp:33: gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from hgfm.h:24, from hgfm.h:24, from hisat2.cpp:33: from hisat2.cpp:33: gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] const SString& s = *(threadParam->s); const SString& s = *(threadParam->s); ^ ^ gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from hgfm.h:24:0, In file included from hgfm.h:24:0, from hisat2.cpp:33: from hisat2.cpp:33: gfm.h: In instantiation of 'void GFM::checkOrigs(const EList >&, bool) const [with index_t = unsigned int]': gfm.h: In instantiation of 'void GFM::checkOrigs(const EList >&, bool) const [with index_t = unsigned int]': hisat2.cpp:3686:27: required from 'void driver(const char*, const string&, const string&) [with TStr = SString; std::string = std::basic_string]' hisat2.cpp:3686:27: required from 'void driver(const char*, const string&, const string&) [with TStr = SString; std::string = std::basic_string]' hisat2.cpp:4115:51: required from here hisat2.cpp:4115:51: required from here gfm.h:6451:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] gfm.h:6451:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; int lastorig = -1; ^ ^ In file included from hgfm.h:24:0, In file included from hgfm.h:24:0, from hisat2.cpp:33: from hisat2.cpp:33: gfm.h: In instantiation of 'void GFM::checkOrigs(const EList >&, bool) const [with index_t = long unsigned int]': gfm.h: In instantiation of 'void GFM::checkOrigs(const EList >&, bool) const [with index_t = long unsigned int]': hisat2.cpp:3686:27: required from 'void driver(const char*, const string&, const string&) [with TStr = SString; std::string = std::basic_string]' hisat2.cpp:3686:27: required from 'void driver(const char*, const string&, const string&) [with TStr = SString; std::string = std::basic_string]' hisat2.cpp:4115:51: required from here hisat2.cpp:4115:51: required from here gfm.h:6451:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] gfm.h:6451:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; int lastorig = -1; ^ ^ In file included from hisat2.cpp:45:0: In file included from hisat2.cpp:45:0: spliced_aligner.h: In instantiation of 'int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long int]': spliced_aligner.h: In instantiation of 'int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long int]': hisat2.cpp:4134:1: required from here hisat2.cpp:4134:1: required from here spliced_aligner.h:282:18: warning: variable 'another_spliced' set but not used [-Wunused-but-set-variable] spliced_aligner.h:282:18: warning: variable 'another_spliced' set but not used [-Wunused-but-set-variable] bool another_spliced = false; bool another_spliced = false; ^ ^ In file included from hisat2.cpp:45:0: In file included from hisat2.cpp:45:0: spliced_aligner.h: In instantiation of 'int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int; int64_t = long int]': spliced_aligner.h: In instantiation of 'int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int; int64_t = long int]': hisat2.cpp:4134:1: required from here hisat2.cpp:4134:1: required from here spliced_aligner.h:282:18: warning: variable 'another_spliced' set but not used [-Wunused-but-set-variable] spliced_aligner.h:282:18: warning: variable 'another_spliced' set but not used [-Wunused-but-set-variable] bool another_spliced = false; bool another_spliced = false; ^ ^ ref_read.cpp: In function 'std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)': ref_read.cpp: In function 'std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)': ref_read.cpp:327:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] ref_read.cpp:327:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(i + 1 >= recs.size() || recs[i+1].first) { if(i + 1 >= recs.size() || recs[i+1].first) { ^ ^ ref_read.cpp: In function 'std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)': ref_read.cpp: In function 'std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)': ref_read.cpp:327:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] ref_read.cpp:327:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(i + 1 >= recs.size() || recs[i+1].first) { if(i + 1 >= recs.size() || recs[i+1].first) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from splice_site.h:34, from splice_site.h:34, from edit.h:30, from edit.h:30, from edit.cpp:21: from edit.cpp:21: gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] RefGraph::RefGraph(const SString& s, RefGraph::RefGraph(const SString& s, ^ ^ gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from splice_site.h:34, from splice_site.h:34, from edit.h:30, from edit.h:30, from edit.cpp:21: from edit.cpp:21: gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from splice_site.h:34, from splice_site.h:34, from edit.h:30, from edit.h:30, from edit.cpp:21: from edit.cpp:21: gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] const SString& s = *(threadParam->s); const SString& s = *(threadParam->s); ^ ^ gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from splice_site.h:34, from splice_site.h:34, from edit.h:30, from edit.h:30, from edit.cpp:21: from edit.cpp:21: gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] RefGraph::RefGraph(const SString& s, RefGraph::RefGraph(const SString& s, ^ ^ gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from splice_site.h:34, from splice_site.h:34, from edit.h:30, from edit.h:30, from edit.cpp:21: from edit.cpp:21: gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from splice_site.h:34, from splice_site.h:34, from edit.h:30, from edit.h:30, from edit.cpp:21: from edit.cpp:21: gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] const SString& s = *(threadParam->s); const SString& s = *(threadParam->s); ^ ^ gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from gfm.cpp:21: from gfm.cpp:21: gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] RefGraph::RefGraph(const SString& s, RefGraph::RefGraph(const SString& s, ^ ^ gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from gfm.cpp:21: from gfm.cpp:21: gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from gfm.cpp:21: from gfm.cpp:21: gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] const SString& s = *(threadParam->s); const SString& s = *(threadParam->s); ^ ^ gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from gfm.cpp:21: from gfm.cpp:21: gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] RefGraph::RefGraph(const SString& s, RefGraph::RefGraph(const SString& s, ^ ^ gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from gfm.cpp:21: from gfm.cpp:21: gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from gfm.cpp:21: from gfm.cpp:21: gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] const SString& s = *(threadParam->s); const SString& s = *(threadParam->s); ^ ^ gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ reference.cpp: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': reference.cpp: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': reference.cpp:456:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] reference.cpp:456:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; uint64_t origBufOff = bufOff; ^ ^ reference.cpp:450:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] reference.cpp:450:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] bool binarySearched = false; bool binarySearched = false; ^ ^ reference.cpp: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': reference.cpp: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': reference.cpp:456:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] reference.cpp:456:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; uint64_t origBufOff = bufOff; ^ ^ reference.cpp:450:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] reference.cpp:450:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] bool binarySearched = false; bool binarySearched = false; ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from splice_site.h:34, from splice_site.h:34, from edit.h:30, from edit.h:30, from aligner_seed.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: from aligner_seed.cpp:21: gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] RefGraph::RefGraph(const SString& s, RefGraph::RefGraph(const SString& s, ^ ^ gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from splice_site.h:34, from splice_site.h:34, from edit.h:30, from edit.h:30, from aligner_seed.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: from aligner_seed.cpp:21: gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from splice_site.h:34, from splice_site.h:34, from edit.h:30, from edit.h:30, from aligner_seed.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: from aligner_seed.cpp:21: gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] const SString& s = *(threadParam->s); const SString& s = *(threadParam->s); ^ ^ gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from splice_site.h:34, from splice_site.h:34, from edit.h:30, from edit.h:30, from aligner_seed.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: from aligner_seed.cpp:21: gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] RefGraph::RefGraph(const SString& s, RefGraph::RefGraph(const SString& s, ^ ^ gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from splice_site.h:34, from splice_site.h:34, from edit.h:30, from edit.h:30, from aligner_seed.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: from aligner_seed.cpp:21: gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from splice_site.h:34, from splice_site.h:34, from edit.h:30, from edit.h:30, from aligner_seed.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: from aligner_seed.cpp:21: gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] const SString& s = *(threadParam->s); const SString& s = *(threadParam->s); ^ ^ gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from splice_site.h:34, from splice_site.h:34, from edit.h:30, from edit.h:30, from aligner_result.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.h:102, from aligner_seed2.cpp:22: from aligner_seed2.cpp:22: gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] RefGraph::RefGraph(const SString& s, RefGraph::RefGraph(const SString& s, ^ ^ gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from splice_site.h:34, from splice_site.h:34, from edit.h:30, from edit.h:30, from aligner_result.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.h:102, from aligner_seed2.cpp:22: from aligner_seed2.cpp:22: gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from splice_site.h:34, from splice_site.h:34, from edit.h:30, from edit.h:30, from aligner_result.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.h:102, from aligner_seed2.cpp:22: from aligner_seed2.cpp:22: gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] const SString& s = *(threadParam->s); const SString& s = *(threadParam->s); ^ ^ gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from splice_site.h:34, from splice_site.h:34, from edit.h:30, from edit.h:30, from aligner_result.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.h:102, from aligner_seed2.cpp:22: from aligner_seed2.cpp:22: gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] RefGraph::RefGraph(const SString& s, RefGraph::RefGraph(const SString& s, ^ ^ gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from splice_site.h:34, from splice_site.h:34, from edit.h:30, from edit.h:30, from aligner_result.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.h:102, from aligner_seed2.cpp:22: from aligner_seed2.cpp:22: gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from splice_site.h:34, from splice_site.h:34, from edit.h:30, from edit.h:30, from aligner_result.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.h:102, from aligner_seed2.cpp:22: from aligner_seed2.cpp:22: gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] const SString& s = *(threadParam->s); const SString& s = *(threadParam->s); ^ ^ gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from splice_site.h:34, from splice_site.h:34, from edit.h:30, from edit.h:30, from aligner_result.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.h:74, from aligner_sw.cpp:25: from aligner_sw.cpp:25: gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:749:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:363:1: warning: matches this 's' under ISO standard rules [enabled by default] RefGraph::RefGraph(const SString& s, RefGraph::RefGraph(const SString& s, ^ ^ gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:639:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from splice_site.h:34, from splice_site.h:34, from edit.h:30, from edit.h:30, from aligner_result.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.h:74, from aligner_sw.cpp:25: from aligner_sw.cpp:25: gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h: In static member function 'static void RefGraph::buildGraph_worker(void*)': gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] gbwt_graph.h:1072:30: warning: name lookup of 's' changed [enabled by default] int nt = s[j]; int nt = s[j]; ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from splice_site.h:34, from splice_site.h:34, from edit.h:30, from edit.h:30, from aligner_result.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.h:74, from aligner_sw.cpp:25: from aligner_sw.cpp:25: gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules [enabled by default] const SString& s = *(threadParam->s); const SString& s = *(threadParam->s); ^ ^ gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] gbwt_graph.h:955:25: warning: matches this 's' under old rules [enabled by default] for(index_t s = 0; s < snpIDs.size(); s++) { for(index_t s = 0; s < snpIDs.size(); s++) { ^ ^ In file included from gfm.h:64:0, In file included from gfm.h:64:0, from splice_site.h:34, from splice_site.h:34, from edit.h:30, from edit.h:30, from aligner_result.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.h:74, from aligner_sw.cpp:25: from aligner_sw.cpp:25: gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString&, const EList&, const EList >&, const EList >&, const string&, int, bool)': gbwt_graph.h: In constructor 'RefGraph::RefGraph(const SString