junaruga/bowtie-1.3.1_fedora_build_flags_build.log

## bowtie-1.3.1_fedora_build_flags_build.log
$ cat result.err/build.log
Mock Version: 3.4
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target x86_64 --nodeps /builddir/build/SPECS/bowtie.spec'], chrootPath='/var/lib/mock/fedora-rawhide-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;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7f70ababb690>timeout=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.guk7ajsi:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=FalseprintOutput=True)
Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.guk7ajsi:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']
Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '1a9d267ed62545e18d25ed035504e135', '-D', '/var/lib/mock/fedora-rawhide-x86_64/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.guk7ajsi:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--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;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target x86_64 --nodeps /builddir/build/SPECS/bowtie.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1676592000
Wrote: /builddir/build/SRPMS/bowtie-1.3.1-1.fc39.src.rpm
Child return code was: 0
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --noclean --target x86_64 --nodeps /builddir/build/SPECS/bowtie.spec'], chrootPath='/var/lib/mock/fedora-rawhide-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;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7f70ababb690>timeout=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.guk7ajsi:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=FalseprintOutput=True)
Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.guk7ajsi:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']
Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '54941ae862954eba91a57cacc470baa0', '-D', '/var/lib/mock/fedora-rawhide-x86_64/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.guk7ajsi:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--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;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb --noclean --target x86_64 --nodeps /builddir/build/SPECS/bowtie.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1676592000
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.OJU5N7
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf bowtie-1.3.1-src
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/bowtie-1.3.1-src.zip
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd bowtie-1.3.1-src
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ rm -rf third_party/
++ find . -name '*.py'
+ for file in $(find . -name "*.py") bowtie bowtie-*
+ sed -E -i '1s|/usr/bin/env python[3]?|/usr/bin/python3|' bowtie
+ for file in $(find . -name "*.py") bowtie bowtie-*
+ sed -E -i '1s|/usr/bin/env python[3]?|/usr/bin/python3|' bowtie-build
+ for file in $(find . -name "*.py") bowtie bowtie-*
+ sed -E -i '1s|/usr/bin/env python[3]?|/usr/bin/python3|' bowtie-inspect
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.jweOCQ
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd bowtie-1.3.1-src
+ /usr/bin/make -O -j8 V=1 VERBOSE=1 allall EXTRA_FLAGS=-g
g++ -O3 \
	-DCOMPILER_OPTIONS="\"-O3 -g -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  \"" -g -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"reproduciblebuild\"" -DBUILD_TIME="\"2023-02-17T00:00:00\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -Wall -Wno-unused-parameter -Wno-reorder \
	 -I third_party -I . \
	-o bowtie-inspect-s bowtie_inspect.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp \
	-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -lz -lpthread
btypes.h:30:26: warning: 'gEbwt_ext' violates the C++ One Definition Rule [-Wodr]
   30 | extern const std::string gEbwt_ext;
      |                          ^
ebwt.cpp:22:13: note: type 'struct string' itself violates the C++ One Definition Rule
   22 | std::string gEbwt_ext("ebwt");
      |             ^
ebwt.cpp:22:13: note: 'gEbwt_ext' was previously declared here
g++ -O3 \
	-DCOMPILER_OPTIONS="\"-O3 -g -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  \"" -g -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"reproduciblebuild\"" -DBUILD_TIME="\"2023-02-17T00:00:00\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DBOWTIE_64BIT_INDEX -Wall -Wno-unused-parameter -Wno-reorder \
	 -I third_party -I . \
	-o bowtie-inspect-l bowtie_inspect.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp \
	-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -lz -lpthread
btypes.h:30:26: warning: 'gEbwt_ext' violates the C++ One Definition Rule [-Wodr]
   30 | extern const std::string gEbwt_ext;
      |                          ^
ebwt.cpp:18:13: note: type 'struct string' itself violates the C++ One Definition Rule
   18 | std::string gEbwt_ext("ebwtl");
      |             ^
ebwt.cpp:18:13: note: 'gEbwt_ext' was previously declared here
g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -g -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  \"" -g -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer    \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"reproduciblebuild\"" -DBUILD_TIME="\"2023-02-17T00:00:00\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder \
	 -I third_party \
	-o bowtie-build-s ebwt_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp  bowtie_build_main.cpp \
	-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -lz -lpthread
btypes.h:30:26: warning: 'gEbwt_ext' violates the C++ One Definition Rule [-Wodr]
   30 | extern const std::string gEbwt_ext;
      |                          ^
ebwt.cpp:22:13: note: type 'struct string' itself violates the C++ One Definition Rule
   22 | std::string gEbwt_ext("ebwt");
      |             ^
ebwt.cpp:22:13: note: 'gEbwt_ext' was previously declared here
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopyExact' at ds.h:965:7,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'resize' at ds.h:569:14,
    inlined from 'resize' at ds.h:562:7,
    inlined from 'buildSamples' at blockwise_sa.h:619:17,
    inlined from 'build' at blockwise_sa.h:384:16:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In member function 'build':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopyExact' at ds.h:965:7,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'resize' at ds.h:569:14,
    inlined from 'resize' at ds.h:562:7,
    inlined from 'buildSamples' at blockwise_sa.h:619:17,
    inlined from 'build' at blockwise_sa.h:384:16:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In member function 'build':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -g -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  \"" -g -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer    \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"reproduciblebuild\"" -DBUILD_TIME="\"2023-02-17T00:00:00\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder \
	 -I third_party \
	-o bowtie-build-l ebwt_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp  bowtie_build_main.cpp \
	-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -lz -lpthread
btypes.h:30:26: warning: 'gEbwt_ext' violates the C++ One Definition Rule [-Wodr]
   30 | extern const std::string gEbwt_ext;
      |                          ^
ebwt.cpp:18:13: note: type 'struct string' itself violates the C++ One Definition Rule
   18 | std::string gEbwt_ext("ebwtl");
      |             ^
ebwt.cpp:18:13: note: 'gEbwt_ext' was previously declared here
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopyExact' at ds.h:965:7,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'resize' at ds.h:569:14,
    inlined from 'resize' at ds.h:562:7,
    inlined from 'buildSamples' at blockwise_sa.h:619:17,
    inlined from 'build' at blockwise_sa.h:384:16:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In member function 'build':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopyExact' at ds.h:965:7,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'resize' at ds.h:569:14,
    inlined from 'resize' at ds.h:562:7,
    inlined from 'buildSamples' at blockwise_sa.h:619:17,
    inlined from 'build' at blockwise_sa.h:384:16:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In member function 'build':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopyExact' at ds.h:965:7,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'resize' at ds.h:569:14,
    inlined from 'resize' at ds.h:562:7,
    inlined from 'bucketSortSufDcU8' at multikey_qsort.h:1034:29,
    inlined from 'mkeyQSortSufDcU8.constprop.isra' at multikey_qsort.h:1154:20:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In function 'mkeyQSortSufDcU8.constprop.isra':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopyExact' at ds.h:965:7,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'push_back' at ds.h:496:29,
    inlined from 'bucketSortSufDcU8' at multikey_qsort.h:1084:23,
    inlined from 'mkeyQSortSufDcU8.constprop.isra' at multikey_qsort.h:1154:20:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In function 'mkeyQSortSufDcU8.constprop.isra':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopyExact' at ds.h:965:7,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'resize' at ds.h:569:14,
    inlined from 'resize' at ds.h:562:7,
    inlined from 'bucketSortSufDcU8' at multikey_qsort.h:1034:29,
    inlined from 'mkeyQSortSufDcU8.constprop.isra' at multikey_qsort.h:1154:20:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In function 'mkeyQSortSufDcU8.constprop.isra':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopyExact' at ds.h:965:7,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'push_back' at ds.h:496:29,
    inlined from 'bucketSortSufDcU8' at multikey_qsort.h:1084:23,
    inlined from 'mkeyQSortSufDcU8.constprop.isra' at multikey_qsort.h:1154:20:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In function 'mkeyQSortSufDcU8.constprop.isra':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
g++ -O0 -g3 \
	-DCOMPILER_OPTIONS="\"-O0 -g3 -g -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  \"" -g -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"reproduciblebuild\"" -DBUILD_TIME="\"2023-02-17T00:00:00\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -Wall -Wno-unused-parameter -Wno-reorder \
	 -I third_party -I . \
	-o bowtie-inspect-s-debug bowtie_inspect.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp \
	-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -lz -lpthread
btypes.h:30:26: warning: 'gEbwt_ext' violates the C++ One Definition Rule [-Wodr]
   30 | extern const std::string gEbwt_ext;
      |                          ^
ebwt.cpp:22:13: note: type 'struct string' itself violates the C++ One Definition Rule
   22 | std::string gEbwt_ext("ebwt");
      |             ^
ebwt.cpp:22:13: note: 'gEbwt_ext' was previously declared here
g++ -O0 -g3 \
	-DCOMPILER_OPTIONS="\"-O0 -g3 -g -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  \"" -g -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"reproduciblebuild\"" -DBUILD_TIME="\"2023-02-17T00:00:00\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DBOWTIE_64BIT_INDEX -Wall -Wno-unused-parameter -Wno-reorder \
	 -I third_party -I . \
	-o bowtie-inspect-l-debug bowtie_inspect.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp \
	-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -lz -lpthread
btypes.h:30:26: warning: 'gEbwt_ext' violates the C++ One Definition Rule [-Wodr]
   30 | extern const std::string gEbwt_ext;
      |                          ^
ebwt.cpp:18:13: note: type 'struct string' itself violates the C++ One Definition Rule
   18 | std::string gEbwt_ext("ebwtl");
      |             ^
ebwt.cpp:18:13: note: 'gEbwt_ext' was previously declared here
g++ -O0 -g3 -DCOMPILER_OPTIONS="\"-O0 -g3 -g -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  \"" -g -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"reproduciblebuild\"" -DBUILD_TIME="\"2023-02-17T00:00:00\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DBOWTIE_64BIT_INDEX -Wall -Wno-unused-parameter -Wno-reorder \
	 -I third_party \
	-o bowtie-build-l-debug ebwt_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp  bowtie_build_main.cpp \
	-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -lz -lpthread
btypes.h:30:26: warning: 'gEbwt_ext' violates the C++ One Definition Rule [-Wodr]
   30 | extern const std::string gEbwt_ext;
      |                          ^
ebwt.cpp:18:13: note: type 'struct string' itself violates the C++ One Definition Rule
   18 | std::string gEbwt_ext("ebwtl");
      |             ^
ebwt.cpp:18:13: note: 'gEbwt_ext' was previously declared here
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'push_back' at ds.h:496:29,
    inlined from 'mkeyQSortSuf2.constprop' at multikey_qsort.h:593:23:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In function 'mkeyQSortSuf2.constprop':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'push_back' at ds.h:496:29,
    inlined from 'mkeyQSortSuf2.constprop' at multikey_qsort.h:593:23:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In function 'mkeyQSortSuf2.constprop':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'resize' at ds.h:569:14,
    inlined from 'resize' at ds.h:562:7,
    inlined from 'bucketSortSufDcU8.constprop' at multikey_qsort.h:1034:29:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In function 'bucketSortSufDcU8.constprop':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'push_back' at ds.h:496:29,
    inlined from 'bucketSortSufDcU8.constprop' at multikey_qsort.h:1084:23:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In function 'bucketSortSufDcU8.constprop':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'resize' at ds.h:569:14,
    inlined from 'resize' at ds.h:562:7,
    inlined from 'bucketSortSufDcU8.constprop' at multikey_qsort.h:1034:29:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In function 'bucketSortSufDcU8.constprop':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'push_back' at ds.h:496:29,
    inlined from 'bucketSortSufDcU8.constprop' at multikey_qsort.h:1084:23:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In function 'bucketSortSufDcU8.constprop':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
g++ -O0 -g3 -DCOMPILER_OPTIONS="\"-O0 -g3 -g -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  \"" -g -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"reproduciblebuild\"" -DBUILD_TIME="\"2023-02-17T00:00:00\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -Wall -Wno-unused-parameter -Wno-reorder \
	 -I third_party \
	-o bowtie-build-s-debug ebwt_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp  bowtie_build_main.cpp \
	-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -lz -lpthread
btypes.h:30:26: warning: 'gEbwt_ext' violates the C++ One Definition Rule [-Wodr]
   30 | extern const std::string gEbwt_ext;
      |                          ^
ebwt.cpp:22:13: note: type 'struct string' itself violates the C++ One Definition Rule
   22 | std::string gEbwt_ext("ebwt");
      |             ^
ebwt.cpp:22:13: note: 'gEbwt_ext' was previously declared here
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'resize' at ds.h:569:14,
    inlined from 'resize' at ds.h:562:7,
    inlined from 'bucketSortSufDcU8.constprop' at multikey_qsort.h:1034:29:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In function 'bucketSortSufDcU8.constprop':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'push_back' at ds.h:496:29,
    inlined from 'bucketSortSufDcU8.constprop' at multikey_qsort.h:1084:23:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In function 'bucketSortSufDcU8.constprop':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'resize' at ds.h:569:14,
    inlined from 'resize' at ds.h:562:7,
    inlined from 'bucketSortSufDcU8.constprop' at multikey_qsort.h:1034:29:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In function 'bucketSortSufDcU8.constprop':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'push_back' at ds.h:496:29,
    inlined from 'bucketSortSufDcU8.constprop' at multikey_qsort.h:1084:23:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In function 'bucketSortSufDcU8.constprop':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -g -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  \"" -g -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"reproduciblebuild\"" -DBUILD_TIME="\"2023-02-17T00:00:00\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder \
	 -I third_party \
	-o bowtie-align-s ebwt_search.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp sam.cpp hit.cpp bowtie_main.cpp \
	-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -lz -lpthread
btypes.h:30:26: warning: 'gEbwt_ext' violates the C++ One Definition Rule [-Wodr]
   30 | extern const std::string gEbwt_ext;
      |                          ^
ebwt.cpp:22:13: note: type 'struct string' itself violates the C++ One Definition Rule
   22 | std::string gEbwt_ext("ebwt");
      |             ^
ebwt.cpp:22:13: note: 'gEbwt_ext' was previously declared here
In member function 'alloc',
    inlined from 'expandNoCopyExact' at ds.h:1003:17,
    inlined from 'expandNoCopy' at ds.h:992:20,
    inlined from 'operator=' at ds.h:405:32,
    inlined from 'operator=' at ds.h:394:15,
    inlined from '__ct_base ' at pat.h:330:37:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In member function '__ct_base ':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function 'alloc',
    inlined from '_ZN5EListI5RangeLi128EE15expandCopyExactEm.part.0' at ds.h:967:17:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In member function '_ZN5EListI5RangeLi128EE15expandCopyExactEm.part.0':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'resize' at ds.h:569:14,
    inlined from 'resize' at ds.h:562:7,
    inlined from '__ct_base .constprop' at hit.h:176:17:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In member function '__ct_base .constprop':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopyExact' at ds.h:965:7,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'resize' at ds.h:569:14,
    inlined from 'resize' at ds.h:562:7,
    inlined from '__ct ' at pat.cpp:379:15,
    inlined from 'patsrcFromStrings' at ebwt_search.cpp:2945:54:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In function 'patsrcFromStrings':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -g -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  \"" -g -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"reproduciblebuild\"" -DBUILD_TIME="\"2023-02-17T00:00:00\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -DBOWTIE_64BIT_INDEX -Wall -Wno-unused-parameter -Wno-reorder \
	 -I third_party \
	-o bowtie-align-l ebwt_search.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp sam.cpp hit.cpp bowtie_main.cpp \
	-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -lz -lpthread
btypes.h:30:26: warning: 'gEbwt_ext' violates the C++ One Definition Rule [-Wodr]
   30 | extern const std::string gEbwt_ext;
      |                          ^
ebwt.cpp:18:13: note: type 'struct string' itself violates the C++ One Definition Rule
   18 | std::string gEbwt_ext("ebwtl");
      |             ^
ebwt.cpp:18:13: note: 'gEbwt_ext' was previously declared here
In member function 'alloc',
    inlined from 'expandNoCopyExact' at ds.h:1003:17,
    inlined from 'expandNoCopy' at ds.h:992:20,
    inlined from 'operator=' at ds.h:405:32,
    inlined from 'operator=' at ds.h:394:15,
    inlined from '__ct_base ' at pat.h:330:37:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In member function '__ct_base ':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function 'alloc',
    inlined from '_ZN5EListI5RangeLi128EE15expandCopyExactEm.part.0' at ds.h:967:17:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In member function '_ZN5EListI5RangeLi128EE15expandCopyExactEm.part.0':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'resize' at ds.h:569:14,
    inlined from 'resize' at ds.h:562:7,
    inlined from '__ct_base .constprop' at hit.h:176:17:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In member function '__ct_base .constprop':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopyExact' at ds.h:965:7,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'resize' at ds.h:569:14,
    inlined from 'resize' at ds.h:562:7,
    inlined from '__ct ' at pat.cpp:379:15,
    inlined from 'patsrcFromStrings' at ebwt_search.cpp:2945:54:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In function 'patsrcFromStrings':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
g++ -O0 -g3 \
	-DCOMPILER_OPTIONS="\"-O0 -g3 -g -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  \"" -g -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"reproduciblebuild\"" -DBUILD_TIME="\"2023-02-17T00:00:00\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -Wall -Wno-unused-parameter -Wno-reorder \
	 -I third_party \
	-o bowtie-align-s-debug ebwt_search.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp sam.cpp hit.cpp bowtie_main.cpp \
	-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -lz -lpthread
btypes.h:30:26: warning: 'gEbwt_ext' violates the C++ One Definition Rule [-Wodr]
   30 | extern const std::string gEbwt_ext;
      |                          ^
ebwt.cpp:22:13: note: type 'struct string' itself violates the C++ One Definition Rule
   22 | std::string gEbwt_ext("ebwt");
      |             ^
ebwt.cpp:22:13: note: 'gEbwt_ext' was previously declared here
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'resize' at ds.h:569:14,
    inlined from 'resize' at ds.h:562:7,
    inlined from '__ct_base .constprop' at hit.h:176:17:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In member function '__ct_base .constprop':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'resize' at ds.h:569:14,
    inlined from 'resize' at ds.h:562:7,
    inlined from 'naiveFind' at ref_aligner.h:251:19,
    inlined from 'anchor64Find' at ref_aligner.h:291:13:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In member function 'anchor64Find':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'resize' at ds.h:569:14,
    inlined from 'resize' at ds.h:562:7,
    inlined from 'naiveFind' at ref_aligner.h:587:20,
    inlined from 'anchor64Find' at ref_aligner.h:632:14:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In member function 'anchor64Find':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'resize' at ds.h:569:14,
    inlined from 'resize' at ds.h:562:7,
    inlined from '__ct ' at pat.cpp:379:15,
    inlined from 'patsrcFromStrings' at ebwt_search.cpp:2945:54:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In function 'patsrcFromStrings':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
g++ -O0 -g3 \
	-DCOMPILER_OPTIONS="\"-O0 -g3 -g -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  \"" -g -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"reproduciblebuild\"" -DBUILD_TIME="\"2023-02-17T00:00:00\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DBOWTIE_64BIT_INDEX -Wall -Wno-unused-parameter -Wno-reorder \
	 -I third_party \
	-o bowtie-align-l-debug ebwt_search.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp sam.cpp hit.cpp bowtie_main.cpp \
	-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -lz -lpthread
btypes.h:30:26: warning: 'gEbwt_ext' violates the C++ One Definition Rule [-Wodr]
   30 | extern const std::string gEbwt_ext;
      |                          ^
ebwt.cpp:18:13: note: type 'struct string' itself violates the C++ One Definition Rule
   18 | std::string gEbwt_ext("ebwtl");
      |             ^
ebwt.cpp:18:13: note: 'gEbwt_ext' was previously declared here
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'resize' at ds.h:569:14,
    inlined from 'resize' at ds.h:562:7,
    inlined from '__ct_base .constprop' at hit.h:176:17:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In member function '__ct_base .constprop':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'resize' at ds.h:569:14,
    inlined from 'resize' at ds.h:562:7,
    inlined from 'naiveFind' at ref_aligner.h:251:19,
    inlined from 'anchor64Find' at ref_aligner.h:291:13:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In member function 'anchor64Find':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'resize' at ds.h:569:14,
    inlined from 'resize' at ds.h:562:7,
    inlined from 'naiveFind' at ref_aligner.h:587:20,
    inlined from 'anchor64Find' at ref_aligner.h:632:14:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In member function 'anchor64Find':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function 'alloc',
    inlined from 'expandCopyExact' at ds.h:967:17,
    inlined from 'expandCopy' at ds.h:958:18,
    inlined from 'resize' at ds.h:569:14,
    inlined from 'resize' at ds.h:562:7,
    inlined from '__ct ' at pat.cpp:379:15,
    inlined from 'patsrcFromStrings' at ebwt_search.cpp:2945:54:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/13/new: In function 'patsrcFromStrings':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.lcgzmq
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64
++ dirname /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd bowtie-1.3.1-src
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64 'INSTALL=/usr/bin/install -p' prefix=/usr
mkdir -p /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64/usr/bin
for file in bowtie-build-s bowtie-build-l bowtie-align-s bowtie-align-l bowtie-inspect-s bowtie-inspect-l bowtie-inspect bowtie-build bowtie ; do \
	cp -f $file /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64/usr/bin ; \
done
+ mkdir -p /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64//usr/share/bowtie
+ cp -a reads /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64//usr/share/bowtie/
+ cp -a indexes /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64//usr/share/bowtie/
+ cp -a genomes /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64//usr/share/bowtie/
+ cp -a scripts /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64//usr/share/bowtie/
+ for cmd in bowtie-*-debug
+ cp -p bowtie-align-l-debug /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64//usr/bin/
+ for cmd in bowtie-*-debug
+ cp -p bowtie-align-s-debug /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64//usr/bin/
+ for cmd in bowtie-*-debug
+ cp -p bowtie-build-l-debug /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64//usr/bin/
+ for cmd in bowtie-*-debug
+ cp -p bowtie-build-s-debug /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64//usr/bin/
+ for cmd in bowtie-*-debug
+ cp -p bowtie-inspect-l-debug /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64//usr/bin/
+ for cmd in bowtie-*-debug
+ cp -p bowtie-inspect-s-debug /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64//usr/bin/
+ /usr/bin/find-debuginfo -j8 --strict-build-id -m -i --build-id-seed 1.3.1-1.fc39 --unique-debug-suffix -1.3.1-1.fc39.x86_64 --unique-debug-src-base bowtie-1.3.1-1.fc39.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/bowtie-1.3.1-src
extracting debug info from /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64/usr/bin/bowtie-align-l-debug
extracting debug info from /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64/usr/bin/bowtie-build-l
extracting debug info from /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64/usr/bin/bowtie-align-l
extracting debug info from /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64/usr/bin/bowtie-align-s
extracting debug info from /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64/usr/bin/bowtie-build-l-debug
extracting debug info from /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64/usr/bin/bowtie-align-s-debug
extracting debug info from /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64/usr/bin/bowtie-build-s-debug
extracting debug info from /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64/usr/bin/bowtie-build-s
extracting debug info from /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64/usr/bin/bowtie-inspect-l
extracting debug info from /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64/usr/bin/bowtie-inspect-l-debug
extracting debug info from /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64/usr/bin/bowtie-inspect-s
extracting debug info from /builddir/build/BUILDROOT/bowtie-1.3.1-1.fc39.x86_64/usr/bin/bowtie-inspect-s-debug
original debug info size: 39268kB, size after compression: 30368kB
/usr/bin/sepdebugcrcfix: Updated 12 CRC32s, 0 CRC32s did match.
2935 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
mangling shebang in /usr/share/bowtie/scripts/make_rn4.sh from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/share/bowtie/scripts/build_test.sh from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/share/bowtie/scripts/make_e_coli.sh from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/share/bowtie/scripts/make_s_cerevisiae.sh from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/share/bowtie/scripts/make_canFam2.sh from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/share/bowtie/scripts/make_m_musculus_ncbi37.sh from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/share/bowtie/scripts/make_b_taurus_UMD3.sh from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/share/bowtie/scripts/make_hg19.sh from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/share/bowtie/scripts/make_mm9.sh from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/share/bowtie/scripts/make_h_sapiens_ncbi36.sh from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/share/bowtie/scripts/make_a_thaliana_tair.sh from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/share/bowtie/scripts/make_d_melanogaster.sh from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/share/bowtie/scripts/make_mm8.sh from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/share/bowtie/scripts/make_c_elegans.sh from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/share/bowtie/scripts/make_hg18.sh from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/share/bowtie/scripts/run-hbb.sh from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/share/bowtie/scripts/bowtie-hbb.sh from /bin/bash to #!/usr/bin/bash
mangling shebang in /usr/share/bowtie/scripts/make_galGal3.sh from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/share/bowtie/scripts/make_h_sapiens_ncbi37.sh from /bin/sh to #!/usr/bin/sh
+ /usr/lib/rpm/brp-remove-la-files
+ env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j8
+ /usr/lib/rpm/redhat/brp-python-hardlink
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.plIBYc
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd bowtie-1.3.1-src
+ for cmd in bowtie bowtie-build bowtie-inspect
+ ./bowtie --version
+ grep 'version 1.3.1'
/builddir/build/BUILD/bowtie-1.3.1-src/bowtie-align-s version 1.3.1
+ for cmd in bowtie bowtie-build bowtie-inspect
+ ./bowtie-build --version
+ grep 'version 1.3.1'
bowtie-build version 1.3.1
+ for cmd in bowtie bowtie-build bowtie-inspect
+ ./bowtie-inspect --version
+ grep 'version 1.3.1'
bowtie-inspect version 1.3.1
+ tar xzvf /builddir/build/SOURCES/bowtie-1.3.1-tests.tgz
scripts/test/
scripts/test/random_bowtie_tests_p.sh
scripts/test/samtools.pl
scripts/test/simple_tests.pl
scripts/test/cs_dec.pl
scripts/test/random_bowtie_tests.sh
scripts/test/btface.py
scripts/test/long_read.pl
scripts/test/dataface.py
scripts/test/inspect.pl
scripts/test/random_bowtie_tests.pl
scripts/test/args.pl
scripts/test/DNA.pm
scripts/test/big_data/
scripts/test/big_data/reads/
scripts/test/big_data/reads/human_reads.fa
scripts/test/big_data/reads/mouse_reads.fa
scripts/test/cs_trim.pl
scripts/test/btdata.py
scripts/test/build_big.py
scripts/test/large_idx.py
scripts/test/all.sh
+ cat /builddir/build/SOURCES/bowtie-test-remove-perl-Sys-Info-dep.patch
+ patch -p1
patching file scripts/test/simple_tests.pl
Hunk #2 succeeded at 993 (offset -135 lines).
+ scripts/test/simple_tests.pl --bowtie=./bowtie --bowtie-build=./bowtie-build
FASTA-continuous 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie-build  --threads 1 --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie --debug   -F 10,9 -S --quiet -a .simple_tests.tmp  .simple_tests
Setting the index via positional argument will be deprecated in a future release. Please use -x option instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:Bowtie	VN:1.3.1	CL:"/builddir/build/BUILD/bowtie-1.3.1-src/bowtie-align-s-debug --wrapper basic-0 -F 10,9 -S --quiet -a .simple_tests.tmp .simple_tests"
# reads processed: 2
# reads with at least one alignment: 2 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 2 alignments
seq1_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	XA:i:0	MD:Z:10	NM:i:0	XM:i:1
seq1_9	0	0	10	255	10M	*	0	0	CAGTATCTGA	IIIIIIIIII	XA:i:0	MD:Z:10	NM:i:0	XM:i:1
FASTA-continuous 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie --debug   -F 10,9 -S --quiet -a .simple_tests.tmp  .simple_tests
Setting the index via positional argument will be deprecated in a future release. Please use -x option instead.
# reads processed: 3
# reads with at least one alignment: 3 (100.00%)@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:Bowtie	VN:1.3.1	CL:"/builddir/build/BUILD/bowtie-1.3.1-src/bowtie-align-s-debug --wrapper basic-0 -F 10,9 -S --quiet -a .simple_tests.tmp .simple_tests"
seq1_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	XA:i:0	MD:Z:10	NM:i:0	XM:i:1
seq2_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	XA:i:0	MD:Z:10	NM:i:0	XM:i:1
seq2_9	0	0	10	255	10M	*	0	0	CAGTATCTGA	IIIIIIIIII	XA:i:0	MD:Z:10	NM:i:0	XM:i:1
# reads that failed to align: 0 (0.00%)
Reported 3 alignments
FASTA-continuous 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie --debug   -F 10,9 -u 1 -S --quiet -a .simple_tests.tmp  .simple_tests
Setting the index via positional argument will be deprecated in a future release. Please use -x option instead.
# reads processed: 1
# reads with at least one alignment: 1 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 1 alignments
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:Bowtie	VN:1.3.1	CL:"/builddir/build/BUILD/bowtie-1.3.1-src/bowtie-align-s-debug --wrapper basic-0 -F 10,9 -u 1 -S --quiet -a .simple_tests.tmp .simple_tests"
seq1_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	XA:i:0	MD:Z:10	NM:i:0	XM:i:1
FASTA-continuous 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie --debug   -F 10,9 -s 1 -S --quiet -a .simple_tests.tmp  .simple_tests
Setting the index via positional argument will be deprecated in a future release. Please use -x option instead.
# reads processed: 1
# reads with at least one alignment: 1 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 1 alignments
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:Bowtie	VN:1.3.1	CL:"/builddir/build/BUILD/bowtie-1.3.1-src/bowtie-align-s-debug --wrapper basic-0 -F 10,9 -s 1 -S --quiet -a .simple_tests.tmp .simple_tests"
seq1_9	0	0	10	255	10M	*	0	0	CAGTATCTGA	IIIIIIIIII	XA:i:0	MD:Z:10	NM:i:0	XM:i:1
FASTA-continuous 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie --debug   -F 10,9 -u 1 -s 1 -S --quiet -a .simple_tests.tmp  .simple_tests
Setting the index via positional argument will be deprecated in a future release. Please use -x option instead.
# reads processed: 1
# reads with at least one alignment: 1 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 1 alignments
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:Bowtie	VN:1.3.1	CL:"/builddir/build/BUILD/bowtie-1.3.1-src/bowtie-align-s-debug --wrapper basic-0 -F 10,9 -u 1 -s 1 -S --quiet -a .simple_tests.tmp .simple_tests"
seq2_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	XA:i:0	MD:Z:10	NM:i:0	XM:i:1
FASTA-continuous 6 (fw:1, sam:1)
References:
>0
AGCATCGATCAG
./bowtie-build  --threads 1 --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie --debug   -F 10,1 -S --quiet -a .simple_tests.tmp  .simple_tests
Setting the index via positional argument will be deprecated in a future release. Please use -x option instead.
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:12
@PG	ID:Bowtie	VN:1.3.1	CL:"/builddir/build/BUILD/bowtie-1.3.1-src/bowtie-align-s-debug --wrapper basic-0 -F 10,1 -S --quiet -a .simple_tests.tmp .simple_tests"
# reads processed: 3
# reads with at least one alignment: 3 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 3 alignments
seq1_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	XA:i:0	MD:Z:10	NM:i:0	XM:i:1
seq1_1	0	0	2	255	10M	*	0	0	GCATCGATCA	IIIIIIIIII	XA:i:0	MD:Z:10	NM:i:0	XM:i:1
seq1_2	0	0	3	255	10M	*	0	0	CATCGATCAG	IIIIIIIIII	XA:i:0	MD:Z:10	NM:i:0	XM:i:1
Cline 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie-build  --threads 2 --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie --debug   --trim3 4 -S --quiet -a .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
Setting the index via positional argument will be deprecated in a future release. Please use -x option instead.
# reads processed: 1
# reads with at least one alignment: 1 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 1 alignments
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:Bowtie	VN:1.3.1	CL:"/builddir/build/BUILD/bowtie-1.3.1-src/bowtie-align-s-debug --wrapper basic-0 --trim3 4 -S --quiet -a .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	XA:i:0	MD:Z:12	NM:i:0	XM:i:1
Cline 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie --debug   --trim5 16 -S --quiet -a .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
Setting the index via positional argument will be deprecated in a future release. Please use -x option instead.
# reads processed: 1
# reads with at least one alignment: 0 (0.00%)
# reads that failed to align: 1 (100.00%)
No alignments
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:Bowtie	VN:1.3.1	CL:"/builddir/build/BUILD/bowtie-1.3.1-src/bowtie-align-s-debug --wrapper basic-0 --trim5 16 -S --quiet -a .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0	4	*	0	0	*	*	0	0			XM:i:0
Cline 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie --debug   -s 1 -S --quiet -a .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
Setting the index via positional argument will be deprecated in a future release. Please use -x option instead.
@HD	VN:1.0	SO:unsorted
# reads processed: 0
# reads with at least one alignment: 0 (0.00%)
# reads that failed to align: 0 (0.00%)
No alignments
@SQ	SN:0	LN:19
@PG	ID:Bowtie	VN:1.3.1	CL:"/builddir/build/BUILD/bowtie-1.3.1-src/bowtie-align-s-debug --wrapper basic-0 -s 1 -S --quiet -a .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
Cline multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie --debug   -u 1 -S --quiet -a .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII
Setting the index via positional argument will be deprecated in a future release. Please use -x option instead.
@HD	VN:1.0	SO:unsorted
# reads processed: 1
# reads with at least one alignment: 1 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 1 alignments
@SQ	SN:0	LN:19
@PG	ID:Bowtie	VN:1.3.1	CL:"/builddir/build/BUILD/bowtie-1.3.1-src/bowtie-align-s-debug --wrapper basic-0 -u 1 -S --quiet -a .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	XA:i:0	MD:Z:16	NM:i:0	XM:i:1
Cline multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie --debug   -u 2 -S --quiet -a .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG
Setting the index via positional argument will be deprecated in a future release. Please use -x option instead.
# reads processed: 2
# reads with at least one alignment: 2 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 2 alignments
@HD	VN:1.0	SO:unsorted
@SQ	SN:0	LN:19
@PG	ID:Bowtie	VN:1.3.1	CL:"/builddir/build/BUILD/bowtie-1.3.1-src/bowtie-align-s-debug --wrapper basic-0 -u 2 -S --quiet -a .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	XA:i:0	MD:Z:16	NM:i:0	XM:i:1
1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTGIIIIIIIIIIIIIII	XA:i:0	MD:Z:15	NM:i:0	XM:i:1
Cline paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie-build  --threads 1 --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie --debug   -s 1 -S --quiet -a .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII
Setting the index via positional argument will be deprecated in a future release. Please use -x option instead.
/usr/include/c++/13/bits/stl_queue.h:725: std::priority_queue<_Tp, _Sequence, _Compare>::const_reference std::priority_queue<_Tp, _Sequence, _Compare>::top() const [with _Tp = Branch*; _Sequence = std::vector<Branch*>; _Compare = CostCompare; const_reference = Branch* const&]: Assertion '!this->empty()' failed.
bowtie aborted with exitlevel 134
error: Bad exit status from /var/tmp/rpm-tmp.plIBYc (%check)
    Bad exit status from /var/tmp/rpm-tmp.plIBYc (%check)
RPM build errors:
Child return code was: 1
EXCEPTION: [Error('Command failed: \n # /usr/bin/systemd-nspawn -q -M 54941ae862954eba91a57cacc470baa0 -D /var/lib/mock/fedora-rawhide-x86_64/root -a -u mockbuild --capability=cap_ipc_lock --bind=/tmp/mock-resolv.guk7ajsi:/etc/resolv.conf --bind=/dev/btrfs-control --bind=/dev/mapper/control --bind=/dev/loop-control --bind=/dev/loop0 --bind=/dev/loop1 --bind=/dev/loop2 --bind=/dev/loop3 --bind=/dev/loop4 --bind=/dev/loop5 --bind=/dev/loop6 --bind=/dev/loop7 --bind=/dev/loop8 --bind=/dev/loop9 --bind=/dev/loop10 --bind=/dev/loop11 --console=pipe --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;<mock-chroot>\\007" --setenv=PS1=<mock-chroot> \\s-\\v\\$  --setenv=LANG=C.UTF-8 --resolv-conf=off bash --login -c /usr/bin/rpmbuild -bb --noclean --target x86_64 --nodeps /builddir/build/SPECS/bowtie.spec\n', 1)]
Traceback (most recent call last):
  File "/usr/lib/python3.11/site-packages/mockbuild/trace_decorator.py", line 93, in trace
    result = func(*args, **kw)
             ^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/site-packages/mockbuild/util.py", line 598, in do_with_status
    raise exception.Error("Command failed: \n # %s\n%s" % (command, output), child.returncode)
mockbuild.exception.Error: Command failed:
 # /usr/bin/systemd-nspawn -q -M 54941ae862954eba91a57cacc470baa0 -D /var/lib/mock/fedora-rawhide-x86_64/root -a -u mockbuild --capability=cap_ipc_lock --bind=/tmp/mock-resolv.guk7ajsi:/etc/resolv.conf --bind=/dev/btrfs-control --bind=/dev/mapper/control --bind=/dev/loop-control --bind=/dev/loop0 --bind=/dev/loop1 --bind=/dev/loop2 --bind=/dev/loop3 --bind=/dev/loop4 --bind=/dev/loop5 --bind=/dev/loop6 --bind=/dev/loop7 --bind=/dev/loop8 --bind=/dev/loop9 --bind=/dev/loop10 --bind=/dev/loop11 --console=pipe --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;<mock-chroot>\007" --setenv=PS1=<mock-chroot> \s-\v\$  --setenv=LANG=C.UTF-8 --resolv-conf=off bash --login -c /usr/bin/rpmbuild -bb --noclean --target x86_64 --nodeps /builddir/build/SPECS/bowtie.spec
$