Mock Version: 3.5
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs  --target i686 --nodeps /builddir/build/SPECS/R-Biostrings.spec'], chrootPath='/var/lib/mock/fedora-rawhide-i686-1671756994.049510/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 0x7fefe6443e50>timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.wvqw_q_y:/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=TrueprintOutput=True)
Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.wvqw_q_y:/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', 'ef69d23a6fee49dda7c418c35f7a39b2', '-D', '/var/lib/mock/fedora-rawhide-i686-1671756994.049510/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.wvqw_q_y:/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  --target i686 --nodeps /builddir/build/SPECS/R-Biostrings.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: i686
Building for target i686
setting SOURCE_DATE_EPOCH=1662163200
Wrote: /builddir/build/SRPMS/R-Biostrings-2.64.1-1.fc38.src.rpm
Child return code was: 0
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb  --target i686 --nodeps /builddir/build/SPECS/R-Biostrings.spec'], chrootPath='/var/lib/mock/fedora-rawhide-i686-1671756994.049510/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 0x7fefe6443e50>timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.wvqw_q_y:/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=TrueprintOutput=True)
Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.wvqw_q_y:/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', '5b7f4ecc4ddc48a9be5d4b832a8ea5f1', '-D', '/var/lib/mock/fedora-rawhide-i686-1671756994.049510/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.wvqw_q_y:/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  --target i686 --nodeps /builddir/build/SPECS/R-Biostrings.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: i686
Building for target i686
setting SOURCE_DATE_EPOCH=1662163200
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.lDZeYq
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf Biostrings
+ /usr/bin/mkdir -p Biostrings
+ cd Biostrings
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/Biostrings_2.64.1.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.TpSh12
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/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/lib:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd Biostrings
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.pMQkfc
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/R-Biostrings-2.64.1-1.fc38.i386 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/R-Biostrings-2.64.1-1.fc38.i386
++ dirname /builddir/build/BUILDROOT/R-Biostrings-2.64.1-1.fc38.i386
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/R-Biostrings-2.64.1-1.fc38.i386
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/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/lib:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd Biostrings
+ rm -rf /builddir/build/BUILDROOT/R-Biostrings-2.64.1-1.fc38.i386
+ mkdir -p /builddir/build/BUILDROOT/R-Biostrings-2.64.1-1.fc38.i386/usr/lib/R/library
+ R CMD INSTALL Biostrings -l /builddir/build/BUILDROOT/R-Biostrings-2.64.1-1.fc38.i386/usr/lib/R/library
* installing *source* package 'Biostrings' ...
** using staged installation
** libs
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c BAB_class.c -o BAB_class.o
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c BitMatrix.c -o BitMatrix.o
BitMatrix.c:299:13: warning: 'BitMatrix_print' defined but not used [-Wunused-function]
  299 | static void BitMatrix_print(BitMatrix *bitmat)
      |             ^~~~~~~~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c MIndex_class.c -o MIndex_class.o
MIndex_class.c: In function 'SparseMIndex_endIndex':
MIndex_class.c:184:27: warning: unused variable 'poffsets_order' [-Wunused-variable]
  184 |         IntAE *poffsets, *poffsets_order;
      |                           ^~~~~~~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c SparseList_utils.c -o SparseList_utils.o
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c XStringSetList_class.c -o XStringSetList_class.o
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c XStringSet_class.c -o XStringSet_class.o
XStringSet_class.c: In function 'new_XStringSet_from_CHARACTER':
XStringSet_class.c:124:17: warning: 'lkup_len' may be used uninitialized [-Wmaybe-uninitialized]
  124 |                 _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt,
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  125 |                                 INTEGER(start)[i], lkup0, lkup_len);
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
XStringSet_class.c:103:22: note: 'lkup_len' was declared here
  103 |         int ans_len, lkup_len, i;
      |                      ^~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c XString_class.c -o XString_class.o
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function 'align_needwunsQS':
align_needwunsQS.c:155:29: warning: 'sc' may be used uninitialized [-Wmaybe-uninitialized]
  155 |         INTEGER(ans_elt)[0] = score;
      |         ~~~~~~~~~~~~~~~~~~~~^~~~~~~
align_needwunsQS.c:27:19: note: 'sc' was declared here
   27 |         int *sco, sc, n1, n2, i1, i2, j1, j2, al_buf_size;
      |                   ^~
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c align_utils.c -o align_utils.o
align_utils.c: In function 'PairwiseAlignmentsSingleSubject_align_aligned':
align_utils.c:232:78: warning: 'indelStartPattern' may be used uninitialized [-Wmaybe-uninitialized]
  232 |                                 if ((numberOfIndelPattern == 0) || (jPattern < indelStartPattern)) {
      |                                                                    ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:221:21: note: 'indelStartPattern' was declared here
  221 |                 int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
      |                     ^~~~~~~~~~~~~~~~~
align_utils.c:238:55: warning: 'indelWidthPattern' may be used uninitialized [-Wmaybe-uninitialized]
  238 |                                         for (k = 0; k < indelWidthPattern; k++) {
      |                                                     ~~^~~~~~~~~~~~~~~~~~~
align_utils.c:221:40: note: 'indelWidthPattern' was declared here
  221 |                 int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
      |                                        ^~~~~~~~~~~~~~~~~
align_utils.c:231:63: warning: 'indelStartSubject' may be used uninitialized [-Wmaybe-uninitialized]
  231 |                         if ((numberOfIndelSubject == 0) || (j < indelStartSubject)) {
      |                                                            ~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:221:59: note: 'indelStartSubject' was declared here
  221 |                 int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
      |                                                           ^~~~~~~~~~~~~~~~~
align_utils.c:250:42: warning: 'indelWidthSubject' may be used uninitialized [-Wmaybe-uninitialized]
  250 |                                 jPattern += indelWidthSubject;
      |                                 ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:221:78: note: 'indelWidthSubject' was declared here
  221 |                 int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
      |                                                                              ^~~~~~~~~~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c find_palindromes.c -o find_palindromes.o
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c gtestsim.c -o gtestsim.o
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c inject_code.c -o inject_code.o
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c letter_frequency.c -o letter_frequency.o
letter_frequency.c: In function 'XStringSet_two_way_letter_frequency':
letter_frequency.c:957:48: warning: unused variable 'x_pos' [-Wunused-variable]
  957 |   int x_width, y_width, x_length, *ans_mat, i, x_pos;
      |                                                ^~~~~
letter_frequency.c:956:13: warning: unused variable 'ans_dimnames' [-Wunused-variable]
  956 |   SEXP ans, ans_dimnames;
      |             ^~~~~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c lowlevel_matching.c -o lowlevel_matching.o
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c match_PWM.c -o match_PWM.o
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c match_pattern.c -o match_pattern.o
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
match_pattern_boyermoore.c: In function '_match_pattern_boyermoore':
match_pattern_boyermoore.c:417:32: warning: 'i1' may be used uninitialized [-Wmaybe-uninitialized]
  417 |                         for (i = i1-1, j = j1-1; j >= 0; i--, j--)
      |                              ~~^~~~~~
match_pattern_boyermoore.c:383:42: note: 'i1' was declared here
  383 |         int nmatches, last_match_end, n, i1, i2, j1, j2, shift, shift1,
      |                                          ^~
match_pattern_boyermoore.c:417:42: warning: 'j1' may be used uninitialized [-Wmaybe-uninitialized]
  417 |                         for (i = i1-1, j = j1-1; j >= 0; i--, j--)
      |                                        ~~^~~~~~
match_pattern_boyermoore.c:383:50: note: 'j1' was declared here
  383 |         int nmatches, last_match_end, n, i1, i2, j1, j2, shift, shift1,
      |                                                  ^~
match_pattern_boyermoore.c:383:46: warning: 'i2' may be used uninitialized [-Wmaybe-uninitialized]
  383 |         int nmatches, last_match_end, n, i1, i2, j1, j2, shift, shift1,
      |                                              ^~
match_pattern_boyermoore.c:445:41: warning: 'c' may be used uninitialized [-Wmaybe-uninitialized]
  445 |                                 shift = get_VSGSshift(c, j1 - 1);
      |                                         ^~~~~~~~~~~~~~~~~~~~~~~~
match_pattern_boyermoore.c:385:23: note: 'c' was declared here
  385 |         char ppP_rmc, c; /* ppP_rmc is 'ppP.seq' right-most char */
      |                       ^
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c match_pattern_indels.c -o match_pattern_indels.o
match_pattern_indels.c:7:13: warning: 'test_match_pattern_indels' defined but not used [-Wunused-function]
    7 | static void test_match_pattern_indels(const char *p, const char *s,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c match_pdict.c -o match_pdict.o
In function 'vcount_PDict3Parts_XStringSet',
    inlined from 'vmatch_PDict3Parts_XStringSet' at match_pdict.c:508:10:
match_pdict.c:419:33: warning: 'ans_col' may be used uninitialized [-Wmaybe-uninitialized]
  419 |                         ans_col += tb_length;
      |                         ~~~~~~~~^~~~~~~~~~~~
match_pdict.c: In function 'vmatch_PDict3Parts_XStringSet':
match_pdict.c:392:65: note: 'ans_col' was declared here
  392 |         int tb_length, S_length, collapse0, i, j, match_count, *ans_col;
      |                                                                 ^~~~~~~
In function 'vcount_XStringSet_XStringSet',
    inlined from 'vmatch_XStringSet_XStringSet' at match_pdict.c:542:10:
match_pdict.c:470:41: warning: 'ans_elt' may be used uninitialized [-Wmaybe-uninitialized]
  470 |                                 ans_elt += P_length;
      |                                 ~~~~~~~~^~~~~~~~~~~
match_pdict.c: In function 'vmatch_XStringSet_XStringSet':
match_pdict.c:441:64: note: 'ans_elt' was declared here
  441 |         int P_length, S_length, collapse0, i, j, match_count, *ans_elt;
      |                                                                ^~~~~~~
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c: In function 'split_and_move_pointers':
match_pdict_ACtree2.c:1031:17: warning: variable 'node0' set but not used [-Wunused-but-set-variable]
 1031 |         ACnode *node0, *node1, *node2;
      |                 ^~~~~
match_pdict_ACtree2.c: In function 'merge_pointers':
match_pdict_ACtree2.c:1076:17: warning: variable 'node0' set but not used [-Wunused-but-set-variable]
 1076 |         ACnode *node0, *node1, *node2;
      |                 ^~~~~
match_pdict_ACtree2.c: At top level:
match_pdict_ACtree2.c:602:21: warning: 'a_nice_max_nodeextbuf_nelt' defined but not used [-Wunused-function]
  602 | static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes)
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~
match_pdict_ACtree2.c:139:13: warning: 'debug_node_counting_functions' defined but not used [-Wunused-function]
  139 | static void debug_node_counting_functions(int maxdepth)
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c match_pdict_Twobit.c -o match_pdict_Twobit.o
In file included from /usr/include/R/Rdefines.h:41,
                 from /usr/lib/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from /usr/lib/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from match_pdict_Twobit.c:10:
In function 'Twobit_asLIST',
    inlined from 'build_Twobit' at match_pdict_Twobit.c:145:2:
match_pdict_Twobit.c:75:27: warning: 'twobit_sign2pos' may be used uninitialized [-Wmaybe-uninitialized]
   75 |         PROTECT(ans_elt = new_XInteger_from_tag("XInteger", twobit_sign2pos));
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/R/Rinternals.h:367:36: note: in definition of macro 'PROTECT'
  367 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
match_pdict_Twobit.c: In function 'build_Twobit':
match_pdict_Twobit.c:110:19: note: 'twobit_sign2pos' was declared here
  110 |         SEXP ans, twobit_sign2pos;
      |                   ^~~~~~~~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c: In function 'match_ppheadtail0':
match_pdict_utils.c:653:56: warning: unused variable 'ncol' [-Wunused-variable]
  653 |         int nelt, min_safe_tb_end, max_safe_tb_end, j, ncol;
      |                                                        ^~~~
match_pdict_utils.c: In function 'match_ppheadtail':
match_pdict_utils.c:713:13: warning: unused variable 'nelt' [-Wunused-variable]
  713 |         int nelt, nkey0, nkey1, nkey2, i, key;
      |             ^~~~
match_pdict_utils.c: In function '_match_pdict_all_flanks':
match_pdict_utils.c:820:51: warning: unused variable 'subtotal_NFC' [-Wunused-variable]
  820 |         static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
      |                                                   ^~~~~~~~~~~~
match_pdict_utils.c:820:34: warning: unused variable 'total_NFC' [-Wunused-variable]
  820 |         static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
      |                                  ^~~~~~~~~
match_pdict_utils.c:819:40: warning: unused variable 'NFC' [-Wunused-variable]
  819 |         unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
      |                                        ^~~
match_pdict_utils.c:819:33: warning: unused variable 'nloci' [-Wunused-variable]
  819 |         unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
      |                                 ^~~~~
match_pdict_utils.c:819:27: warning: unused variable 'ndup' [-Wunused-variable]
  819 |         unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
      |                           ^~~~
match_pdict_utils.c: At top level:
match_pdict_utils.c:820:34: warning: 'total_NFC' defined but not used [-Wunused-variable]
  820 |         static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
      |                                  ^~~~~~~~~
match_pdict_utils.c:820:51: warning: 'subtotal_NFC' defined but not used [-Wunused-variable]
  820 |         static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
      |                                                   ^~~~~~~~~~~~
match_pdict_utils.c:261:13: warning: 'match_headtail_by_loc' defined but not used [-Wunused-function]
  261 | static void match_headtail_by_loc(const HeadTail *headtail,
      |             ^~~~~~~~~~~~~~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c match_reporting.c -o match_reporting.o
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c matchprobes.c -o matchprobes.o
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c pmatchPattern.c -o pmatchPattern.o
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c read_fasta_files.c -o read_fasta_files.o
In function 'new_FASTAloaderExt',
    inlined from 'read_fasta_files' at read_fasta_files.c:430:15:
read_fasta_files.c:186:16: warning: 'loader_ext.seq_elt_holder.ptr' may be used uninitialized [-Wmaybe-uninitialized]
  186 |         return loader_ext;
      |                ^~~~~~~~~~
read_fasta_files.c: In function 'read_fasta_files':
read_fasta_files.c:182:24: note: 'loader_ext' declared here
  182 |         FASTAloaderExt loader_ext;
      |                        ^~~~~~~~~~
In function 'new_FASTAloaderExt',
    inlined from 'read_fasta_files' at read_fasta_files.c:430:15:
read_fasta_files.c:186:16: warning: 'loader_ext.seq_elt_holder.length' may be used uninitialized [-Wmaybe-uninitialized]
  186 |         return loader_ext;
      |                ^~~~~~~~~~
read_fasta_files.c: In function 'read_fasta_files':
read_fasta_files.c:182:24: note: 'loader_ext' declared here
  182 |         FASTAloaderExt loader_ext;
      |                        ^~~~~~~~~~
In function 'new_FASTAloaderExt',
    inlined from 'read_fasta_blocks' at read_fasta_files.c:596:15:
read_fasta_files.c:186:16: warning: 'loader_ext.seq_elt_holder.ptr' is used uninitialized [-Wuninitialized]
  186 |         return loader_ext;
      |                ^~~~~~~~~~
read_fasta_files.c: In function 'read_fasta_blocks':
read_fasta_files.c:182:24: note: 'loader_ext' declared here
  182 |         FASTAloaderExt loader_ext;
      |                        ^~~~~~~~~~
In function 'new_FASTAloaderExt',
    inlined from 'read_fasta_blocks' at read_fasta_files.c:596:15:
read_fasta_files.c:186:16: warning: 'loader_ext.seq_elt_holder.length' is used uninitialized [-Wuninitialized]
  186 |         return loader_ext;
      |                ^~~~~~~~~~
read_fasta_files.c: In function 'read_fasta_blocks':
read_fasta_files.c:182:24: note: 'loader_ext' declared here
  182 |         FASTAloaderExt loader_ext;
      |                        ^~~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c read_fastq_files.c -o read_fastq_files.o
read_fastq_files.c: In function 'parse_FASTQ_file':
read_fastq_files.c:406:28: warning: 'dont_load' may be used uninitialized [-Wmaybe-uninitialized]
  406 |                         if (dont_load || loader->new_qualid_hook == NULL)
      |                            ^
read_fastq_files.c:309:26: note: 'dont_load' was declared here
  309 |             lineinrecno, dont_load;
      |                          ^~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c replaceAt.c -o replaceAt.o
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c replace_letter_at.c -o replace_letter_at.o
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c strutils.c -o strutils.o
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c translate.c -o translate.o
In function 'translate',
    inlined from 'DNAStringSet_translate' at translate.c:195:4:
translate.c:99:36: warning: 'if_non_ambig0' may be used uninitialized [-Wmaybe-uninitialized]
   99 |                                 if (if_non_ambig == TRANSLATE_ERROR) {
      |                                    ^
translate.c: In function 'DNAStringSet_translate':
translate.c:136:21: note: 'if_non_ambig0' was declared here
  136 |         int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
      |                     ^~~~~~~~~~~~~
In function 'translate',
    inlined from 'DNAStringSet_translate' at translate.c:195:4:
translate.c:110:36: warning: 'if_ambig0' may be used uninitialized [-Wmaybe-uninitialized]
  110 |                                 if (if_ambig == TRANSLATE_ERROR) {
      |                                    ^
translate.c: In function 'DNAStringSet_translate':
translate.c:136:36: note: 'if_ambig0' was declared here
  136 |         int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
      |                                    ^~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c unstrsplit_methods.c -o unstrsplit_methods.o
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c utils.c -o utils.o
utils.c: In function '_get_twobit_signature':
utils.c:157:16: warning: 'twobit_sign' may be used uninitialized [-Wmaybe-uninitialized]
  157 |         return twobit_sign;
      |                ^~~~~~~~~~~
utils.c:150:16: note: 'twobit_sign' was declared here
  150 |         int i, twobit_sign;
      |                ^~~~~~~~~~~
utils.c: In function '_get_twobit_signature_at':
utils.c:174:16: warning: 'twobit_sign' may be used uninitialized [-Wmaybe-uninitialized]
  174 |         return twobit_sign;
      |                ^~~~~~~~~~~
utils.c:164:19: note: 'twobit_sign' was declared here
  164 |         int i, j, twobit_sign;
      |                   ^~~~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG  -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I/usr/local/include   -fpic  -O2  -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c xscat.c -o xscat.o
In file included from /usr/include/R/Rdefines.h:41,
                 from /usr/lib/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from /usr/lib/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
xscat.c: In function 'XString_xscat':
/usr/include/R/Rdefines.h:91:33: warning: 'ans_length' may be used uninitialized [-Wmaybe-uninitialized]
   91 | #define NEW_RAW(n)              Rf_allocVector(RAWSXP,n)
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/R/Rinternals.h:367:36: note: in definition of macro 'PROTECT'
  367 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
xscat.c:38:27: note: in expansion of macro 'NEW_RAW'
   38 |         PROTECT(ans_tag = NEW_RAW(ans_length));
      |                           ^~~~~~~
xscat.c:18:20: note: 'ans_length' was declared here
   18 |         int nargs, ans_length, tag_offset, j;
      |                    ^~~~~~~~~~
xscat.c:52:23: warning: 'ans_classname' may be used uninitialized [-Wmaybe-uninitialized]
   52 |         PROTECT(ans = new_XRaw_from_tag(ans_classname, ans_tag));
      |                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/R/Rinternals.h:367:36: note: in definition of macro 'PROTECT'
  367 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
xscat.c:20:21: note: 'ans_classname' was declared here
   20 |         const char *ans_classname;
      |                     ^~~~~~~~~~~~~
xscat.c: In function 'XStringSet_xscat':
/usr/include/R/Rdefines.h:85:33: warning: 'ans_length' may be used uninitialized [-Wmaybe-uninitialized]
   85 | #define NEW_INTEGER(n)          Rf_allocVector(INTSXP,n)
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/R/Rinternals.h:367:36: note: in definition of macro 'PROTECT'
  367 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
xscat.c:91:29: note: in expansion of macro 'NEW_INTEGER'
   91 |         PROTECT(ans_width = NEW_INTEGER(ans_length));
      |                             ^~~~~~~~~~~
xscat.c:66:39: note: 'ans_length' was declared here
   66 |         int nargs, *arg_lengths, *ii, ans_length, i, j, *width;
      |                                       ^~~~~~~~~~
xscat.c:108:23: warning: 'ans_element_type' may be used uninitialized [-Wmaybe-uninitialized]
  108 |         PROTECT(ans = _alloc_XStringSet(ans_element_type, ans_width));
      |                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/R/Rinternals.h:367:36: note: in definition of macro 'PROTECT'
  367 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
xscat.c:68:21: note: 'ans_element_type' was declared here
   68 |         const char *ans_element_type;
      |                     ^~~~~~~~~~~~~~~~
gcc -shared -L/usr/lib/R/lib -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 -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o read_fasta_files.o read_fastq_files.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -L/usr/lib/R/lib -lR
installing to /builddir/build/BUILDROOT/R-Biostrings-2.64.1-1.fc38.i386/usr/lib/R/library/00LOCK-Biostrings/00new/Biostrings/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for 'twoWayAlphabetFrequencyByQuality' with signature '"QualityScaledXStringSet"': no definition for class "QualityScaledXStringSet"
Creating a new generic function for 'strsplit' in package 'Biostrings'
Creating a generic function for 'ls' from package 'base' in package 'Biostrings'
Creating a new generic function for 'pattern' in package 'Biostrings'
Creating a new generic function for 'offset' in package 'Biostrings'
** help
*** installing help indices
  converting help for package 'Biostrings'
    finding HTML links ... done
    AAString-class                          html  
    AMINO_ACID_CODE                         html  
    AlignedXStringSet-class                 html  
    Biostrings-internals                    html  
    DNAString-class                         html  
    GENETIC_CODE                            html  
    HNF4alpha                               html  
    IUPAC_CODE_MAP                          html  
    InDel-class                             html  
    MIndex-class                            html  
    MaskedXString-class                     html  
    MultipleAlignment-class                 html  
    finding level-2 HTML links ... done
    PDict-class                             html  
    PairwiseAlignments-class                html  
    PairwiseAlignments-io                   html  
    QualityScaledXStringSet-class           html  
    RNAString-class                         html  
    XString-class                           html  
    XStringPartialMatches-class             html  
    XStringQuality-class                    html  
    XStringSet-class                        html  
    XStringSet-comparison                   html  
    XStringSet-io                           html  
    XStringSetList-class                    html  
    XStringViews-class                      html  
    align-utils                             html  
    chartr                                  html  
    detail                                  html  
    dinucleotideFrequencyTest               html  
    findPalindromes                         html  
    getSeq                                  html  
    gregexpr2                               html  
    injectHardMask                          html  
    letter                                  html  
    letterFrequency                         html  
    longestConsecutive                      html  
    lowlevel-matching                       html  
    maskMotif                               html  
    match-utils                             html  
    matchLRPatterns                         html  
    matchPDict-exact                        html  
    matchPDict-inexact                      html  
    matchPWM                                html  
    matchPattern                            html  
    matchProbePair                          html  
    matchprobes                             html  
    misc                                    html  
    needwunsQS                              html  
    nucleotideFrequency                     html  
    padAndClip                              html  
    pairwiseAlignment                       html  
    phiX174Phage                            html  
    pid                                     html  
    pmatchPattern                           html  
    replaceAt                               html  
    replaceLetterAt                         html  
    reverseComplement                       html  
    seqinfo                                 html  
    stringDist                              html  
    substitution_matrices                   html  
    toComplex                               html  
    translate                               html  
    trimLRPatterns                          html  
    xscat                                   html  
    yeastSEQCHR1                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Biostrings)
+ test -d Biostrings/src
+ cd Biostrings/src
+ rm -f BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o read_fasta_files.o read_fastq_files.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o Biostrings.so
+ rm -rf /builddir/build/BUILDROOT/R-Biostrings-2.64.1-1.fc38.i386/usr/lib/R/library/R.css
+ rm -f /builddir/build/BUILDROOT/R-Biostrings-2.64.1-1.fc38.i386/usr/lib/R/library/Biostrings/doc/GenomeSearching.R
+ /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 2.64.1-1.fc38 --unique-debug-suffix -2.64.1-1.fc38.i386 --unique-debug-src-base R-Biostrings-2.64.1-1.fc38.i386 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/Biostrings
extracting debug info from /builddir/build/BUILDROOT/R-Biostrings-2.64.1-1.fc38.i386/usr/lib/R/library/Biostrings/libs/Biostrings.so
original debug info size: 600kB, size after compression: 552kB
/usr/bin/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match.
807 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
+ /usr/lib/rpm/brp-remove-la-files
+ /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0
+ /usr/lib/rpm/redhat/brp-python-hardlink
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.WoHRoa
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/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/lib:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd Biostrings
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: R-Biostrings-2.64.1-1.fc38.i686
Provides: R(Biostrings) = 2.64.1 R-Biostrings = 2.64.1-1.fc38 R-Biostrings(x86-32) = 2.64.1-1.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: R(ABI) = 4.2 R(BiocGenerics) >= 0.37.0 R(GenomeInfoDb) R(IRanges) >= 2.30.1 R(S4Vectors) >= 0.27.12 R(XVector) >= 0.29.2 R(crayon) R(grDevices) R(graphics) R(methods) R(stats) R(utils) R-core >= 4.0.0 libR.so libc.so.6 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1.3) libc.so.6(GLIBC_2.3.4) libc.so.6(GLIBC_2.4) libc.so.6(GLIBC_2.7) rtld(GNU_HASH)
Suggests: R(BSgenome) >= 1.13.14 R(BSgenome.Celegans.UCSC.ce2) >= 1.3.11 R(BSgenome.Dmelanogaster.UCSC.dm3) >= 1.3.11 R(BSgenome.Hsapiens.UCSC.hg18) R(GenomicFeatures) >= 1.3.14 R(RUnit) R(affy) >= 1.41.3 R(affydata) >= 1.11.5 R(drosophila2probe) R(hgu133aprobe) R(hgu95av2cdf) R(hgu95av2probe)
Enhances: R(Rmpi)
Processing files: R-Biostrings-devel-2.64.1-1.fc38.i686
Provides: R-Biostrings-devel = 2.64.1-1.fc38 R-Biostrings-devel(x86-32) = 2.64.1-1.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: R-Biostrings-debugsource-2.64.1-1.fc38.i686
Provides: R-Biostrings-debugsource = 2.64.1-1.fc38 R-Biostrings-debugsource(x86-32) = 2.64.1-1.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: R-Biostrings-debuginfo-2.64.1-1.fc38.i686
Provides: R-Biostrings-debuginfo = 2.64.1-1.fc38 R-Biostrings-debuginfo(x86-32) = 2.64.1-1.fc38 debuginfo(build-id) = 06798ccfa2691c9641ecece68da65b5341fe23b9
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: R-Biostrings-debugsource(x86-32) = 2.64.1-1.fc38
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-Biostrings-2.64.1-1.fc38.i386
Wrote: /builddir/build/RPMS/R-Biostrings-debuginfo-2.64.1-1.fc38.i686.rpm
Wrote: /builddir/build/RPMS/R-Biostrings-debugsource-2.64.1-1.fc38.i686.rpm
Wrote: /builddir/build/RPMS/R-Biostrings-devel-2.64.1-1.fc38.i686.rpm
Wrote: /builddir/build/RPMS/R-Biostrings-2.64.1-1.fc38.i686.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.tGQDIv
+ umask 022
+ cd /builddir/build/BUILD
+ cd Biostrings
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/R-Biostrings-2.64.1-1.fc38.i386
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.73maRx
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf Biostrings Biostrings.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0
Child return code was: 0