Mock Version: 5.5
Mock Version: 5.5
Mock Version: 5.5
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target x86_64 --nodeps /builddir/build/SPECS/lagan.spec'], chrootPath='/var/lib/mock/f41-build-50456272-6038281/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 0x7fb4c915eab0>timeout=201600uid=1000gid=425user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.kiioy_70:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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=False)
Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.kiioy_70:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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', 'c6a3fc7b5ea24f7c8f50a4991f827d93', '-D', '/var/lib/mock/f41-build-50456272-6038281/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.kiioy_70:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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/lagan.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
warning: %patchN is deprecated (3 usages found), use %patch N (or %patch -P N)
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1706140800
Wrote: /builddir/build/SRPMS/lagan-2.0-41.fc41.src.rpm
RPM build warnings:
    %patchN is deprecated (3 usages found), use %patch N (or %patch -P N)
Child return code was: 0
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --noclean --target x86_64 --nodeps /builddir/build/SPECS/lagan.spec'], chrootPath='/var/lib/mock/f41-build-50456272-6038281/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 0x7fb4c915eab0>timeout=201600uid=1000gid=425user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.kiioy_70:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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=False)
Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.kiioy_70:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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', 'c8c0de2495fd47bbac5df5c22f27e4f4', '-D', '/var/lib/mock/f41-build-50456272-6038281/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.kiioy_70:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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/lagan.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
warning: %patchN is deprecated (3 usages found), use %patch N (or %patch -P N)
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1706140800
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.UW85jk
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf lagan20
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/lagan20.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd lagan20
+ rm -rf /builddir/build/BUILD/lagan20-SPECPARTS
+ /usr/bin/mkdir -p /builddir/build/BUILD/lagan20-SPECPARTS
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
Patch #0 (lagan20-chris.patch):
+ echo 'Patch #0 (lagan20-chris.patch):'
+ /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .chris --fuzz=0
patching file Readmes/README.FIRST
patching file Readmes/README.shuffle
patching file Readmes/README.chaos
patching file Readmes/README.lagan
patching file src/utils/scorealign.c
patching file src/utils/Glue.cpp
patching file src/utils/mrun.pl
patching file src/utils/mrunfile.pl
patching file src/utils/mrunpairs.pl
patching file src/utils/mviz.pl
patching file src/mlagan.c
patching file src/prolagan.c
patching file src/slagan-mfa.pl
patching file src/supermap.pl
patching file src/xmfa2mfa.pl
patching file utils/mrunpairs.pl
patching file utils/draft.pl
patching file utils/mrunfile.pl
patching file utils/mviz.pl
patching file utils/mrun.pl
patching file slagan.pl
patching file lagan.pl
patching file rechaos.pl
patching file slagan-mfa.pl
patching file supermap.pl
patching file xmfa2mfa.pl
patching file src/glocal/rightinfluence.cpp
patching file src/glocal/score.cpp
Patch #1 (lagan20-gcc10.patch):
+ echo 'Patch #1 (lagan20-gcc10.patch):'
+ /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .gcc10 --fuzz=0
patching file src/multial.c
patching file src/order.c
patching file src/utils/scorecontigs.c
Hunk #1 succeeded at 258 (offset -1 lines).
Patch #2 (lagan-c99.patch):
+ echo 'Patch #2 (lagan-c99.patch):'
+ /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0
patching file src/multial.h
patching file src/order.c
+ sed -i 's/^CC .*$/CC = gcc $(RPM_OPT_FLAGS)/;
        s/^CPP .*$/CPP = g++ $(RPM_OPT_FLAGS)/' Makefile
+ sed -i 's|getenv ("LAGAN_DIR")|"/usr/lib64/lagan"|g' src/anchors.c src/diagmatrix.c src/fchaos.c src/filebuffer.c src/global.c src/mempage.c src/mlagan.c src/multial.c src/order.c src/prolagan.c src/skiplist.c src/sortlist.c src/thrtrie.c src/translate.c src/utils/bin2bl.c src/utils/bin2mf.c src/utils/cextract.c src/utils/contigorder.c src/utils/cstat.c src/utils/fa2xfa.c src/utils/getbounds.c src/utils/getcontigpos.c src/utils/getlength.c src/utils/getoverlap.c src/utils/overlay.c src/utils/rc.c src/utils/scorealign.c src/utils/scorecontigs.c src/utils/seqmerge.c
+ sed -i 's|getenv ("LAGAN_DIR")|"/usr/lib64/lagan"|g' src/utils/Glue.cpp src/utils/dotplot.cpp
+ sed -i 's|$ENV{LAGAN_DIR}|"/usr/lib64/lagan"|g' anal_gloc.pl lagan.pl rechaos.pl slagan-mfa.pl slagan.pl supermap.pl xmfa2mfa.pl src/anal_gloc.pl src/lagan.pl src/rechaos.pl src/slagan-mfa.pl src/slagan.pl src/supermap.pl src/xmfa2mfa.pl utils/cmerge2.pl utils/draft.pl utils/flipchaos.pl utils/mextract.pl utils/mf2bin.pl utils/mpretty.pl utils/mproject.pl utils/mrun.pl utils/mrunfile.pl utils/mrunpairs.pl utils/msplit.pl utils/mviz.pl src/utils/cmerge2.pl src/utils/draft.pl src/utils/mextract.pl src/utils/mf2bin.pl src/utils/mpretty.pl src/utils/mproject.pl src/utils/mrun.pl src/utils/mrunfile.pl src/utils/mrunpairs.pl src/utils/mviz.pl
+ sed -i 's|$LAGAN_DIR|/usr/lib64/lagan|g' Readmes/README.shuffle src/anchors.c src/diagmatrix.c src/fchaos.c src/filebuffer.c src/global.c src/mempage.c src/mlagan.c src/multial.c src/order.c src/prolagan.c src/skiplist.c src/sortlist.c src/thrtrie.c src/translate.c
+ sed -i s/getline/GetLine/g src/anchors.c
+ sed -i 's/^inline /inline __attribute__ ((always_inline)) /' src/fchaos.c
+ sed -i '/<stdio.h>/a#include <ctype.h>' src/filebuffer.c
+ sed -i '/<stdio.h>/a#include <ctype.h>' src/utils/scorecontigs.c
+ sed -i '/<stdio.h>/a#include <ctype.h>' src/utils/overlay.c
+ sed -i '/<stdio.h>/a#include <ctype.h>' src/utils/cstat.c
+ sed -i 's/^int indeces/extern int indeces/' src/thrtrie.h
+ sed -i '/^int nnodes=0;/aint indeces[256];' src/thrtrie.c
+ rm prolagan
+ chmod -x src/glocal/Makefile src/glocal/default.score src/glocal/glocal src/glocal/glocal.cpp src/glocal/glocal.h src/glocal/io.cpp src/glocal/io.h src/glocal/leftinfluence.cpp src/glocal/leftinfluence.h src/glocal/rightinfluence.cpp src/glocal/rightinfluence.cpp.chris src/glocal/rightinfluence.h src/glocal/score.cpp src/glocal/score.cpp.chris src/glocal/score.h src/glocal/structs.h src/glocal/test.score
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.vnrjE4
+ 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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 lagan20
+ make -j48 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' 'CXXFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer'
(cd src; make)
make[1]: Entering directory '/builddir/build/BUILD/lagan20/src'
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -o ../anchors anchors.c skiplist.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -o ../chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -o ../order order.c diagmatrix.c filebuffer.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -o ../mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -o ../prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -o ../utils/bin2mf utils/bin2mf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -o ../utils/bin2bl utils/bin2bl.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -o ../utils/cextract utils/cextract.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -o ../utils/cstat utils/cstat.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -o ../utils/contigorder utils/contigorder.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -o ../utils/getbounds utils/getbounds.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -o ../utils/getlength utils/getlength.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -o ../utils/getoverlap utils/getoverlap.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -o ../utils/rc utils/rc.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -o ../utils/seqmerge utils/seqmerge.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -o ../utils/scorealign utils/scorealign.c -lm
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -o ../utils/scorecontigs utils/scorecontigs.c -lm
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -o ../utils/getcontigpos utils/getcontigpos.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -o ../utils/fa2xfa utils/fa2xfa.c
g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -o ../utils/Glue utils/Glue.cpp
g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -o ../utils/dotplot utils/dotplot.cpp
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -o ../utils/overlay utils/overlay.c
utils/bin2bl.c: In function ‘main’:
utils/bin2bl.c:52:6: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
   52 |   if (argv[1][0] == '-')
      |      ^
utils/bin2bl.c:22:7: warning: unused variable ‘width’ [-Wunused-variable]
   22 |   int width = 60;
      |       ^~~~~
utils/contigorder.c: In function ‘getFileInfo’:
utils/contigorder.c:15:57: warning: format ‘%s’ expects a matching ‘char *’ argument [-Wformat=]
   15 |     fprintf (stderr, "contigorder: Error opening file: %s\n");
      |                                                        ~^
      |                                                         |
      |                                                         char *
utils/contigorder.c:26:25: warning: unknown conversion type character ‘&’ in format [-Wformat=]
   26 |         fscanf (file, "%&d", &dummy);
      |                         ^
utils/contigorder.c:26:23: warning: too many arguments for format [-Wformat-extra-args]
   26 |         fscanf (file, "%&d", &dummy);
      |                       ^~~~~
utils/contigorder.c: In function ‘getScores’:
utils/contigorder.c:52:57: warning: format ‘%s’ expects a matching ‘char *’ argument [-Wformat=]
   52 |     fprintf (stderr, "contigorder: Error opening file: %s\n");
      |                                                        ~^
      |                                                         |
      |                                                         char *
utils/contigorder.c: In function ‘solveOrder’:
utils/contigorder.c:176:30: warning: unused variable ‘ptr’ [-Wunused-variable]
  176 |   int **best, *first, *last, ptr, newScore, **scoreOf;
      |                              ^~~
utils/getbounds.c: In function ‘main’:
utils/getbounds.c:32:27: warning: unused variable ‘ext’ [-Wunused-variable]
   32 |   int S1B, S1E, S2B, S2E, ext, len1, len2;
      |                           ^~~
utils/getbounds.c: In function ‘getLength’:
utils/getbounds.c:18:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   18 |   fgets (buffer, 1024, file);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~
utils/contigorder.c: In function ‘getFileInfo’:
utils/contigorder.c:19:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   19 |   fscanf (file, "numContigs = %d\n", numContigs);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils/contigorder.c:20:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   20 |   fscanf (file, "seqLen = %d\n", seqLen);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils/contigorder.c:26:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   26 |         fscanf (file, "%&d", &dummy);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils/getlength.c: In function ‘main’:
utils/rc.c: In function ‘main’:
utils/getlength.c:20:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   20 |   fgets (buffer, BUF_SIZE, file);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils/rc.c:39:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   39 |   fgets(temp, 255, stdin);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
utils/contigorder.c: In function ‘getScores’:
utils/contigorder.c:56:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   56 |   fscanf (file, "numContigs = %*d\n");
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils/contigorder.c:57:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   57 |   fscanf (file, "seqLen = %*d\n");
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils/contigorder.c:63:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   63 |         fscanf (file, "%d", &((*score)[i][j]));
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
order.c: In function ‘readAncFile’:
order.c:238:35: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  238 |     if ((tt->seq1start >= s1start && tt->seq1end <= s1end || s1start == 0 && s1end == 0) &&
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
order.c:239:35: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  239 |         (tt->seq2start >= s2start && tt->seq2end <= s2end || s2start == 0 && s2end == 0)){
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
utils/cextract.c: In function ‘getLength’:
utils/cextract.c:16:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   16 |   fgets (buffer, 1024, file);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~
utils/getcontigpos.c: In function ‘print’:
utils/getcontigpos.c:66:46: warning: unused variable ‘j’ [-Wunused-variable]
   66 |   int i = 0, pos = 0, pos2 = 0, written = 0, j = 0;
      |                                              ^
utils/getcontigpos.c:66:33: warning: unused variable ‘written’ [-Wunused-variable]
   66 |   int i = 0, pos = 0, pos2 = 0, written = 0, j = 0;
      |                                 ^~~~~~~
order.c: In function ‘mkBarrel’:
order.c:275:7: warning: unused variable ‘incr’ [-Wunused-variable]
  275 |   int incr;
      |       ^~~~
utils/cextract.c: In function ‘readfile’:
utils/cextract.c:41:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   41 |     fgets (buffer, 1024, file);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~
utils/getcontigpos.c: In function ‘getLength’:
utils/getcontigpos.c:16:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   16 |   fgets (buffer, 1024, file);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~
utils/overlay.c: In function ‘read_align’:
utils/overlay.c:102:30: warning: unused variable ‘tt’ [-Wunused-variable]
  102 |   char currchar, checkchar, *tt;
      |                              ^~
utils/seqmerge.c: In function ‘main’:
utils/getcontigpos.c: In function ‘readfile’:
utils/seqmerge.c:33:15: warning: suggest parentheses around comparison in operand of ‘^’ [-Wparentheses]
   33 |   if (written ^ 60 != 0) printf ("\n");
      |               ^
utils/getcontigpos.c:41:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   41 |     fgets (buffer, 1024, file);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~
utils/overlay.c: In function ‘read_sequences’:
utils/overlay.c:177:19: warning: unused variable ‘breaker’ [-Wunused-variable]
  177 |   int i, j, kmer, breaker;
      |                   ^~~~~~~
utils/overlay.c:177:13: warning: unused variable ‘kmer’ [-Wunused-variable]
  177 |   int i, j, kmer, breaker;
      |             ^~~~
utils/overlay.c:177:10: warning: unused variable ‘j’ [-Wunused-variable]
  177 |   int i, j, kmer, breaker;
      |          ^
utils/fa2xfa.c: In function ‘print’:
utils/fa2xfa.c:81:36: warning: unused variable ‘j’ [-Wunused-variable]
   81 |   int i = 0, pos = 0, written = 0, j = 0;
      |                                    ^
utils/fa2xfa.c:81:14: warning: unused variable ‘pos’ [-Wunused-variable]
   81 |   int i = 0, pos = 0, written = 0, j = 0;
      |              ^~~
utils/seqmerge.c:19:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   19 |     fgets (buffer, 1024, file);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~
order.c: In function ‘getChain’:
utils/overlay.c: In function ‘main’:
utils/overlay.c:233:16: warning: unused variable ‘test’ [-Wunused-variable]
  233 |   float ttree, test;
      |                ^~~~
utils/overlay.c:233:9: warning: unused variable ‘ttree’ [-Wunused-variable]
  233 |   float ttree, test;
      |         ^~~~~
utils/overlay.c:232:7: warning: unused variable ‘moved’ [-Wunused-variable]
  232 |   int moved, i;
      |       ^~~~~
utils/overlay.c:231:8: warning: unused variable ‘string_tree’ [-Wunused-variable]
  231 |   char string_tree[16537]; //noone will ever need more :)))
      |        ^~~~~~~~~~~
order.c:487:7: warning: unused variable ‘temp’ [-Wunused-variable]
  487 |   int temp;
      |       ^~~~
order.c: In function ‘saveNeck’:
order.c:562:6: warning: unused variable ‘second’ [-Wunused-variable]
  562 |     *second = DMgetDiagStart(mydm, neckdiag, &size2, &x2, &y2);
      |      ^~~~~~
utils/fa2xfa.c: In function ‘getLength’:
utils/fa2xfa.c:30:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   30 |   fgets (buffer, 1024, file);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~
order.c:561:9: warning: unused variable ‘first’ [-Wunused-variable]
  561 |   alel *first = DMgetDiagStart(mydm, neckdiag-1, &size1, &x1, &y1),
      |         ^~~~~
order.c: In function ‘joinAligns’:
order.c:587:10: warning: unused variable ‘n’ [-Wunused-variable]
  587 |   align *n = a->nextalign, *t;
      |          ^
utils/overlay.c: In function ‘read_align’:
utils/overlay.c:110:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  110 |   fgets(temp, 255, input);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
utils/fa2xfa.c: In function ‘readfile’:
utils/fa2xfa.c:55:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   55 |     fgets (buffer, 1024, file);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~
order.c: In function ‘printBinAlign’:
order.c:719:23: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  719 |       left = lets[seq1[s1++]];
      |                   ~~~~^~~~~~
order.c:721:24: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  721 |       right = lets[seq2[s2++]];
      |                    ~~~~^~~~~~
order.c: In function ‘printMFAAlign’:
order.c:774:27: warning: unused variable ‘nlets’ [-Wunused-variable]
  774 |   int nm=0, nga=0, ngb=0, nlets=0;
      |                           ^~~~~
order.c:774:7: warning: unused variable ‘nm’ [-Wunused-variable]
  774 |   int nm=0, nga=0, ngb=0, nlets=0;
      |       ^~
order.c: In function ‘printXMFAAlign’:
order.c:806:27: warning: unused variable ‘nlets’ [-Wunused-variable]
  806 |   int nm=0, nga=0, ngb=0, nlets=0;
      |                           ^~~~~
order.c:806:7: warning: unused variable ‘nm’ [-Wunused-variable]
  806 |   int nm=0, nga=0, ngb=0, nlets=0;
      |       ^~
prolagan.c: In function ‘hptrcomp’:
prolagan.c:41:7: warning: unused variable ‘jt’ [-Wunused-variable]
   41 |   int jt = ((hptr*)p2)->isstart;
      |       ^~
mlagan.c: In function ‘hptrcomp’:
mlagan.c:38:7: warning: unused variable ‘jt’ [-Wunused-variable]
   38 |   int jt = ((hptr*)p2)->isstart;
      |       ^~
order.c: In function ‘readfile’:
order.c:62:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   62 |   fgets(temp, 255, input);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
prolagan.c: In function ‘readfile’:
prolagan.c:93:25: warning: too many arguments for format [-Wformat-extra-args]
   93 |         fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mlagan.c: In function ‘readfile’:
utils/cstat.c: In function ‘main’:
mlagan.c:93:25: warning: too many arguments for format [-Wformat-extra-args]
   93 |         fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils/cstat.c:235:7: warning: unused variable ‘i’ [-Wunused-variable]
  235 |   int i;
      |       ^
order.c: In function ‘readSubstMatrix’:
order.c:146:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  146 |       fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]]));
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
prolagan.c: In function ‘appendAlignProfile’:
order.c:150:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  150 |   fscanf (file, "%d", &gapstart);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
order.c:151:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  151 |   fscanf (file, "%d", &gapcont);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
prolagan.c:163:9: warning: unused variable ‘j’ [-Wunused-variable]
  163 |   int i,j,k;
      |         ^
prolagan.c: In function ‘readProfile’:
utils/cstat.c: In function ‘cntlets’:
utils/cstat.c:45:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   45 |   fgets(temp, 255, input);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
prolagan.c:198:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  198 |   while ( myseq = FileRead( with_gaps,0,0,VER_MLAGAN )) {
      |           ^~~~~
mlagan.c: In function ‘getAnchsFromFile’:
mlagan.c:161:29: warning: unused variable ‘first’ [-Wunused-variable]
  161 |   hll *myres = 0, *tt = 0, *first = 0;
      |                             ^~~~~
mlagan.c: In function ‘generateAnchors’:
fchaos.c: In function ‘removeDups’:
utils/cstat.c: In function ‘readseq’:
utils/cstat.c:68:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   68 |   fgets(temp, 255, input);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
fchaos.c:302:24: warning: unused variable ‘temp’ [-Wunused-variable]
  302 |   hll *i, *j, *jprev, *temp;
      |                        ^~~~
mlagan.c:213:8: warning: unused variable ‘flip’ [-Wunused-variable]
  213 |   char flip = 0;
      |        ^~~~
mlagan.c:211:10: warning: unused variable ‘temp’ [-Wunused-variable]
  211 |   align* temp;
      |          ^~~~
prolagan.c: In function ‘getAnchsFromFile’:
prolagan.c:246:29: warning: unused variable ‘first’ [-Wunused-variable]
  246 |   hll *myres = 0, *tt = 0, *first = 0;
      |                             ^~~~~
fchaos.c: In function ‘readfile’:
fchaos.c:357:25: warning: too many arguments for format [-Wformat-extra-args]
  357 |         fprintf(stderr, "WARNING %c converted to N\n", currchar, alpha);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
prolagan.c: In function ‘generateAnchors’:
mlagan.c: In function ‘remakeHLL’:
prolagan.c:298:8: warning: unused variable ‘flip’ [-Wunused-variable]
  298 |   char flip = 0;
      |        ^~~~
mlagan.c:310:10: warning: unused variable ‘bestscore’ [-Wunused-variable]
  310 |   int i, bestscore=-1;
      |          ^~~~~~~~~
prolagan.c:296:10: warning: unused variable ‘temp’ [-Wunused-variable]
  296 |   align* temp;
      |          ^~~~
mlagan.c:310:7: warning: unused variable ‘i’ [-Wunused-variable]
  310 |   int i, bestscore=-1;
      |       ^
mlagan.c:309:20: warning: unused variable ‘t3’ [-Wunused-variable]
  309 |   hll *temp, *t2, *t3;
      |                    ^~
fchaos.c: In function ‘chain’:
fchaos.c:401:16: warning: unused variable ‘d2’ [-Wunused-variable]
  401 |   int i, d1=0, d2=0;
      |                ^~
mlagan.c:309:15: warning: unused variable ‘t2’ [-Wunused-variable]
  309 |   hll *temp, *t2, *t3;
      |               ^~
fchaos.c:401:10: warning: unused variable ‘d1’ [-Wunused-variable]
  401 |   int i, d1=0, d2=0;
      |          ^~
mlagan.c:307:7: warning: unused variable ‘len’ [-Wunused-variable]
  307 |   int len;
      |       ^~~
fchaos.c:401:7: warning: unused variable ‘i’ [-Wunused-variable]
  401 |   int i, d1=0, d2=0;
      |       ^
prolagan.c: In function ‘remakeHLL’:
prolagan.c:395:10: warning: unused variable ‘bestscore’ [-Wunused-variable]
  395 |   int i, bestscore=-1;
      |          ^~~~~~~~~
prolagan.c:395:7: warning: unused variable ‘i’ [-Wunused-variable]
  395 |   int i, bestscore=-1;
      |       ^
prolagan.c:394:20: warning: unused variable ‘t3’ [-Wunused-variable]
  394 |   hll *temp, *t2, *t3;
      |                    ^~
prolagan.c:394:15: warning: unused variable ‘t2’ [-Wunused-variable]
  394 |   hll *temp, *t2, *t3;
      |               ^~
prolagan.c:392:7: warning: unused variable ‘len’ [-Wunused-variable]
  392 |   int len;
      |       ^~~
fchaos.c: In function ‘findPrev’:
fchaos.c:440:7: warning: unused variable ‘doneset’ [-Wunused-variable]
  440 |   int doneset = 0;
      |       ^~~~~~~
mlagan.c: In function ‘iterativeImprovement’:
mlagan.c:485:10: warning: unused variable ‘readd’ [-Wunused-variable]
  485 |   align *readd, *old, *new;
      |          ^~~~~
mlagan.c:483:12: warning: unused variable ‘oldscore’ [-Wunused-variable]
  483 |   int i=0, oldscore, cutoff;
      |            ^~~~~~~~
fchaos.c: In function ‘doAlgo’:
fchaos.c:543:24: warning: unused variable ‘bestdbaseloc’ [-Wunused-variable]
  543 |   int bestqueryloc=-1, bestdbaseloc=-1, numhits;
      |                        ^~~~~~~~~~~~
fchaos.c:543:7: warning: unused variable ‘bestqueryloc’ [-Wunused-variable]
  543 |   int bestqueryloc=-1, bestdbaseloc=-1, numhits;
      |       ^~~~~~~~~~~~
prolagan.c: In function ‘processAnchors’:
mlagan.c: In function ‘treeToRPN’:
fchaos.c:542:9: warning: unused variable ‘bestscore’ [-Wunused-variable]
  542 |   float bestscore=-1, baseval;
      |         ^~~~~~~~~
order.c: In function ‘printBinAlign’:
mlagan.c:528:16: warning: unused variable ‘j’ [-Wunused-variable]
  528 |   int i=0; int j, k;
      |                ^
prolagan.c:539:36: warning: unused variable ‘uni’ [-Wunused-variable]
  539 |   align *first, *second, *result, *uni;
      |                                    ^~~
order.c:726:1: warning: control reaches end of non-void function [-Wreturn-type]
  726 | }
      | ^
order.c: In function ‘printTextAlign’:
prolagan.c: In function ‘iterativeImprovement’:
order.c:770:1: warning: control reaches end of non-void function [-Wreturn-type]
  770 | }
      | ^
prolagan.c:587:10: warning: unused variable ‘readd’ [-Wunused-variable]
  587 |   align *readd, *old, *new;
      |          ^~~~~
order.c: In function ‘printMFAAlign’:
prolagan.c:585:12: warning: unused variable ‘oldscore’ [-Wunused-variable]
  585 |   int i=0, oldscore, cutoff;
      |            ^~~~~~~~
order.c:802:1: warning: control reaches end of non-void function [-Wreturn-type]
  802 | }
      | ^
prolagan.c: In function ‘treeToRPN’:
order.c: In function ‘printXMFAAlign’:
anchors.c: In function ‘hptrcomp’:
anchors.c:49:7: warning: unused variable ‘jt’ [-Wunused-variable]
   49 |   int jt = ((hptr*)p2)->isstart;
      |       ^~
prolagan.c:630:16: warning: unused variable ‘j’ [-Wunused-variable]
  630 |   int i=0; int j, k;
      |                ^
order.c:834:1: warning: control reaches end of non-void function [-Wreturn-type]
  834 | }
      | ^
utils/scorecontigs.c: In function ‘analyze’:
utils/scorecontigs.c:345:13: warning: unused variable ‘k’ [-Wunused-variable]
  345 |   int i, j, k;
      |             ^
utils/scorecontigs.c: In function ‘main’:
utils/scorecontigs.c:385:38: warning: format ‘%s’ expects argument of type ‘char *’, but argument 6 has type ‘char (*)[1024]’ [-Wformat=]
  385 |     if (fscanf (filelist, "%d %d %d %s\n", &(num[numseqs]), &(offs1[numseqs]), &(offs2[numseqs]), &(contignames[numseqs])) == 4){
      |                                     ~^                                                            ~~~~~~~~~~~~~~~~~~~~~~~
      |                                      |                                                            |
      |                                      char *                                                       char (*)[1024]
fchaos.c: In function ‘main’:
utils/scorecontigs.c: In function ‘cntlets’:
fchaos.c:885:7: warning: unused variable ‘i’ [-Wunused-variable]
  885 |   int i;
      |       ^
utils/scorecontigs.c:56:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   56 |   fgets(temp, 1024, input);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~
anchors.c: In function ‘doOutput’:
fchaos.c: In function ‘saveScore’:
anchors.c:171:17: warning: unused variable ‘bestscore’ [-Wunused-variable]
  171 |   int chl=0, i, bestscore=-1;
      |                 ^~~~~~~~~
utils/dotplot.cpp: In function ‘int main(int, char**)’:
utils/dotplot.cpp:6:27: warning: variable ‘pa’ set but not used [-Wunused-but-set-variable]
    6 |   int s1b, s1e, s2b, s2e, pa, pb, maxa = 0, maxb = 0;
      |                           ^~
utils/dotplot.cpp:6:31: warning: variable ‘pb’ set but not used [-Wunused-but-set-variable]
    6 |   int s1b, s1e, s2b, s2e, pa, pb, maxa = 0, maxb = 0;
      |                               ^~
anchors.c:171:14: warning: unused variable ‘i’ [-Wunused-variable]
  171 |   int chl=0, i, bestscore=-1;
      |              ^
anchors.c:168:7: warning: variable ‘len’ set but not used [-Wunused-but-set-variable]
  168 |   int len;
      |       ^~~
fchaos.c:970:7: warning: unused variable ‘temp’ [-Wunused-variable]
  970 |   int temp;
      |       ^~~~
utils/scorecontigs.c: In function ‘readseq’:
utils/scorecontigs.c:82:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   82 |   fgets (temp, 1024, input);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~
utils/dotplot.cpp:37:11: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   37 |     fgets (buffer, 105, file);
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~
utils/dotplot.cpp:74:11: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   74 |     fgets (buffer, 105, file);
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~
utils/dotplot.cpp:97:11: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   97 |     fgets (buffer, 105, file);
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~
mlagan.c: In function ‘main’:
mlagan.c:942:8: warning: unused variable ‘command’ [-Wunused-variable]
  942 |   char command[256];
      |        ^~~~~~~
prolagan.c: In function ‘main’:
mlagan.c:941:24: warning: unused variable ‘y’ [-Wunused-variable]
  941 |   int i = 1, j = 1, x, y;
      |                        ^
prolagan.c:966:8: warning: unused variable ‘table’ [-Wunused-variable]
  966 |   hll* table[MAX_SEQ][MAX_SEQ];
      |        ^~~~~
mlagan.c:941:21: warning: unused variable ‘x’ [-Wunused-variable]
  941 |   int i = 1, j = 1, x, y;
      |                     ^
prolagan.c:960:8: warning: unused variable ‘command’ [-Wunused-variable]
  960 |   char command[256];
      |        ^~~~~~~
mlagan.c:939:14: warning: unused variable ‘seqfile’ [-Wunused-variable]
  939 |   FileBuffer seqfile;
      |              ^~~~~~~
prolagan.c:954:14: warning: unused variable ‘seqfile’ [-Wunused-variable]
  954 |   FileBuffer seqfile;
      |              ^~~~~~~
fchaos.c: In function ‘savenfreeLList’:
fchaos.c:1137:9: warning: variable ‘j’ set but not used [-Wunused-but-set-variable]
 1137 |   int i,j;
      |         ^
mlagan.c: In function ‘readfile’:
mlagan.c:79:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   79 |   fgets(temp, 255, input);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
prolagan.c: In function ‘readfile’:
prolagan.c:79:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   79 |   fgets(temp, 255, input);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
anchors.c: In function ‘GetLine’:
anchors.c:232:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  232 |   fgets(temp, 1024, infile);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~
fchaos.c: In function ‘readfile’:
fchaos.c:344:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  344 |   fgets(temp, 255, input);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
mlagan.c: In function ‘treeToRPN’:
mlagan.c:565:1: warning: control reaches end of non-void function [-Wreturn-type]
  565 | }
      | ^
prolagan.c: In function ‘treeToRPN’:
prolagan.c:667:1: warning: control reaches end of non-void function [-Wreturn-type]
  667 | }
      | ^
fchaos.c: In function ‘readSubstMatrix’:
fchaos.c:622:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  622 |       fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]]));
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fchaos.c:627:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  627 |   fscanf (file, "%d", &gappenstart);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fchaos.c:628:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  628 |   fscanf (file, "%d", &gappenext);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils/getcontigpos.c:59:8: warning: ‘ch’ may be used uninitialized [-Wmaybe-uninitialized]
   59 |     if (ch == '>') ungetc (ch, file);
      |        ^
utils/getcontigpos.c:29:22: note: ‘ch’ was declared here
   29 |   char buffer[1024], ch;
      |                      ^~
utils/cextract.c:59:8: warning: ‘ch’ may be used uninitialized [-Wmaybe-uninitialized]
   59 |     if (ch == '>') ungetc (ch, file);
      |        ^
utils/cextract.c:29:22: note: ‘ch’ was declared here
   29 |   char buffer[1024], ch;
      |                      ^~
utils/scorealign.c: In function ‘getSequence’:
utils/scorealign.c:262:8: warning: variable ‘prevch’ set but not used [-Wunused-but-set-variable]
  262 |   char prevch = '~';
      |        ^~~~~~
utils/scorealign.c: In function ‘getSequences’:
utils/scorealign.c:322:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  322 |   while (newseq = getSequence (file, &si, &ss, &se, &sd, &sc)){
      |          ^~~~~~
utils/scorealign.c:310:7: warning: unused variable ‘i’ [-Wunused-variable]
  310 |   int i, si, ss, se;
      |       ^
utils/scorealign.c: In function ‘processSequences’:
utils/scorealign.c:353:10: warning: unused variable ‘j’ [-Wunused-variable]
  353 |   int i, j;
      |          ^
utils/scorealign.c: In function ‘getSequence’:
utils/scorealign.c:266:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  266 |   fgets (line, 1024, file);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~
utils/fa2xfa.c:74:8: warning: ‘ch’ may be used uninitialized [-Wmaybe-uninitialized]
   74 |     if (ch == '>') ungetc (ch, file);
      |        ^
utils/fa2xfa.c:43:22: note: ‘ch’ was declared here
   43 |   char buffer[1024], ch;
      |                      ^~
utils/scorealign.c: In function ‘readScoreMatrix’:
utils/scorealign.c:411:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  411 |   fgets (line, 1024, file);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~
utils/scorealign.c:419:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  419 |     fscanf (file, "%1s", &(line[0]));
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils/scorealign.c:421:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  421 |       fscanf (file, "%d", &k);
      |       ^~~~~~~~~~~~~~~~~~~~~~~
utils/scorealign.c:426:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  426 |   fscanf (file, "%d%d", &gapopen, &gapcont);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils/overlay.c:135:5: warning: ‘__strncpy_chk’ specified bound depends on the length of the source argument [-Wstringop-truncation]
  135 |     strncpy(allseqs[target]->seqname, temp, strlen(temp)+1);
      |     ^
utils/overlay.c:135:45: note: length computed here
  135 |     strncpy(allseqs[target]->seqname, temp, strlen(temp)+1);
      |                                             ^~~~~~~~~~~~
anchors.c: In function ‘findBestChain’:
anchors.c:164:10: warning: ‘bestptr’ may be used uninitialized [-Wmaybe-uninitialized]
  164 |   return (hll*)bestptr->myelem;
      |          ^~~~~~~~~~~~~~~~~~~~~
anchors.c:126:15: note: ‘bestptr’ was declared here
  126 |   sle* help, *bestptr;
      |               ^~~~~~~
utils/scorecontigs.c: In function ‘getranges’:
utils/scorecontigs.c:188:31: warning: ‘*_29’ may be used uninitialized [-Wmaybe-uninitialized]
  188 |   states[len - 1] = (scores[0][len - 1] > scores[1][len - 1]) ? 0 : 1;
      |                      ~~~~~~~~~^~~~~~~~~
utils/scorecontigs.c:188:52: warning: ‘*_305’ may be used uninitialized [-Wmaybe-uninitialized]
  188 |   states[len - 1] = (scores[0][len - 1] > scores[1][len - 1]) ? 0 : 1;
      |                                           ~~~~~~~~~^~~~~~~~~
skiplist.c: In function ‘printSLE’:
skiplist.c:12:19: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘void *’ [-Wformat=]
   12 |   printf("  %d   %x\n", tbp->index, tbp->myelem);
      |                  ~^                 ~~~~~~~~~~~
      |                   |                    |
      |                   unsigned int         void *
      |                  %p
skiplist.c: In function ‘makeSkLst’:
skiplist.c:33:7: warning: unused variable ‘i’ [-Wunused-variable]
   33 |   int i;
      |       ^
skiplist.c: In function ‘SLinsert’:
skiplist.c:100:37: warning: unused variable ‘tbe’ [-Wunused-variable]
  100 |   sle* prev = SLfind(trgt, index), *tbe;
      |                                     ^~~
utils/contigorder.c: In function ‘solveOrder’:
utils/contigorder.c:247:44: warning: ‘bestState’ may be used uninitialized [-Wmaybe-uninitialized]
  247 |     for (i = 0; k && i < numCols; i++) if (bestState & (1 << i)){
      |                                            ^~~~~~~~~
utils/contigorder.c:177:22: note: ‘bestState’ was declared here
  177 |   int bestScore = 0, bestState, bestRange, newBest, addedScore;
      |                      ^~~~~~~~~
utils/contigorder.c:249:63: warning: ‘bestRange’ may be used uninitialized [-Wmaybe-uninitialized]
  249 |       for (j = 0; k && j < numRanges; j++) if (last[j] < first[bestRange]){
      |                                                               ^
utils/contigorder.c:177:33: note: ‘bestRange’ was declared here
  177 |   int bestScore = 0, bestState, bestRange, newBest, addedScore;
      |                                 ^~~~~~~~~
mlagan.c: In function ‘buildTree’:
mlagan.c:662:8: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized]
  662 |     if (names[i] != result)
      |        ^
mlagan.c:599:9: note: ‘result’ was declared here
  599 |   char *result, *temp;
      |         ^~~~~~
diagmatrix.c: In function ‘DMsetPtr’:
diagmatrix.c:155:8: warning: unused variable ‘res’ [-Wunused-variable]
  155 |   char res;
      |        ^~~
diagmatrix.c:154:19: warning: unused variable ‘loc’ [-Wunused-variable]
  154 |   int dn = x+y-1, loc;
      |                   ^~~
utils/Glue.cpp: In function ‘void readScoreMatrix(char*)’:
utils/Glue.cpp:33:15: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
   33 |   lagan_dir = "/usr/lib64/lagan";
      |               ^~~~~~~~~~~~~~~~~~
utils/Glue.cpp: In function ‘void calculateScoreMatrix(int)’:
utils/Glue.cpp:60:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
   60 |   char *alpha = "ATCG";
      |                 ^~~~~~
utils/Glue.cpp:11:32: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
   11 | #define NUCLEOTIDE_MATRIX_FILE "nucmatrix.txt"
      |                                ^~~~~~~~~~~~~~~
utils/Glue.cpp:68:22: note: in expansion of macro ‘NUCLEOTIDE_MATRIX_FILE’
   68 |     readScoreMatrix (NUCLEOTIDE_MATRIX_FILE);
      |                      ^~~~~~~~~~~~~~~~~~~~~~
utils/Glue.cpp: In function ‘int countLets(SafeVector<char>&)’:
utils/Glue.cpp:228:24: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  228 |     if (data[i] >= 'A' && data[i] <= 'Z' || data[i] >= 'a' && data[i] <= 'z')
utils/Glue.cpp: In function ‘int main(int, char**)’:
utils/Glue.cpp:372:19: warning: variable ‘end1’ set but not used [-Wunused-but-set-variable]
  372 |   int begin1 = 1, end1 = 1;
      |                   ^~~~
multial.c: In function ‘getAnchsFromAlign’:
multial.c:104:9: warning: unused variable ‘peakfrac’ [-Wunused-variable]
  104 |   float peakfrac;
      |         ^~~~~~~~
multial.c:103:19: warning: unused variable ‘isfrst’ [-Wunused-variable]
  103 |   char ingap = 0, isfrst = 1;
      |                   ^~~~~~
multial.c:99:30: warning: unused variable ‘peakscore’ [-Wunused-variable]
   99 |   int currscore=0, oldscore, peakscore;
      |                              ^~~~~~~~~
multial.c:99:20: warning: unused variable ‘oldscore’ [-Wunused-variable]
   99 |   int currscore=0, oldscore, peakscore;
      |                    ^~~~~~~~
multial.c: In function ‘unifyAlign’:
multial.c:188:28: warning: unused variable ‘tgc’ [-Wunused-variable]
  188 |   int s1 = 0, s2 = 0, tgs, tgc;
      |                            ^~~
multial.c:188:23: warning: unused variable ‘tgs’ [-Wunused-variable]
  188 |   int s1 = 0, s2 = 0, tgs, tgc;
      |                       ^~~
multial.c:187:19: warning: unused variable ‘brcount’ [-Wunused-variable]
  187 |   int i,j,k, cbc, brcount;
      |                   ^~~~~~~
multial.c:187:14: warning: unused variable ‘cbc’ [-Wunused-variable]
  187 |   int i,j,k, cbc, brcount;
      |              ^~~
multial.c: In function ‘getChain’:
multial.c:247:7: warning: unused variable ‘temp’ [-Wunused-variable]
  247 |   int temp;
      |       ^~~~
multial.c: In function ‘saveNeck’:
multial.c:358:6: warning: unused variable ‘second’ [-Wunused-variable]
  358 |     *second = DMgetDiagStart(mydm, neckdiag, &size2, &x2, &y2);
      |      ^~~~~~
multial.c:357:9: warning: unused variable ‘first’ [-Wunused-variable]
  357 |   alel *first = DMgetDiagStart(mydm, neckdiag-1, &size1, &x1, &y1),
      |         ^~~~~
multial.c: In function ‘joinAligns’:
multial.c:381:10: warning: unused variable ‘n’ [-Wunused-variable]
  381 |   align *n = a->nextalign, *t;
      |          ^
multial.c: In function ‘openGap’:
multial.c:594:25: warning: unused variable ‘i’ [-Wunused-variable]
  594 |   int alopen, pen, sav, i;
      |                         ^
multial.c:594:15: warning: unused variable ‘pen’ [-Wunused-variable]
  594 |   int alopen, pen, sav, i;
      |               ^~~
multial.c: In function ‘mkBarrel’:
multial.c: In function ‘getAnchsFromAlign’:
multial.c:104:9: warning: unused variable ‘peakfrac’ [-Wunused-variable]
  104 |   float peakfrac;
      |         ^~~~~~~~
multial.c:103:19: warning: unused variable ‘isfrst’ [-Wunused-variable]
  103 |   char ingap = 0, isfrst = 1;
      |                   ^~~~~~
multial.c:99:30: warning: unused variable ‘peakscore’ [-Wunused-variable]
   99 |   int currscore=0, oldscore, peakscore;
      |                              ^~~~~~~~~
multial.c:99:20: warning: unused variable ‘oldscore’ [-Wunused-variable]
   99 |   int currscore=0, oldscore, peakscore;
      |                    ^~~~~~~~
multial.c:615:7: warning: unused variable ‘incr’ [-Wunused-variable]
  615 |   int incr;
      |       ^~~~
multial.c: In function ‘unifyAlign’:
multial.c:188:28: warning: unused variable ‘tgc’ [-Wunused-variable]
  188 |   int s1 = 0, s2 = 0, tgs, tgc;
      |                            ^~~
multial.c:188:23: warning: unused variable ‘tgs’ [-Wunused-variable]
  188 |   int s1 = 0, s2 = 0, tgs, tgc;
      |                       ^~~
multial.c:187:19: warning: unused variable ‘brcount’ [-Wunused-variable]
  187 |   int i,j,k, cbc, brcount;
      |                   ^~~~~~~
multial.c:187:14: warning: unused variable ‘cbc’ [-Wunused-variable]
  187 |   int i,j,k, cbc, brcount;
      |              ^~~
multial.c: In function ‘getChain’:
multial.c:247:7: warning: unused variable ‘temp’ [-Wunused-variable]
  247 |   int temp;
      |       ^~~~
multial.c: In function ‘saveNeck’:
multial.c:358:6: warning: unused variable ‘second’ [-Wunused-variable]
  358 |     *second = DMgetDiagStart(mydm, neckdiag, &size2, &x2, &y2);
      |      ^~~~~~
multial.c:357:9: warning: unused variable ‘first’ [-Wunused-variable]
  357 |   alel *first = DMgetDiagStart(mydm, neckdiag-1, &size1, &x1, &y1),
      |         ^~~~~
multial.c: In function ‘doNW’:
multial.c: In function ‘joinAligns’:
multial.c:811:20: warning: variable ‘oldneck’ set but not used [-Wunused-but-set-variable]
  811 |   int numNecks =0, oldneck =0;
      |                    ^~~~~~~
multial.c:381:10: warning: unused variable ‘n’ [-Wunused-variable]
  381 |   align *n = a->nextalign, *t;
      |          ^
multial.c:808:8: warning: unused variable ‘rh’ [-Wunused-variable]
  808 |   char rh, ptr=0, isneck;
      |        ^~
multial.c:807:14: warning: unused variable ‘b’ [-Wunused-variable]
  807 |   align* a, *b;
      |              ^
multial.c:805:11: warning: unused variable ‘prevgap’ [-Wunused-variable]
  805 |   int tt, prevgap;
      |           ^~~~~~~
multial.c:805:7: warning: unused variable ‘tt’ [-Wunused-variable]
  805 |   int tt, prevgap;
      |       ^~
multial.c:804:7: warning: unused variable ‘gapend’ [-Wunused-variable]
  804 |   int gapend[3];
      |       ^~~~~~
multial.c: In function ‘openGap’:
multial.c:594:25: warning: unused variable ‘i’ [-Wunused-variable]
  594 |   int alopen, pen, sav, i;
      |                         ^
multial.c:594:15: warning: unused variable ‘pen’ [-Wunused-variable]
  594 |   int alopen, pen, sav, i;
      |               ^~~
multial.c: In function ‘mkBarrel’:
multial.c:615:7: warning: unused variable ‘incr’ [-Wunused-variable]
  615 |   int incr;
      |       ^~~~
multial.c: In function ‘removeSeqByName’:
multial.c:1062:8: warning: variable ‘removed’ set but not used [-Wunused-but-set-variable]
 1062 |   seq *removed;
      |        ^~~~~~~
multial.c: In function ‘getSeqNum’:
multial.c:1073:8: warning: unused variable ‘removed’ [-Wunused-variable]
 1073 |   seq *removed;
      |        ^~~~~~~
multial.c: In function ‘doNW’:
multial.c: In function ‘remapHLLs’:
multial.c:811:20: warning: variable ‘oldneck’ set but not used [-Wunused-but-set-variable]
  811 |   int numNecks =0, oldneck =0;
      |                    ^~~~~~~
multial.c:1262:24: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
 1262 |         if (which == 0 && anchs->seq1end - anchs->seq1start < ANCHOR_LENGTH_CUTOFF ||
      |                        ^
multial.c:808:8: warning: unused variable ‘rh’ [-Wunused-variable]
  808 |   char rh, ptr=0, isneck;
      |        ^~
multial.c:807:14: warning: unused variable ‘b’ [-Wunused-variable]
  807 |   align* a, *b;
      |              ^
multial.c:805:11: warning: unused variable ‘prevgap’ [-Wunused-variable]
  805 |   int tt, prevgap;
      |           ^~~~~~~
multial.c:1104:43: warning: unused variable ‘olen’ [-Wunused-variable]
 1104 |   int mybp, i, *searchint, stmybp, mylen, olen, osize;
      |                                           ^~~~
multial.c:805:7: warning: unused variable ‘tt’ [-Wunused-variable]
  805 |   int tt, prevgap;
      |       ^~
multial.c:804:7: warning: unused variable ‘gapend’ [-Wunused-variable]
  804 |   int gapend[3];
      |       ^~~~~~
multial.c: In function ‘hllJoin’:
multial.c:1352:10: warning: unused variable ‘j’ [-Wunused-variable]
 1352 |   int i, j;
      |          ^
multial.c:1352:7: warning: unused variable ‘i’ [-Wunused-variable]
 1352 |   int i, j;
      |       ^
multial.c: In function ‘minHLL’:
multial.c:1368:10: warning: unused variable ‘j’ [-Wunused-variable]
 1368 |   int i, j;
      |          ^
multial.c: In function ‘removeSeqByName’:
multial.c:1062:8: warning: variable ‘removed’ set but not used [-Wunused-but-set-variable]
 1062 |   seq *removed;
      |        ^~~~~~~
multial.c: In function ‘getSeqNum’:
multial.c: In function ‘mergeHLLs’:
multial.c:1073:8: warning: unused variable ‘removed’ [-Wunused-variable]
 1073 |   seq *removed;
      |        ^~~~~~~
multial.c:1408:10: warning: unused variable ‘j’ [-Wunused-variable]
 1408 |   int i, j, mscore;
      |          ^
multial.c:1408:7: warning: unused variable ‘i’ [-Wunused-variable]
 1408 |   int i, j, mscore;
      |       ^
multial.c: In function ‘printTextAlign’:
multial.c:1466:7: warning: unused variable ‘nlets’ [-Wunused-variable]
 1466 |   int nlets=0;
      |       ^~~~~
multial.c: In function ‘remapHLLs’:
multial.c:1262:24: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
 1262 |         if (which == 0 && anchs->seq1end - anchs->seq1start < ANCHOR_LENGTH_CUTOFF ||
      |                        ^
multial.c:1465:13: warning: unused variable ‘s2’ [-Wunused-variable]
 1465 |   int s1=0, s2=0, c, k, i;
      |             ^~
multial.c:1465:7: warning: unused variable ‘s1’ [-Wunused-variable]
 1465 |   int s1=0, s2=0, c, k, i;
      |       ^~
multial.c:1104:43: warning: unused variable ‘olen’ [-Wunused-variable]
 1104 |   int mybp, i, *searchint, stmybp, mylen, olen, osize;
      |                                           ^~~~
multial.c: In function ‘printFASTAAlign’:
multial.c:1525:7: warning: unused variable ‘nlets’ [-Wunused-variable]
 1525 |   int nlets=0;
      |       ^~~~~
multial.c: In function ‘hllJoin’:
multial.c:1524:13: warning: unused variable ‘s2’ [-Wunused-variable]
 1524 |   int s1=0, s2=0, c, k, i;
      |             ^~
multial.c:1352:10: warning: unused variable ‘j’ [-Wunused-variable]
 1352 |   int i, j;
      |          ^
multial.c:1524:7: warning: unused variable ‘s1’ [-Wunused-variable]
 1524 |   int s1=0, s2=0, c, k, i;
      |       ^~
multial.c:1352:7: warning: unused variable ‘i’ [-Wunused-variable]
 1352 |   int i, j;
      |       ^
multial.c: In function ‘minHLL’:
multial.c: In function ‘printXMFAAlign’:
multial.c:1368:10: warning: unused variable ‘j’ [-Wunused-variable]
 1368 |   int i, j;
      |          ^
multial.c:1553:7: warning: unused variable ‘nlets’ [-Wunused-variable]
 1553 |   int nlets=0;
      |       ^~~~~
multial.c: In function ‘mergeHLLs’:
multial.c:1552:13: warning: unused variable ‘s2’ [-Wunused-variable]
 1552 |   int s1=0, s2=0, c, k, i;
      |             ^~
multial.c:1408:10: warning: unused variable ‘j’ [-Wunused-variable]
 1408 |   int i, j, mscore;
      |          ^
multial.c:1552:7: warning: unused variable ‘s1’ [-Wunused-variable]
 1552 |   int s1=0, s2=0, c, k, i;
      |       ^~
multial.c:1408:7: warning: unused variable ‘i’ [-Wunused-variable]
 1408 |   int i, j, mscore;
      |       ^
multial.c: At top level:
multial.c:581:10: warning: ‘gapcache’ is static but used in inline function ‘endGap2’ which is not static
  581 |   return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) |
      |          ^~~~~~~~
multial.c: In function ‘printTextAlign’:
multial.c:576:10: warning: ‘gapcache’ is static but used in inline function ‘endGap1’ which is not static
  576 |   return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) |
      |          ^~~~~~~~
multial.c:570:10: warning: ‘gapcache’ is static but used in inline function ‘endGap0’ which is not static
  570 |   return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) |
      |          ^~~~~~~~
multial.c:563:10: warning: ‘matchcache’ is static but used in inline function ‘scoreOpp’ which is not static
  563 |   return matchcache[v(other->cnts[0][ow]) |
      |          ^~~~~~~~~~
multial.c:1466:7: warning: unused variable ‘nlets’ [-Wunused-variable]
 1466 |   int nlets=0;
      |       ^~~~~
multial.c:1465:13: warning: unused variable ‘s2’ [-Wunused-variable]
 1465 |   int s1=0, s2=0, c, k, i;
      |             ^~
multial.c:1465:7: warning: unused variable ‘s1’ [-Wunused-variable]
 1465 |   int s1=0, s2=0, c, k, i;
      |       ^~
multial.c: In function ‘scoreLocal’:
multial.c:84:1: warning: control reaches end of non-void function [-Wreturn-type]
   84 | }
      | ^
multial.c: In function ‘printFASTAAlign’:
multial.c:1525:7: warning: unused variable ‘nlets’ [-Wunused-variable]
 1525 |   int nlets=0;
      |       ^~~~~
multial.c:1524:13: warning: unused variable ‘s2’ [-Wunused-variable]
 1524 |   int s1=0, s2=0, c, k, i;
      |             ^~
multial.c:1524:7: warning: unused variable ‘s1’ [-Wunused-variable]
 1524 |   int s1=0, s2=0, c, k, i;
      |       ^~
multial.c: In function ‘printXMFAAlign’:
multial.c: In function ‘readSubstMatrix’:
multial.c:478:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  478 |       fscanf (file, "%d", &k);
      |       ^~~~~~~~~~~~~~~~~~~~~~~
multial.c:486:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  486 |   fscanf (file, "%d", &gapstart);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multial.c:487:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  487 |   fscanf (file, "%d", &gapcont);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multial.c:1553:7: warning: unused variable ‘nlets’ [-Wunused-variable]
 1553 |   int nlets=0;
      |       ^~~~~
multial.c:1552:13: warning: unused variable ‘s2’ [-Wunused-variable]
 1552 |   int s1=0, s2=0, c, k, i;
      |             ^~
multial.c:1552:7: warning: unused variable ‘s1’ [-Wunused-variable]
 1552 |   int s1=0, s2=0, c, k, i;
      |       ^~
multial.c: At top level:
multial.c:581:10: warning: ‘gapcache’ is static but used in inline function ‘endGap2’ which is not static
  581 |   return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) |
      |          ^~~~~~~~
multial.c:576:10: warning: ‘gapcache’ is static but used in inline function ‘endGap1’ which is not static
  576 |   return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) |
      |          ^~~~~~~~
multial.c:570:10: warning: ‘gapcache’ is static but used in inline function ‘endGap0’ which is not static
  570 |   return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) |
      |          ^~~~~~~~
multial.c:563:10: warning: ‘matchcache’ is static but used in inline function ‘scoreOpp’ which is not static
  563 |   return matchcache[v(other->cnts[0][ow]) |
      |          ^~~~~~~~~~
multial.c: In function ‘scoreLocal’:
multial.c:84:1: warning: control reaches end of non-void function [-Wreturn-type]
   84 | }
      | ^
multial.c: In function ‘removeSeqByName’:
multial.c:1068:1: warning: control reaches end of non-void function [-Wreturn-type]
 1068 | }
      | ^
multial.c: In function ‘readSubstMatrix’:
multial.c:478:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  478 |       fscanf (file, "%d", &k);
      |       ^~~~~~~~~~~~~~~~~~~~~~~
multial.c:486:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  486 |   fscanf (file, "%d", &gapstart);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multial.c:487:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  487 |   fscanf (file, "%d", &gapcont);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multial.c: In function ‘printTextAlign’:
multial.c:1521:1: warning: control reaches end of non-void function [-Wreturn-type]
 1521 | }
      | ^
multial.c: In function ‘printFASTAAlign’:
multial.c:1549:1: warning: control reaches end of non-void function [-Wreturn-type]
 1549 | }
      | ^
multial.c: In function ‘printXMFAAlign’:
multial.c:1579:1: warning: control reaches end of non-void function [-Wreturn-type]
 1579 | }
      | ^
multial.c: In function ‘removeSeqByName’:
multial.c:1068:1: warning: control reaches end of non-void function [-Wreturn-type]
 1068 | }
      | ^
multial.c: In function ‘printTextAlign’:
multial.c:1521:1: warning: control reaches end of non-void function [-Wreturn-type]
 1521 | }
      | ^
multial.c: In function ‘printFASTAAlign’:
multial.c:1549:1: warning: control reaches end of non-void function [-Wreturn-type]
 1549 | }
      | ^
multial.c: In function ‘printXMFAAlign’:
multial.c:1579:1: warning: control reaches end of non-void function [-Wreturn-type]
 1579 | }
      | ^
fchaos.c: In function ‘doTranslated’:
fchaos.c:865:7: warning: ‘temp’ may be used uninitialized [-Wmaybe-uninitialized]
  865 |       procPairs(currquery, currdbase);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fchaos.c:805:32: note: ‘temp’ was declared here
  805 |   seq *currquery, *currdbase, *temp;
      |                                ^~~~
fchaos.c: In function ‘main’:
fchaos.c:955:7: warning: ‘temp’ may be used uninitialized [-Wmaybe-uninitialized]
  955 |       procPairs(currquery, currdbase);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fchaos.c:882:32: note: ‘temp’ was declared here
  882 |   seq *currquery, *currdbase, *temp;
      |                                ^~~~
thrtrie.c: In function ‘makeAlpha’:
thrtrie.c:34:15: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   34 |       indeces[*alpha] = i;
      |               ^~~~~~
thrtrie.c:36:19: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   36 |     else indeces [*alpha] = i++;
      |                   ^~~~~~
thrtrie.c: In function ‘lookup’:
thrtrie.c:43:17: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   43 |   return indeces[c];
      |                 ^
thrtrie.c: In function ‘insertString’:
thrtrie.c:175:10: warning: unused variable ‘j’ [-Wunused-variable]
  175 |   int i, j, wordlen = root->height, letprev, letcurr;
      |          ^
In file included from thrtrie.c:14:
mempage.c: In function ‘MPallfree’:
mempage.c:48:1: warning: control reaches end of non-void function [-Wreturn-type]
   48 | }
      | ^
utils/Glue.cpp: In function ‘void readScoreMatrix(char*)’:
utils/Glue.cpp:40:9: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   40 |   fgets (line, 1024, file);
      |   ~~~~~~^~~~~~~~~~~~~~~~~~
utils/Glue.cpp:48:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   48 |     fscanf (file, "%1s", &(line[0]));
      |     ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
utils/Glue.cpp:50:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   50 |       fscanf (file, "%d", &k);
      |       ~~~~~~~^~~~~~~~~~~~~~~~
utils/Glue.cpp:55:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   55 |   fscanf (file, "%d%d", &gapopen, &gapcont);
      |   ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
skiplist.c: In function ‘printSLE’:
skiplist.c:12:19: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘void *’ [-Wformat=]
   12 |   printf("  %d   %x\n", tbp->index, tbp->myelem);
      |                  ~^                 ~~~~~~~~~~~
      |                   |                    |
      |                   unsigned int         void *
      |                  %p
skiplist.c: In function ‘makeSkLst’:
skiplist.c:33:7: warning: unused variable ‘i’ [-Wunused-variable]
   33 |   int i;
      |       ^
skiplist.c: In function ‘SLinsert’:
skiplist.c:100:37: warning: unused variable ‘tbe’ [-Wunused-variable]
  100 |   sle* prev = SLfind(trgt, index), *tbe;
      |                                     ^~~
global.c: In function ‘ismatch’:
global.c:12:17: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   12 |   return indeces[a] == indeces[b];
      |                 ^
global.c:12:31: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   12 |   return indeces[a] == indeces[b];
      |                               ^
global.c: In function ‘global’:
global.c:34:31: warning: unused variable ‘score’ [-Wunused-variable]
   34 |   int mm = end2 - start2 + 1, score;
      |                               ^~~~~
global.c: In function ‘printalign’:
global.c:172:1: warning: control reaches end of non-void function [-Wreturn-type]
  172 | }
      | ^
translate.c: In function ‘toPeptide’:
translate.c:9:10: warning: unused variable ‘j’ [-Wunused-variable]
    9 |   int i, j, sum=0, mask = 0;
      |          ^
diagmatrix.c: In function ‘DMsetPtr’:
diagmatrix.c:155:8: warning: unused variable ‘res’ [-Wunused-variable]
  155 |   char res;
      |        ^~~
diagmatrix.c:154:19: warning: unused variable ‘loc’ [-Wunused-variable]
  154 |   int dn = x+y-1, loc;
      |                   ^~~
diagmatrix.c: In function ‘DMsetPtr’:
diagmatrix.c:155:8: warning: unused variable ‘res’ [-Wunused-variable]
  155 |   char res;
      |        ^~~
diagmatrix.c:154:19: warning: unused variable ‘loc’ [-Wunused-variable]
  154 |   int dn = x+y-1, loc;
      |                   ^~~
skiplist.c: In function ‘printSLE’:
skiplist.c:12:19: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘void *’ [-Wformat=]
   12 |   printf("  %d   %x\n", tbp->index, tbp->myelem);
      |                  ~^                 ~~~~~~~~~~~
      |                   |                    |
      |                   unsigned int         void *
      |                  %p
skiplist.c: In function ‘makeSkLst’:
skiplist.c:33:7: warning: unused variable ‘i’ [-Wunused-variable]
   33 |   int i;
      |       ^
skiplist.c: In function ‘SLinsert’:
skiplist.c:100:37: warning: unused variable ‘tbe’ [-Wunused-variable]
  100 |   sle* prev = SLfind(trgt, index), *tbe;
      |                                     ^~~
skiplist.c: In function ‘printSLE’:
skiplist.c:12:19: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘void *’ [-Wformat=]
   12 |   printf("  %d   %x\n", tbp->index, tbp->myelem);
      |                  ~^                 ~~~~~~~~~~~
      |                   |                    |
      |                   unsigned int         void *
      |                  %p
skiplist.c: In function ‘makeSkLst’:
skiplist.c:33:7: warning: unused variable ‘i’ [-Wunused-variable]
   33 |   int i;
      |       ^
skiplist.c: In function ‘SLinsert’:
skiplist.c:100:37: warning: unused variable ‘tbe’ [-Wunused-variable]
  100 |   sle* prev = SLfind(trgt, index), *tbe;
      |                                     ^~~
(cd glocal; make)
make[2]: Entering directory '/builddir/build/BUILD/lagan20/src/glocal'
g++ -Wno-deprecated -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I./ -c glocal.cpp
g++ -Wno-deprecated -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I./ -c io.cpp
g++ -Wno-deprecated -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I./ -c rightinfluence.cpp
g++ -Wno-deprecated -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I./ -c leftinfluence.cpp
g++ -Wno-deprecated -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I./ -c score.cpp
In file included from ./leftinfluence.h:4,
                 from leftinfluence.cpp:1:
leftinfluence.cpp: In function ‘void InitLI(LI*, long long int)’:
./structs.h:30:34: warning: suggest parentheses around ‘+’ inside ‘>>’ [-Wparentheses]
   30 | #define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS
      |                                  ^
leftinfluence.cpp:135:29: note: in expansion of macro ‘RELPOSSHIFT’
  135 |         if (((scoreIndex >> RELPOSSHIFT) & 1) == LEFT) {
      |                             ^~~~~~~~~~~
In file included from ./rightinfluence.h:4,
                 from rightinfluence.cpp:1:
rightinfluence.cpp: In function ‘void initRI(RI*, long long int)’:
./structs.h:30:34: warning: suggest parentheses around ‘+’ inside ‘>>’ [-Wparentheses]
   30 | #define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS
      |                                  ^
rightinfluence.cpp:9:29: note: in expansion of macro ‘RELPOSSHIFT’
    9 |         if (((scoreIndex >> RELPOSSHIFT) & 1) == LEFT) {
      |                             ^~~~~~~~~~~
rightinfluence.cpp: In function ‘long long int RICommitEndPoint(RI*, Fragment*)’:
./structs.h:30:34: warning: suggest parentheses around ‘+’ inside ‘<<’ [-Wparentheses]
   30 | #define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS
      |                                  ^
rightinfluence.cpp:119:85: note: in expansion of macro ‘RELPOSSHIFT’
  119 | int possibleCase = NEGATIVE << DOWNSTRANDSHIFT | NEGATIVE <<UPSTRANDSHIFT | LEFT << RELPOSSHIFT;
      |                                                                                     ^~~~~~~~~~~
leftinfluence.cpp: In function ‘void printState(LI*)’:
leftinfluence.cpp:619:23: warning: variable ‘colCount’ set but not used [-Wunused-but-set-variable]
  619 |         long long int colCount, diagCount, ownerCount;
      |                       ^~~~~~~~
leftinfluence.cpp:619:33: warning: variable ‘diagCount’ set but not used [-Wunused-but-set-variable]
  619 |         long long int colCount, diagCount, ownerCount;
      |                                 ^~~~~~~~~
leftinfluence.cpp:619:44: warning: variable ‘ownerCount’ set but not used [-Wunused-but-set-variable]
  619 |         long long int colCount, diagCount, ownerCount;
      |                                            ^~~~~~~~~~
In file included from score.cpp:1:
score.cpp: In function ‘void createScoreFunctionObjects(char*)’:
./structs.h:30:34: warning: suggest parentheses around ‘+’ inside ‘<<’ [-Wparentheses]
   30 | #define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS
      |                                  ^
score.cpp:92:120: note: in expansion of macro ‘RELPOSSHIFT’
   92 |                 cases[i]= charToCase(updir)<<UPSTRANDSHIFT | charToCase(downdir)<<DOWNSTRANDSHIFT |charToCase(relpos)<<RELPOSSHIFT;
      |                                                                                                                        ^~~~~~~~~~~
In file included from ./score.h:4,
                 from glocal.cpp:1:
glocal.cpp: In function ‘int main(int, char**)’:
./structs.h:31:50: warning: suggest parentheses around ‘+’ inside ‘<<’ [-Wparentheses]
   31 | #define TOTALSHIFT UPSTRANDBITS + DOWNSTRANDBITS + RELPOSBITS
      |                                                  ^
glocal.cpp:64:23: note: in expansion of macro ‘TOTALSHIFT’
   64 |         for (i=0;i<1<<TOTALSHIFT;i++) {
      |                       ^~~~~~~~~~
score.cpp: In function ‘float scoreAll(Fragment*, Fragment*, long long int)’:
./structs.h:30:34: warning: suggest parentheses around ‘+’ inside ‘>>’ [-Wparentheses]
   30 | #define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS
      |                                  ^
score.cpp:143:33: note: in expansion of macro ‘RELPOSSHIFT’
  143 |                 if (ret_case >> RELPOSSHIFT != UNRELATED) {
      |                                 ^~~~~~~~~~~
score.cpp: In function ‘float fragmentSetScore(Fragment*, Fragment*, LI*, RI*, long long int)’:
./structs.h:30:34: warning: suggest parentheses around ‘+’ inside ‘<<’ [-Wparentheses]
   30 | #define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS
      |                                  ^
score.cpp:185:134: note: in expansion of macro ‘RELPOSSHIFT’
  185 |                 tempScore = scoreAll(owner,current, current->strand << DOWNSTRANDSHIFT | owner->strand <<UPSTRANDSHIFT | UNRELATED<< RELPOSSHIFT);
      |                                                                                                                                      ^~~~~~~~~~~
glocal.cpp: In function ‘long long int startPointHandler()’:
./structs.h:30:34: warning: suggest parentheses around ‘+’ inside ‘<<’ [-Wparentheses]
   30 | #define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS
      |                                  ^
glocal.cpp:131:100: note: in expansion of macro ‘RELPOSSHIFT’
  131 |                 possibleCase = downStrand << DOWNSTRANDSHIFT | upStrand <<UPSTRANDSHIFT | relPos<< RELPOSSHIFT;
      |                                                                                                    ^~~~~~~~~~~
./structs.h:30:34: warning: suggest parentheses around ‘+’ inside ‘<<’ [-Wparentheses]
   30 | #define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS
      |                                  ^
glocal.cpp:142:101: note: in expansion of macro ‘RELPOSSHIFT’
  142 |                 possibleCase = downStrand << DOWNSTRANDSHIFT | upStrand <<UPSTRANDSHIFT | relPos << RELPOSSHIFT;
      |                                                                                                     ^~~~~~~~~~~
glocal.cpp:120:15: warning: variable ‘current_score’ set but not used [-Wunused-but-set-variable]
  120 |         float current_score;
      |               ^~~~~~~~~~~~~
glocal.cpp: In function ‘long long int endPointHandler()’:
./structs.h:30:34: warning: suggest parentheses around ‘+’ inside ‘<<’ [-Wparentheses]
   30 | #define RELPOSSHIFT UPSTRANDBITS + DOWNSTRANDBITS
      |                                  ^
glocal.cpp:224:116: note: in expansion of macro ‘RELPOSSHIFT’
  224 |                                 possibleCase = downStrand << DOWNSTRANDSHIFT | upStrand <<UPSTRANDSHIFT | relPos<< RELPOSSHIFT;
      |                                                                                                                    ^~~~~~~~~~~
io.cpp: In function ‘long long int getline(FILE*, hll*)’:
io.cpp:60:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   60 |         fgets(temp, 1024, infile);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~
glocal.cpp: In function ‘intersectionPointHandler()’:
glocal.cpp:257:37: warning: ‘curr.seq1’ is used uninitialized [-Wuninitialized]
  257 |         } while (current_seq1==curr.seq1);
      |                                ~~~~~^~~~
glocal.cpp:243:17: note: ‘curr’ declared here
  243 |         Point p,curr;
      |                 ^~~~
In function ‘intersectionPointHandler()’,
    inlined from ‘main’ at glocal.cpp:91:29:
glocal.cpp:257:37: warning: ‘curr.seq1’ may be used uninitialized [-Wmaybe-uninitialized]
  257 |         } while (current_seq1==curr.seq1);
      |                                ~~~~~^~~~
glocal.cpp: In function ‘main’:
glocal.cpp:243:17: note: ‘curr’ declared here
  243 |         Point p,curr;
      |                 ^~~~
In function ‘intersectionPointHandler()’,
    inlined from ‘main’ at glocal.cpp:101:29:
glocal.cpp:257:37: warning: ‘curr.seq1’ may be used uninitialized [-Wmaybe-uninitialized]
  257 |         } while (current_seq1==curr.seq1);
      |                                ~~~~~^~~~
glocal.cpp: In function ‘main’:
glocal.cpp:243:17: note: ‘curr’ declared here
  243 |         Point p,curr;
      |                 ^~~~
glocal.cpp: In function ‘intersectionPointHandler()’:
glocal.cpp:257:37: warning: ‘curr.seq1’ is used uninitialized [-Wuninitialized]
  257 |         } while (current_seq1==curr.seq1);
      |                                ~~~~~^~~~
glocal.cpp:243:17: note: ‘curr’ declared here
  243 |         Point p,curr;
      |                 ^~~~
g++   glocal.o io.o rightinfluence.o leftinfluence.o score.o -o ../../glocal -lm
make[2]: Leaving directory '/builddir/build/BUILD/lagan20/src/glocal'
make[1]: Leaving directory '/builddir/build/BUILD/lagan20/src'
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.qStJyK
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64
++ dirname /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/lagan-2.0-41.fc41.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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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 -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 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 lagan20
+ rm -rf /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64
+ mkdir -p /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/bin /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan/utils
+ install -m755 chaos /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64/usr/bin
+ install -m755 mlagan /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64/usr/bin
+ install -m755 prolagan /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64/usr/bin
+ install -m755 lagan.pl /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64/usr/bin/lagan
+ install -m755 slagan.pl /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64/usr/bin/slagan
+ for f in anal_gloc.pl anchors glocal order rechaos.pl supermap.pl xmfa2mfa.pl
+ install -m755 anal_gloc.pl /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan
+ for f in anal_gloc.pl anchors glocal order rechaos.pl supermap.pl xmfa2mfa.pl
+ install -m755 anchors /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan
+ for f in anal_gloc.pl anchors glocal order rechaos.pl supermap.pl xmfa2mfa.pl
+ install -m755 glocal /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan
+ for f in anal_gloc.pl anchors glocal order rechaos.pl supermap.pl xmfa2mfa.pl
+ install -m755 order /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan
+ for f in anal_gloc.pl anchors glocal order rechaos.pl supermap.pl xmfa2mfa.pl
+ install -m755 rechaos.pl /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan
+ for f in anal_gloc.pl anchors glocal order rechaos.pl supermap.pl xmfa2mfa.pl
+ install -m755 supermap.pl /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan
+ for f in anal_gloc.pl anchors glocal order rechaos.pl supermap.pl xmfa2mfa.pl
+ install -m755 xmfa2mfa.pl /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/bin2bl /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/bin2mf /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/cextract /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/cmerge2.pl /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/contigorder /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/cstat /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/dotplot /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/draft.pl /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/fa2xfa /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/getbounds /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/getcontigpos /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/getlength /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/getoverlap /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/Glue /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/mextract.pl /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/mf2bin.pl /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/mpretty.pl /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/mproject.pl /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/mrunfile.pl /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/mrunpairs.pl /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/mrun.pl /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/mviz.pl /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/rc /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/scorealign /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/scorecontigs /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/seqmerge /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan/utils
+ for f in bin2bl bin2mf cextract cmerge2.pl contigorder cstat dotplot draft.pl fa2xfa getbounds getcontigpos getlength getoverlap Glue mextract.pl mf2bin.pl mpretty.pl mproject.pl mrunfile.pl mrunpairs.pl mrun.pl mviz.pl rc scorealign scorecontigs seqmerge overlay
+ install -m755 utils/overlay /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan/utils
+ install -m644 blosum62.txt blosum62s.txt nucmatrix.txt test.score /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64//usr/lib64/lagan
+ rm -f Readmes/README.FIRST.chris Readmes/README.chaos.chris Readmes/README.lagan.chris Readmes/README.shuffle.chris
+ /usr/bin/find-debuginfo -j48 --strict-build-id -m -i --build-id-seed 2.0-41.fc41 --unique-debug-suffix -2.0-41.fc41.x86_64 --unique-debug-src-base lagan-2.0-41.fc41.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/lagan20
find-debuginfo: starting
Extracting debug info from 23 files
DWARF-compressing 23 files
sepdebugcrcfix: Updated 23 CRC32s, 0 CRC32s did match.
Creating .debug symlinks for symlinks to ELF files
Copying sources found by 'debugedit -l' to /usr/src/debug/lagan-2.0-41.fc41.x86_64
676 blocks
find-debuginfo: done
+ /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/bin/lagan from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/lib64/lagan/utils/cmerge2.pl from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/lib64/lagan/utils/draft.pl from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/lib64/lagan/utils/mextract.pl from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/lib64/lagan/utils/mf2bin.pl from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/lib64/lagan/utils/mpretty.pl from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/lib64/lagan/utils/mproject.pl from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/lib64/lagan/utils/mrunfile.pl from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/lib64/lagan/utils/mrunpairs.pl from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/lib64/lagan/utils/mrun.pl from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/lib64/lagan/utils/mviz.pl from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/lib64/lagan/anal_gloc.pl from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/lib64/lagan/rechaos.pl from /usr/bin/env perl to #!/usr/bin/perl
+ /usr/lib/rpm/brp-remove-la-files
+ env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j48
+ /usr/lib/rpm/redhat/brp-python-hardlink
Processing files: lagan-2.0-41.fc41.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.nl4MEj
+ umask 022
+ cd /builddir/build/BUILD
+ cd lagan20
+ DOCDIR=/builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64/usr/share/doc/lagan
+ export LC_ALL=
+ LC_ALL=
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64/usr/share/doc/lagan
+ cp -pr /builddir/build/BUILD/lagan20/Readmes/LICENSE /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64/usr/share/doc/lagan
+ cp -pr /builddir/build/BUILD/lagan20/Readmes/README.FIRST /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64/usr/share/doc/lagan
+ cp -pr /builddir/build/BUILD/lagan20/Readmes/README.chaos /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64/usr/share/doc/lagan
+ cp -pr /builddir/build/BUILD/lagan20/Readmes/README.lagan /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64/usr/share/doc/lagan
+ cp -pr /builddir/build/BUILD/lagan20/Readmes/README.mlagan /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64/usr/share/doc/lagan
+ cp -pr /builddir/build/BUILD/lagan20/Readmes/README.shuffle /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64/usr/share/doc/lagan
+ cp -pr /builddir/build/BUILD/lagan20/Readmes/README.tools /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64/usr/share/doc/lagan
+ cp -pr /builddir/build/BUILD/lagan20/sample.fasta /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64/usr/share/doc/lagan
+ cp -pr /builddir/build/BUILD/lagan20/sample.params /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64/usr/share/doc/lagan
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: lagan = 2.0-41.fc41 lagan(x86-64) = 2.0-41.fc41
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/perl libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) perl(:VERSION) >= 5.5.0 perl(Cwd) perl(File::Basename) perl(File::Copy) perl(File::Path) perl(Getopt::Long) perl(IO::Handle) perl(IPC::Open2) perl(constant) perl(strict) perl(warnings) rtld(GNU_HASH)
Processing files: lagan-debugsource-2.0-41.fc41.x86_64
Provides: lagan-debugsource = 2.0-41.fc41 lagan-debugsource(x86-64) = 2.0-41.fc41
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: lagan-debuginfo-2.0-41.fc41.x86_64
Provides: debuginfo(build-id) = 0cbeee2ca3f67c2c92d4e3e57746a3358f911391 debuginfo(build-id) = 12971f3db6c729fcaed79a38df9079c6f0a8d60a debuginfo(build-id) = 2bf1609c7d0238ae7ca8bfed93084740873afcfc debuginfo(build-id) = 2ff24ce8c1da418ba566536cf4de2e7927d7baed debuginfo(build-id) = 3b161d3855117e80f3b99e2398d105136b87f950 debuginfo(build-id) = 457a0a201f4de9747ccedc9e88ae89af1291f248 debuginfo(build-id) = 4b4968c2507ecabfbd32555d21b6b257b132156f debuginfo(build-id) = 5047179cf14ae4dfb8cfaa823cedf855a0a7158f debuginfo(build-id) = 62428872908edae160649497991f1fa84c5bdb7c debuginfo(build-id) = 6d378008b31035bce7e5a8cb1f54f7c9b80d34e9 debuginfo(build-id) = 77cd352ffa45c1bbcea18fbd41defc51dc5a0e8e debuginfo(build-id) = 895c6aca258c4d020adf9341ad35ed84a6bcb210 debuginfo(build-id) = 8e53f4759c12da391a4bf6ba294f8eea9622f944 debuginfo(build-id) = 9bb70347b6c2a4cf6b867a65027e7065fe351c3a debuginfo(build-id) = 9dcdb5c9139c19ad245dd070118cf8c4a6b3d215 debuginfo(build-id) = ab926e03141874bea2c2d70e1d80a05898e37463 debuginfo(build-id) = b4eb06eaaaef235946c17176272b5671fc2365b8 debuginfo(build-id) = bd19a8d75154d276c3467b2833192eca66747aa2 debuginfo(build-id) = c5e02283126d03073ce0812708b5c8ab48b839f5 debuginfo(build-id) = d2fb401a6d1ed7aa12ca3c25315848df7c32f199 debuginfo(build-id) = d738f2218de9cedae2561cfd68fb4245d33ff2c1 debuginfo(build-id) = ec1b43b6d3fd4ed7f4eb4fc6fd36297e0cccb052 debuginfo(build-id) = ee73763e42f558f655fee9c33e79e987b3b96660 lagan-debuginfo = 2.0-41.fc41 lagan-debuginfo(x86-64) = 2.0-41.fc41
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: lagan-debugsource(x86-64) = 2.0-41.fc41
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/lagan-2.0-41.fc41.x86_64
Wrote: /builddir/build/RPMS/lagan-debugsource-2.0-41.fc41.x86_64.rpm
Wrote: /builddir/build/RPMS/lagan-2.0-41.fc41.x86_64.rpm
Wrote: /builddir/build/RPMS/lagan-debuginfo-2.0-41.fc41.x86_64.rpm
RPM build warnings:
    %patchN is deprecated (3 usages found), use %patch N (or %patch -P N)
Child return code was: 0