Mock Version: 3.5
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs  --target i686 --nodeps /builddir/build/SPECS/hmmer.spec'], chrootPath='/var/lib/mock/fedora-rawhide-i686-1672268095.305560/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 0x7fa2a2f1cf50>timeout=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.p4ec5xwc:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True)
Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.p4ec5xwc:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']
Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '4f3e8d07b7374f96be768404f7351a48', '-D', '/var/lib/mock/fedora-rawhide-i686-1672268095.305560/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.p4ec5xwc:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs  --target i686 --nodeps /builddir/build/SPECS/hmmer.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False
Building target platforms: i686
Building for target i686
setting SOURCE_DATE_EPOCH=1659312000
Wrote: /builddir/build/SRPMS/hmmer-3.3.2-2.fc38.src.rpm
Child return code was: 0
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb  --target i686 --nodeps /builddir/build/SPECS/hmmer.spec'], chrootPath='/var/lib/mock/fedora-rawhide-i686-1672268095.305560/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 0x7fa2a2f1cf50>timeout=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.p4ec5xwc:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True)
Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.p4ec5xwc:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']
Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '94345065f58f4600a254cefdce73771a', '-D', '/var/lib/mock/fedora-rawhide-i686-1672268095.305560/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.p4ec5xwc:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb  --target i686 --nodeps /builddir/build/SPECS/hmmer.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False
Building target platforms: i686
Building for target i686
setting SOURCE_DATE_EPOCH=1659312000
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.wbJfII
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf hmmer-3.3.2
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/hmmer-3.3.2.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd hmmer-3.3.2
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.79tQFU
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd hmmer-3.3.2
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']'
++ find . -type f -name configure -print
+ for file in $(find . -type f -name configure -print)
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure
+ diff -u ./configure.backup ./configure
--- ./configure.backup	2020-11-26 21:19:58.000000000 +0000
+++ ./configure	2022-12-28 22:56:06.726037205 +0000
@@ -1898,7 +1898,7 @@
 #ifdef __cplusplus
 extern "C"
 #endif
-char $2 ();
+__attribute__ ((used)) char $2 ();
 /* The GNU C library defines this for functions which it implements
     to always fail with ENOSYS.  Some functions are actually named
     something starting with __ and the normal name is an alias.  */
+ /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ '[' 1 = 1 ']'
+++ dirname ./configure
++ find . -name config.guess -o -name config.sub
+ for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub)
++ basename ./easel/config.sub
+ '[' -f /usr/lib/rpm/redhat/config.sub ']'
+ /usr/bin/rm -f ./easel/config.sub
++ basename ./easel/config.sub
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./easel/config.sub
'/usr/lib/rpm/redhat/config.sub' -> './easel/config.sub'
+ for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub)
++ basename ./easel/config.guess
+ '[' -f /usr/lib/rpm/redhat/config.guess ']'
+ /usr/bin/rm -f ./easel/config.guess
++ basename ./easel/config.guess
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./easel/config.guess
'/usr/lib/rpm/redhat/config.guess' -> './easel/config.guess'
+ for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub)
++ basename ./config.sub
+ '[' -f /usr/lib/rpm/redhat/config.sub ']'
+ /usr/bin/rm -f ./config.sub
++ basename ./config.sub
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./config.sub
'/usr/lib/rpm/redhat/config.sub' -> './config.sub'
+ for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub)
++ basename ./config.guess
+ '[' -f /usr/lib/rpm/redhat/config.guess ']'
+ /usr/bin/rm -f ./config.guess
++ basename ./config.guess
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./config.guess
'/usr/lib/rpm/redhat/config.guess' -> './config.guess'
+ '[' 1 = 1 ']'
+ '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']'
++ find . -name ltmain.sh
++ grep -q runstatedir=DIR ./configure
+ ./configure --build=i686-redhat-linux-gnu --host=i686-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info
configure: WARNING: unrecognized options: --disable-dependency-tracking
configure: Configuring HMMER3 for your system.
checking build system type... i686-redhat-linux-gnu
checking host system type... i686-redhat-linux-gnu
checking whether to compile using MPI... no
checking for i686-redhat-linux-gnu-gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gcc option to accept ISO C99... none needed
checking for gcc option to accept ISO Standard C... (cached) none needed
checking how to run the C preprocessor... gcc -E
checking for a BSD-compatible install... /usr/bin/install -c
checking for i686-redhat-linux-gnu-strip... no
checking for strip... strip
checking for i686-redhat-linux-gnu-ranlib... no
checking for ranlib... ranlib
checking for ar... /usr/bin/ar
checking whether ln -s works... yes
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking whether gcc is Clang... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking whether more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking whether gcc can compile our Altivec/VMX code... no
checking whether gcc can compile our SSE code... yes
configure: Activating Intel/AMD SSE vector DP implementation
checking whether _MM_SET_FLUSH_ZERO_MODE is supported... yes
checking compiler support --start-group... yes
checking for gzip... /usr/bin/gzip
checking for python3... yes
checking for library containing clock_gettime... none required
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking endian.h usability... yes
checking endian.h presence... yes
checking for endian.h... yes
checking for inttypes.h... (cached) yes
checking for stdint.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/types.h... (cached) yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking for sys/sysctl.h... no
checking for uint8_t... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking for off_t... yes
checking whether byte ordering is bigendian... no
checking for __attribute__((noreturn))... yes
checking for __attribute__((format))... yes
checking for mkstemp... yes
checking for popen... yes
checking for putenv... yes
checking for strcasecmp... yes
checking for strsep... yes
checking for times... yes
checking for getpid... yes
checking for sysctl... no
checking for sysconf... yes
checking for getcwd... yes
checking for chmod... yes
checking for stat... yes
checking for fstat... yes
checking for erfc... no
checking for library containing ntohs... none required
checking for library containing ntohl... none required
checking for library containing htons... none required
checking for library containing htonl... none required
checking for library containing socket... none required
checking for library containing inet_pton... none required
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating testsuite/Makefile
config.status: creating profmark/Makefile
config.status: creating src/impl_sse/Makefile
config.status: creating documentation/Makefile
config.status: creating documentation/man/Makefile
config.status: creating documentation/userguide/Makefile
config.status: creating documentation/userguide/inclusions/Makefile
config.status: creating libdivsufsort/Makefile
config.status: creating easel/Makefile
config.status: creating easel/miniapps/Makefile
config.status: creating easel/testsuite/Makefile
config.status: creating easel/documentation/Makefile
config.status: creating documentation/userguide/titlepage.tex
config.status: creating documentation/userguide/titlepage_daemon.tex
config.status: creating documentation/userguide/copyright.tex
config.status: creating documentation/man/alimask.man
config.status: creating documentation/man/hmmalign.man
config.status: creating documentation/man/hmmbuild.man
config.status: creating documentation/man/hmmc2.man
config.status: creating documentation/man/hmmconvert.man
config.status: creating documentation/man/hmmemit.man
config.status: creating documentation/man/hmmer.man
config.status: creating documentation/man/hmmfetch.man
config.status: creating documentation/man/hmmlogo.man
config.status: creating documentation/man/hmmpgmd.man
config.status: creating documentation/man/hmmpgmd_shard.man
config.status: creating documentation/man/hmmpress.man
config.status: creating documentation/man/hmmscan.man
config.status: creating documentation/man/hmmsearch.man
config.status: creating documentation/man/hmmsim.man
config.status: creating documentation/man/hmmstat.man
config.status: creating documentation/man/jackhmmer.man
config.status: creating documentation/man/makehmmerdb.man
config.status: creating documentation/man/nhmmer.man
config.status: creating documentation/man/nhmmscan.man
config.status: creating documentation/man/phmmer.man
config.status: creating easel/miniapps/esl-afetch.man
config.status: creating easel/miniapps/esl-alimanip.man
config.status: creating easel/miniapps/esl-alimap.man
config.status: creating easel/miniapps/esl-alimask.man
config.status: creating easel/miniapps/esl-alimerge.man
config.status: creating easel/miniapps/esl-alipid.man
config.status: creating easel/miniapps/esl-alirev.man
config.status: creating easel/miniapps/esl-alistat.man
config.status: creating easel/miniapps/esl-compalign.man
config.status: creating easel/miniapps/esl-compstruct.man
config.status: creating easel/miniapps/esl-construct.man
config.status: creating easel/miniapps/esl-histplot.man
config.status: creating easel/miniapps/esl-mask.man
config.status: creating easel/miniapps/esl-mixdchlet.man
config.status: creating easel/miniapps/esl-reformat.man
config.status: creating easel/miniapps/esl-selectn.man
config.status: creating easel/miniapps/esl-seqrange.man
config.status: creating easel/miniapps/esl-seqstat.man
config.status: creating easel/miniapps/esl-sfetch.man
config.status: creating easel/miniapps/esl-shuffle.man
config.status: creating easel/miniapps/esl-ssdraw.man
config.status: creating easel/miniapps/esl-translate.man
config.status: creating easel/miniapps/esl-weight.man
config.status: creating easel/decoy_config.h
config.status: creating src/p7_config.h
config.status: creating easel/esl_config.h
config.status: creating libdivsufsort/divsufsort.h
config.status: linking src/impl_sse to src/impl
configure: WARNING: unrecognized options: --disable-dependency-tracking
HMMER configuration:
   compiler:             gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection   -pthread 
   host:                 i686-redhat-linux-gnu
   linker:               -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes
   libraries:              
   DP implementation:    sse
Now do 'make'  to build HMMER, and optionally:
       'make check'  to run self tests,
       'make install'  to install programs and man pages,
       '(cd easel; make install)'  to install Easel tools.
+ make -j2
     SUBDIR easel
     CC easel.o
     CC esl_alloc.o
     CC esl_alphabet.o
easel.c: In function 'esl_fail':
easel.c:79:12: warning: 'ap' may be used uninitialized [-Wmaybe-uninitialized]
   79 |       else vsyslog(LOG_ERR, format, ap); // SRE: TODO: check this.
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
easel.c:69:15: note: 'ap' was declared here
   69 |       va_list ap;
      |               ^~
easel.c: In function 'esl_exception':
easel.c:157:12: warning: 'argp' may be used uninitialized [-Wmaybe-uninitialized]
  157 |       else vsyslog(LOG_ERR, format, argp);
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
easel.c:131:11: note: 'argp' was declared here
  131 |   va_list argp;
      |           ^~~~
easel.c: In function 'esl_fatal':
easel.c:308:8: warning: 'argp' may be used uninitialized [-Wmaybe-uninitialized]
  308 |   else vsyslog(LOG_ERR, format, argp);
      |        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
easel.c:295:11: note: 'argp' was declared here
  295 |   va_list argp;
      |           ^~~~
     CC esl_arr2.o
     CC esl_arr3.o
     CC esl_bitfield.o
     CC esl_buffer.o
     CC esl_cluster.o
     CC esl_composition.o
     CC esl_cpu.o
     CC esl_dirichlet.o
     CC esl_distance.o
     CC esl_dmatrix.o
     CC esl_dsqdata.o
     CC esl_exponential.o
     CC esl_fileparser.o
     CC esl_gamma.o
     CC esl_gencode.o
     CC esl_getopts.o
     CC esl_gev.o
     CC esl_graph.o
     CC esl_gumbel.o
     CC esl_heap.o
     CC esl_histogram.o
     CC esl_hmm.o
     CC esl_huffman.o
     CC esl_hyperexp.o
     CC esl_json.o
esl_json.c: In function 'esl_json_Validate':
esl_json.c:752:33: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  752 |           case eslJSON_BOOLEAN: if (! esl_memstrcmp(bf->mem + pos1, pos2-pos1+1, "true")  &&
      |                                 ^~
esl_json.c:753:167: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  753 |                                     ! esl_memstrcmp(bf->mem + pos1, pos2-pos1+1, "false"))   ESL_FAIL(eslFAIL, errbuf, "boolean isn't a boolean, tok %d",         i); break;
      |                                                                                                                                                                       ^~~~~
     CC esl_keyhash.o
     CC esl_matrixops.o
     CC esl_mem.o
     CC esl_minimizer.o
esl_minimizer.c: In function 'esl_min_ConjugateGradientDescent':
esl_minimizer.c:243:23: warning: 'fx' may be used uninitialized [-Wmaybe-uninitialized]
  243 |   if (opt_fx) *opt_fx = fx;
      |               ~~~~~~~~^~~~
esl_minimizer.c:119:10: note: 'fx' was declared here
  119 |   double fx;
      |          ^~
In function 'brent',
    inlined from 'esl_min_ConjugateGradientDescent' at esl_minimizer.c:192:7:
esl_minimizer.c:720:21: warning: 'ax' may be used uninitialized [-Wmaybe-uninitialized]
  720 |       m   = 0.5 * (a+b);
      |                   ~~^~~
esl_minimizer.c: In function 'esl_min_ConjugateGradientDescent':
esl_minimizer.c:118:10: note: 'ax' was declared here
  118 |   double ax,bx,cx;
      |          ^~
In function 'brent',
    inlined from 'esl_min_ConjugateGradientDescent' at esl_minimizer.c:192:7:
esl_minimizer.c:720:21: warning: 'cx' may be used uninitialized [-Wmaybe-uninitialized]
  720 |       m   = 0.5 * (a+b);
      |                   ~~^~~
esl_minimizer.c: In function 'esl_min_ConjugateGradientDescent':
esl_minimizer.c:118:16: note: 'cx' was declared here
  118 |   double ax,bx,cx;
      |                ^~
     CC esl_mixdchlet.o
     CC esl_mixgev.o
     CC esl_mpi.o
     CC esl_msa.o
     CC esl_msacluster.o
     CC esl_msafile.o
     CC esl_msafile2.o
     CC esl_msafile_a2m.o
     CC esl_msafile_afa.o
     CC esl_msafile_clustal.o
esl_msafile_clustal.c: In function 'esl_msafile_clustal_Read':
esl_msafile_clustal.c:247:12: warning: 'block_seq_start' may be used uninitialized [-Wmaybe-uninitialized]
  247 |         if (seq_start != block_seq_start) ESL_XFAIL(eslEFORMAT, afp->errmsg, "sequence start is misaligned");
      |            ^
esl_msafile_clustal.c:203:13: note: 'block_seq_start' was declared here
  203 |   esl_pos_t block_seq_start, block_seq_len;
      |             ^~~~~~~~~~~~~~~
esl_msafile_clustal.c:248:12: warning: 'block_seq_len' may be used uninitialized [-Wmaybe-uninitialized]
  248 |         if (seq_len   != block_seq_len)   ESL_XFAIL(eslEFORMAT, afp->errmsg, "sequence end is misaligned");
      |            ^
esl_msafile_clustal.c:203:30: note: 'block_seq_len' was declared here
  203 |   esl_pos_t block_seq_start, block_seq_len;
      |                              ^~~~~~~~~~~~~
     CC esl_msafile_phylip.o
     CC esl_msafile_psiblast.o
esl_msafile_psiblast.c: In function 'esl_msafile_psiblast_Read':
esl_msafile_psiblast.c:228:12: warning: 'block_seq_start' may be used uninitialized [-Wmaybe-uninitialized]
  228 |         if (seq_start != block_seq_start) ESL_XFAIL(eslEFORMAT, afp->errmsg, "sequence start is misaligned");
      |            ^
esl_msafile_psiblast.c:195:13: note: 'block_seq_start' was declared here
  195 |   esl_pos_t block_seq_start, block_seq_len;
      |             ^~~~~~~~~~~~~~~
esl_msafile_psiblast.c:229:12: warning: 'block_seq_len' may be used uninitialized [-Wmaybe-uninitialized]
  229 |         if (seq_len   != block_seq_len)   ESL_XFAIL(eslEFORMAT, afp->errmsg, "sequence end is misaligned");
      |            ^
esl_msafile_psiblast.c:195:30: note: 'block_seq_len' was declared here
  195 |   esl_pos_t block_seq_start, block_seq_len;
      |                              ^~~~~~~~~~~~~
In function 'phylip_check_interleaved',
    inlined from 'esl_msafile_phylip_CheckFileFormat' at esl_msafile_phylip.c:389:13:
esl_msafile_phylip.c:739:16: warning: 'nres1' may be used uninitialized [-Wmaybe-uninitialized]
  739 |       if (nres1+nres2 == alen) break;
      |           ~~~~~^~~~~~
esl_msafile_phylip.c: In function 'esl_msafile_phylip_CheckFileFormat':
esl_msafile_phylip.c:687:13: note: 'nres1' was declared here
  687 |   int       nres1;
      |             ^~~~~
In function 'phylip_deduce_namewidth',
    inlined from 'phylip_check_interleaved' at esl_msafile_phylip.c:747:22,
    inlined from 'esl_msafile_phylip_CheckFileFormat' at esl_msafile_phylip.c:389:13:
esl_msafile_phylip.c:1048:10: warning: 'ncols0' may be used uninitialized [-Wmaybe-uninitialized]
 1048 |   for (c = ncols0-1; nres1 && c >= 0; c--)
      |        ~~^~~~~~~~~~
esl_msafile_phylip.c: In function 'esl_msafile_phylip_CheckFileFormat':
esl_msafile_phylip.c:683:20: note: 'ncols0' was declared here
  683 |   int       ncols, ncols0;
      |                    ^~~~~~
     CC esl_msafile_selex.o
     CC esl_msafile_stockholm.o
     CC esl_msashuffle.o
     CC esl_msaweight.o
     CC esl_normal.o
     CC esl_paml.o
     CC esl_quicksort.o
     CC esl_random.o
esl_msaweight.c: In function 'esl_msaweight_IDFilter_adv':
esl_msaweight.c:1035:9: warning: 'conscols_112' may be used uninitialized [-Wmaybe-uninitialized]
 1035 |         collect_counts(cfg, msa, conscols, ncons, ct, NULL);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
esl_msaweight.c:435:1: note: by argument 3 of type 'const int *' to 'collect_counts.isra.0' declared here
  435 | collect_counts(const ESL_MSAWEIGHT_CFG *cfg, const ESL_MSA *msa, const int *conscols, int ncons, int **ct, ESL_MSAWEIGHT_DAT *dat)
      | ^~~~~~~~~~~~~~
     CC esl_rand64.o
     CC esl_randomseq.o
     CC esl_ratematrix.o
     CC esl_recorder.o
     CC esl_red_black.o
     CC esl_regexp.o
     CC esl_rootfinder.o
     CC esl_scorematrix.o
     CC esl_sq.o
     CC esl_sqio.o
     CC esl_sqio_ascii.o
     CC esl_sqio_ncbi.o
     CC esl_ssi.o
     CC esl_stack.o
     CC esl_stats.o
     CC esl_stopwatch.o
     CC esl_stretchexp.o
     CC esl_subcmd.o
     CC esl_threads.o
     CC esl_tree.o
     CC esl_varint.o
esl_varint.c: In function 'esl_varint_google_decode':
esl_varint.c:474:11: warning: 'grp' may be used uninitialized [-Wmaybe-uninitialized]
  474 |   if (grp & cmask) { status = eslEOD; goto ERROR; }
      |       ~~~~^~~~~~~
esl_varint.c:464:12: note: 'grp' was declared here
  464 |   uint64_t grp;                     // current k-bit code group
      |            ^~~
     CC esl_vectorops.o
     CC esl_weibull.o
     CC esl_workqueue.o
     CC esl_wuss.o
     CC esl_sse.o
esl_wuss.c: In function 'esl_wuss2ct':
esl_wuss.c:136:10: warning: 'status' may be used uninitialized [-Wmaybe-uninitialized]
  136 |   return status;
      |          ^~~~~~
esl_wuss.c:56:14: note: 'status' was declared here
   56 |   int        status;      /* success or failure return status */
      |              ^~~~~~
     CC esl_avx.o
     CC esl_avx512.o
     CC esl_neon.o
     CC esl_vmx.o
     AR libeasel.a
     SUBDIR miniapps
     GEN esl-afetch
     GEN esl-alimanip
     GEN esl-alimap
     GEN esl-alimask
In function 'mask_based_on_postprobs',
    inlined from 'main' at esl-alimask.c:482:18:
esl-alimask.c:1085:33: warning: 'ppidx_thresh' may be used uninitialized [-Wmaybe-uninitialized]
 1085 |           for(ppidx = 10; ppidx >= ppidx_thresh; ppidx--) {
      |                           ~~~~~~^~~~~~~~~~~~~~~
esl-alimask.c: In function 'main':
esl-alimask.c:1007:7: note: 'ppidx_thresh' was declared here
 1007 |   int ppidx_thresh;
      |       ^~~~~~~~~~~~
     GEN esl-alimerge
esl-alimerge.c: In function 'validate_and_copy_msa_annotation':
esl-alimerge.c:732:7: warning: 'found_tag' may be used uninitialized [-Wmaybe-uninitialized]
  732 |   int found_tag;
      |       ^~~~~~~~~
In file included from /usr/include/stdio.h:906,
                 from esl-alimerge.c:26:
In function 'fprintf',
    inlined from 'main' at esl-alimerge.c:366:2:
/usr/include/bits/stdio2.h:79:10: warning: 'namewidth' may be used uninitialized [-Wmaybe-uninitialized]
   79 |   return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   80 |                         __va_arg_pack ());
      |                         ~~~~~~~~~~~~~~~~~
esl-alimerge.c: In function 'main':
esl-alimerge.c:136:14: note: 'namewidth' was declared here
  136 |   int        namewidth;                        /* max width of file name         */
      |              ^~~~~~~~~
esl-alimerge.c:412:16: warning: 'clen' may be used uninitialized [-Wmaybe-uninitialized]
  412 |   if((status = validate_and_copy_msa_annotation(go, outfmt, mmsa, msaA, nali_tot, clen, alen_mmsa, maxgap, maxmis, errbuf)) != eslOK)
      |                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
esl-alimerge.c:118:17: note: 'clen' was declared here
  118 |   int           clen;                          /* consensus length (non-gap #=GC RF length) of all alignments */
      |                 ^~~~
     GEN esl-alipid
     GEN esl-alirev
     GEN esl-alistat
In file included from /usr/include/stdio.h:906,
                 from esl-alistat.c:6:
In function 'printf',
    inlined from 'main' at esl-alistat.c:293:6:
/usr/include/bits/stdio2.h:86:10: warning: 'small' may be used uninitialized [-Wmaybe-uninitialized]
   86 |   return __printf_chk (__USE_FORTIFY_LEVEL - 1, __fmt, __va_arg_pack ());
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
esl-alistat.c: In function 'main':
esl-alistat.c:74:17: note: 'small' was declared here
   74 |   int64_t       small, large;                  /* smallest, largest sequence      */
      |                 ^~~~~
In function 'printf',
    inlined from 'main' at esl-alistat.c:294:6:
/usr/include/bits/stdio2.h:86:10: warning: 'large' may be used uninitialized [-Wmaybe-uninitialized]
   86 |   return __printf_chk (__USE_FORTIFY_LEVEL - 1, __fmt, __va_arg_pack ());
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
esl-alistat.c: In function 'main':
esl-alistat.c:74:24: note: 'large' was declared here
   74 |   int64_t       small, large;                  /* smallest, largest sequence      */
      |                        ^~~~~
     GEN esl-compalign
esl-compalign.c: In function 'main':
esl-compalign.c:231:13: warning: 'masklen' may be used uninitialized [-Wmaybe-uninitialized]
  231 |           if(masklen != rflen) {
      |             ^
esl-compalign.c:90:7: note: 'masklen' was declared here
   90 |   int masklen;
      |       ^~~~~~~
esl-compalign.c:326:30: warning: 'ppidx' may be used uninitialized [-Wmaybe-uninitialized]
  326 |               if(do_post) pti[ppidx]++;
      |                              ^
esl-compalign.c:104:7: note: 'ppidx' was declared here
  104 |   int ppidx;           /* index of PP */
      |       ^~~~~
     GEN esl-compstruct
     GEN esl-construct
esl-construct.c: In function 'main':
esl-construct.c:573:24: warning: 'fmin' may be used uninitialized [-Wmaybe-uninitialized]
  573 |         if(do_fmin)  { printf("#\n# <x> determined to be %.3f\n", fthresh); }
      |                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
esl-construct.c:129:9: note: 'fmin' was declared here
  129 |   float fmin;
      |         ^~~~
     GEN esl-histplot
     GEN esl-mask
     GEN esl-mixdchlet
     GEN esl-reformat
esl-reformat.c: In function 'main':
esl-reformat.c:416:9: warning: 'mapfp' may be used uninitialized [-Wmaybe-uninitialized]
  416 |         fclose(mapfp);
      |         ^~~~~~~~~~~~~
esl-reformat.c:304:20: note: 'mapfp' was declared here
  304 |       FILE        *mapfp;    /* output stream for the map file                       */
      |                    ^~~~~
esl-reformat.c:212:13: warning: 'reached_eof' may be used uninitialized [-Wmaybe-uninitialized]
  212 |           if(! reached_eof) esl_fatal("Input file contains >1 alignments, but afa formatted output file can only contain 1");
      |             ^
esl-reformat.c:103:10: note: 'reached_eof' was declared here
  103 |   int    reached_eof;           /* reached EOF? used only in small mem mode  */
      |          ^~~~~~~~~~~
     GEN esl-selectn
     GEN esl-seqrange
     GEN esl-seqstat
     GEN esl-sfetch
     GEN esl-shuffle
     GEN esl-ssdraw
esl-ssdraw.c: In function 'get_insert_info_from_ifile.constprop.0':
esl-ssdraw.c:6664:32: warning: 'rfpos' may be used uninitialized [-Wmaybe-uninitialized]
 6664 |   if(! seen_end_of_model_line) esl_fatal("Error reading insert file, didn't read the special '//' line at the end of file %s.\n", rfpos, efp->linenumber, ifile);
      |                                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
esl-ssdraw.c:6500:19: note: 'rfpos' was declared here
 6500 |   int             rfpos; /* current nongap RF position */
      |                   ^~~~~
In file included from esl-ssdraw.c:16:
In function 'draw_header_and_footer',
    inlined from 'draw_sspostscript.isra.0' at esl-ssdraw.c:2491:18:
esl-ssdraw.c:6263:56: warning: 'split_idx' may be used uninitialized [-Wmaybe-uninitialized]
 6263 |         ESL_ALLOC(desc2print, sizeof(char) * (split_idx+1));
      |                                              ~~~~~~~~~~^~~
esl-ssdraw.c: In function 'draw_sspostscript.isra.0':
esl-ssdraw.c:6164:10: note: 'split_idx' was declared here
 6164 |   int i, split_idx;
      |          ^~~~~~~~~
     GEN esl-translate
In file included from /usr/include/stdio.h:906,
                 from esl-ssdraw.c:10:
In function 'fprintf',
    inlined from 'individuals_sspostscript.constprop.0' at esl-ssdraw.c:3663:7:
/usr/include/bits/stdio2.h:79:10: warning: 'namewidth' may be used uninitialized [-Wmaybe-uninitialized]
   79 |   return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   80 |                         __va_arg_pack ());
      |                         ~~~~~~~~~~~~~~~~~
esl-ssdraw.c: In function 'individuals_sspostscript.constprop.0':
esl-ssdraw.c:3347:7: note: 'namewidth' was declared here
 3347 |   int namewidth;        /* length in chars of longest seq name we'll print */
      |       ^~~~~~~~~
esl-ssdraw.c: In function 'parse_template_file.isra.0':
esl-ssdraw.c:2716:10: warning: 'ps' may be used uninitialized [-Wmaybe-uninitialized]
 2716 |     if(ps->rflen == msa_rflen) { found_match = TRUE; }
      |        ~~^~~~~~~
esl-ssdraw.c:2703:19: note: 'ps' was declared here
 2703 |   SSPostscript_t *ps;
      |                   ^~
     GEN esl-weight
     CC cmd_alistat.o
     CC cmd_downsample.o
     CC cmd_filter.o
     CC cmd_index.o
     GEN easel
     SUBDIR libdivsufsort
     CC divsufsort.o
     AR libdivsufsort.a
     SUBDIR src
     CC alimask.o
     CC build.o
alimask.c: In function 'main':
alimask.c:313:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  313 |     if (puts("Must specify mask range with --modelrange, --alirange, --model2ali, or --ali2model\n") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto ERROR;
      |     ^~
alimask.c:313:154: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  313 |     if (puts("Must specify mask range with --modelrange, --alirange, --model2ali, or --ali2model\n") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto ERROR;
      |                                                                                                                                                          ^~~~
     CC cachedb.o
     CC cachedb_shard.o
     CC emit.o
     CC errors.o
     CC evalues.o
     CC eweight.o
     CC generic_decoding.o
     CC generic_fwdback.o
     CC generic_fwdback_chk.o
     CC generic_fwdback_banded.o
     CC generic_null2.o
     CC generic_msv.o
     CC generic_optacc.o
     CC generic_stotrace.o
generic_stotrace.c: In function 'p7_GStochasticTrace':
generic_stotrace.c:172:21: warning: 'scur' may be used uninitialized [-Wmaybe-uninitialized]
  172 |       if ((status = p7_trace_Append(tr, scur, k, i)) != eslOK) goto ERROR;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
generic_stotrace.c:57:11: note: 'scur' was declared here
   57 |   int     scur, sprv;
      |           ^~~~
     CC generic_viterbi.o
     CC generic_vtrace.o
     CC h2_io.o
     CC heatmap.o
     CC hmmlogo.o
     CC hmmdmstr.o
     CC hmmdmstr_shard.o
In function 'process_ServerCmd',
    inlined from 'clientside_loop' at hmmdmstr.c:1134:5:
hmmdmstr.c:1020:24: warning: array subscript 'struct HMMD_COMMAND[0]' is partly outside array bounds of 'unsigned char[12]' [-Warray-bounds=]
 1020 |       cmd->hdr.command = HMMD_CMD_SHUTDOWN;
hmmdmstr.c:1017:18: note: object of size 12 allocated by 'malloc'
 1017 |       if ((cmd = malloc(sizeof(HMMD_HEADER))) == NULL) LOG_FATAL_MSG("malloc", errno);
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
hmmdmstr.c:1046:3: warning: array subscript 'struct HMMD_COMMAND[0]' is partly outside array bounds of 'unsigned char[12]' [-Warray-bounds=]
 1046 |   printf("Queuing command %d from %s (%d)\n", cmd->hdr.command, parms->ip_addr, parms->sock);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hmmdmstr.c:1017:18: note: object of size 12 allocated by 'malloc'
 1017 |       if ((cmd = malloc(sizeof(HMMD_HEADER))) == NULL) LOG_FATAL_MSG("malloc", errno);
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'process_ServerCmd',
    inlined from 'clientside_loop' at hmmdmstr_shard.c:1173:5:
hmmdmstr_shard.c:1059:24: warning: array subscript 'struct HMMD_COMMAND_SHARD[0]' is partly outside array bounds of 'unsigned char[12]' [-Warray-bounds=]
 1059 |       cmd->hdr.command = HMMD_CMD_SHUTDOWN;
hmmdmstr_shard.c:1056:18: note: object of size 12 allocated by 'malloc'
 1056 |       if ((cmd = malloc(sizeof(HMMD_HEADER))) == NULL) LOG_FATAL_MSG("malloc", errno);
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
hmmdmstr_shard.c:1085:3: warning: array subscript 'struct HMMD_COMMAND_SHARD[0]' is partly outside array bounds of 'unsigned char[12]' [-Warray-bounds=]
 1085 |   printf("Queuing command %d from %s (%d)\n", cmd->hdr.command, parms->ip_addr, parms->sock);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hmmdmstr_shard.c:1056:18: note: object of size 12 allocated by 'malloc'
 1056 |       if ((cmd = malloc(sizeof(HMMD_HEADER))) == NULL) LOG_FATAL_MSG("malloc", errno);
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:535,
                 from hmmdmstr.c:10:
In function 'memset',
    inlined from 'destroy_worker' at hmmdmstr.c:948:5,
    inlined from 'update_workers.part.0' at hmmdmstr.c:285:7:
/usr/include/bits/string_fortified.h:59:10: warning: argument 1 null where non-null expected [-Wnonnull]
   59 |   return __builtin___memset_chk (__dest, __ch, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   60 |                                  __glibc_objsize0 (__dest));
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/bits/string_fortified.h:59:10: note: in a call to built-in function 'memset'
In file included from /usr/include/string.h:535,
                 from hmmdmstr_shard.c:10:
In function 'memset',
    inlined from 'destroy_worker' at hmmdmstr_shard.c:987:5,
    inlined from 'update_workers.part.0' at hmmdmstr_shard.c:306:7:
/usr/include/bits/string_fortified.h:59:10: warning: argument 1 null where non-null expected [-Wnonnull]
   59 |   return __builtin___memset_chk (__dest, __ch, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   60 |                                  __glibc_objsize0 (__dest));
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/bits/string_fortified.h:59:10: note: in a call to built-in function 'memset'
     CC hmmd_search_status.o
     CC hmmdwrkr.o
     CC hmmdwrkr_shard.o
     CC hmmdutils.o
     CC hmmer.o
     CC logsum.o
     CC modelconfig.o
     CC modelstats.o
     CC mpisupport.o
     CC seqmodel.o
     CC tracealign.o
     CC p7_alidisplay.o
     CC p7_bg.o
     CC p7_builder.o
     CC p7_domain.o
p7_domain.c: In function 'p7_domain_Serialize':
p7_domain.c:191:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  191 |   network_32bit = esl_hton32(*((uint32_t *) &(obj->envsc)));  // ow, this hurts, but is probably the best way to get the
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~
p7_domain.c:198:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  198 |   network_32bit = esl_hton32(*((uint32_t *) &(obj->domcorrection)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
p7_domain.c:203:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  203 |   network_32bit = esl_hton32(*((uint32_t *) &(obj->dombias)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
p7_domain.c:208:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  208 |   network_32bit = esl_hton32(*((uint32_t *) &(obj->oasc)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~
p7_domain.c:213:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  213 |   network_32bit = esl_hton32(*((uint32_t *) &(obj->bitscore)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
p7_domain.c:218:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  218 |   network_64bit = esl_hton64(*((uint64_t *) &(obj->lnP)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~
p7_domain.c: In function 'p7_domain_Deserialize':
p7_domain.c:341:22: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  341 |   ret_obj->envsc = *((float *) &host_32bit);
      |                     ~^~~~~~~~~~~~~~~~~~~~~~
p7_domain.c:347:30: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  347 |   ret_obj->domcorrection = *((float *) &host_32bit);
      |                             ~^~~~~~~~~~~~~~~~~~~~~~
p7_domain.c:353:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  353 |   ret_obj->dombias = *((float *) &host_32bit);
      |                       ~^~~~~~~~~~~~~~~~~~~~~~
p7_domain.c:359:21: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  359 |   ret_obj->oasc = *((float *) &host_32bit);
      |                    ~^~~~~~~~~~~~~~~~~~~~~~
p7_domain.c:365:25: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  365 |   ret_obj->bitscore = *((float *) &host_32bit);
      |                        ~^~~~~~~~~~~~~~~~~~~~~~
p7_domain.c:371:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  371 |   ret_obj->lnP = *((double *) &host_64bit);
      |                   ~^~~~~~~~~~~~~~~~~~~~~~~
p7_domain.c:398:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  398 |       ret_obj->scores_per_pos[i] = *((float *) &host_32bit);
      |                                     ~^~~~~~~~~~~~~~~~~~~~~~
     CC p7_domaindef.o
     CC p7_gbands.o
p7_domaindef.c: In function 'rescore_isolated_domain':
p7_domaindef.c:932:5: warning: 'orig_L' may be used uninitialized [-Wmaybe-uninitialized]
  932 |     p7_oprofile_ReconfigRestLength(om, orig_L);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
p7_domaindef.c:827:18: note: 'orig_L' was declared here
  827 |   int            orig_L;
      |                  ^~~~~~
     CC p7_gmx.o
     CC p7_gmxb.o
     CC p7_gmxchk.o
     CC p7_hit.o
     CC p7_hmm.o
p7_hit.c: In function 'p7_hit_Serialize':
p7_hit.c:226:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  226 |   network_64bit = esl_hton64(*((uint64_t *) &(obj->sortkey)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
p7_hit.c:231:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  231 |   network_32bit = esl_hton32(*((uint32_t *) &(obj->score)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~
p7_hit.c:236:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  236 |   network_32bit = esl_hton32(*((uint32_t *) &(obj->pre_score)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
p7_hit.c:241:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  241 |   network_32bit = esl_hton32(*((uint32_t *) &(obj->sum_score)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
p7_hit.c:246:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  246 |   network_64bit = esl_hton64(*((uint64_t *) &(obj->lnP)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~
p7_hit.c:251:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  251 |   network_64bit = esl_hton64(*((uint64_t *) &(obj->pre_lnP)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
p7_hit.c:256:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  256 |   network_64bit = esl_hton64(*((uint64_t *) &(obj->sum_lnP)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
p7_hit.c:261:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  261 |   network_32bit = esl_hton32(*((uint32_t *) &(obj->nexpected)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
p7_hit.c: In function 'p7_hit_Deserialize':
p7_hit.c:408:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  408 |   ret_obj->sortkey = *((double *) &host_64bit);
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
p7_hit.c:414:22: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  414 |   ret_obj->score = *((float *) &host_32bit);
      |                     ~^~~~~~~~~~~~~~~~~~~~~~
p7_hit.c:420:26: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  420 |   ret_obj->pre_score = *((float *) &host_32bit);
      |                         ~^~~~~~~~~~~~~~~~~~~~~~
p7_hit.c:426:26: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  426 |   ret_obj->sum_score = *((float *) &host_32bit);
      |                         ~^~~~~~~~~~~~~~~~~~~~~~
p7_hit.c:432:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  432 |   ret_obj->lnP = *((double *) &host_64bit);
      |                   ~^~~~~~~~~~~~~~~~~~~~~~~
p7_hit.c:438:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  438 |   ret_obj->pre_lnP = *((double *) &host_64bit);
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
p7_hit.c:444:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  444 |   ret_obj->sum_lnP = *((double *) &host_64bit);
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
p7_hit.c:450:26: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  450 |   ret_obj->nexpected = *((float *) &host_32bit);
      |                         ~^~~~~~~~~~~~~~~~~~~~~~
     CC p7_hmmcache.o
     CC p7_hmmd_search_stats.o
p7_hmmd_search_stats.c: In function 'p7_hmmd_search_stats_Serialize':
p7_hmmd_search_stats.c:89:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   89 |   network_64bit = esl_hton64(*((uint64_t *) &(obj->elapsed)));  // ow, this hurts, but is probably the best way to get the
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
p7_hmmd_search_stats.c:97:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   97 |   network_64bit = esl_hton64(*((uint64_t *) &(obj->user)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~
p7_hmmd_search_stats.c:103:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  103 |   network_64bit = esl_hton64(*((uint64_t *) &(obj->sys)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~
p7_hmmd_search_stats.c:109:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  109 |   network_64bit = esl_hton64(*((uint64_t *) &(obj->Z)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~
p7_hmmd_search_stats.c:115:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  115 |   network_64bit = esl_hton64(*((uint64_t *) &(obj->domZ)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~
p7_hmmd_search_stats.c: In function 'p7_hmmd_search_stats_Deserialize':
p7_hmmd_search_stats.c:256:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  256 |   ret_obj->elapsed = *((double *) &host_64bit);
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
p7_hmmd_search_stats.c:262:21: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  262 |   ret_obj->user = *((double *) &host_64bit);
      |                    ~^~~~~~~~~~~~~~~~~~~~~~~
p7_hmmd_search_stats.c:268:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  268 |   ret_obj->sys = *((double *) &host_64bit);
      |                   ~^~~~~~~~~~~~~~~~~~~~~~~
p7_hmmd_search_stats.c:274:18: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  274 |   ret_obj->Z = *((double *) &host_64bit);
      |                 ~^~~~~~~~~~~~~~~~~~~~~~~
p7_hmmd_search_stats.c:280:21: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  280 |   ret_obj->domZ = *((double *) &host_64bit);
      |                    ~^~~~~~~~~~~~~~~~~~~~~~~
     CC p7_hmmfile.o
     CC p7_hmmwindow.o
     CC p7_pipeline.o
     CC p7_prior.o
     CC p7_profile.o
     CC p7_spensemble.o
     CC p7_tophits.o
In file included from p7_spensemble.c:7:
p7_spensemble.c: In function 'p7_spensemble_Cluster':
p7_spensemble.c:344:43: warning: 'imax' may be used uninitialized [-Wmaybe-uninitialized]
  344 |       cwindow_width = ESL_MAX(ESL_MAX(imax-imin+1, jmax-jmin+1),
      |                                       ~~~~^~~~~
p7_spensemble.c:294:7: note: 'imax' was declared here
  294 |   int imax, jmax, kmax, mmax;
      |       ^~~~
p7_spensemble.c:344:56: warning: 'jmin' may be used uninitialized [-Wmaybe-uninitialized]
  344 |       cwindow_width = ESL_MAX(ESL_MAX(imax-imin+1, jmax-jmin+1),
      |                                                    ~~~~^~~~~
p7_spensemble.c:293:13: note: 'jmin' was declared here
  293 |   int imin, jmin, kmin, mmin;
      |             ^~~~
p7_spensemble.c:345:43: warning: 'kmin' may be used uninitialized [-Wmaybe-uninitialized]
  345 |                               ESL_MAX(kmax-kmin+1, mmax-mmin+1));
      |                                       ~~~~^~~~~
p7_spensemble.c:293:19: note: 'kmin' was declared here
  293 |   int imin, jmin, kmin, mmin;
      |                   ^~~~
p7_spensemble.c:345:56: warning: 'mmin' may be used uninitialized [-Wmaybe-uninitialized]
  345 |                               ESL_MAX(kmax-kmin+1, mmax-mmin+1));
      |                                                    ~~~~^~~~~
p7_spensemble.c:293:25: note: 'mmin' was declared here
  293 |   int imin, jmin, kmin, mmin;
      |                         ^~~~
p7_spensemble.c:344:56: warning: 'jmax' may be used uninitialized [-Wmaybe-uninitialized]
  344 |       cwindow_width = ESL_MAX(ESL_MAX(imax-imin+1, jmax-jmin+1),
      |                                                    ~~~~^~~~~
p7_spensemble.c:294:13: note: 'jmax' was declared here
  294 |   int imax, jmax, kmax, mmax;
      |             ^~~~
p7_spensemble.c:345:43: warning: 'kmax' may be used uninitialized [-Wmaybe-uninitialized]
  345 |                               ESL_MAX(kmax-kmin+1, mmax-mmin+1));
      |                                       ~~~~^~~~~
p7_spensemble.c:294:19: note: 'kmax' was declared here
  294 |   int imax, jmax, kmax, mmax;
      |                   ^~~~
p7_spensemble.c:345:56: warning: 'mmax' may be used uninitialized [-Wmaybe-uninitialized]
  345 |                               ESL_MAX(kmax-kmin+1, mmax-mmin+1));
      |                                                    ~~~~^~~~~
p7_spensemble.c:294:25: note: 'mmax' was declared here
  294 |   int imax, jmax, kmax, mmax;
      |                         ^~~~
     CC p7_trace.o
In file included from /usr/include/stdio.h:906,
                 from ../easel/easel.h:22,
                 from p7_tophits.c:16:
In function 'fprintf',
    inlined from 'p7_tophits_Targets' at p7_tophits.c:1142:12:
/usr/include/bits/stdio2.h:79:10: warning: 'posw' may be used uninitialized [-Wmaybe-uninitialized]
   79 |   return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   80 |                         __va_arg_pack ());
      |                         ~~~~~~~~~~~~~~~~~
p7_tophits.c: In function 'p7_tophits_Targets':
p7_tophits.c:1068:10: note: 'posw' was declared here
 1068 |   int    posw;
      |          ^~~~
     CC p7_scoredata.o
     CC hmmpgmd2msa.o
     CC fm_alphabet.o
     CC fm_general.o
     CC fm_sse.o
     CC fm_ssv.o
     CC hmmalign.o
In function 'FM_extendSeed',
    inlined from 'p7_SSVFM_longlarget' at fm_ssv.c:806:5:
fm_ssv.c:696:32: warning: 'max_hit_start' may be used uninitialized [-Wmaybe-uninitialized]
  696 |   diag->k       = model_start  + max_hit_start - 1;
      |                   ~~~~~~~~~~~~~^~~~~~~~~~~~~~~
fm_ssv.c: In function 'p7_SSVFM_longlarget':
fm_ssv.c:648:22: note: 'max_hit_start' was declared here
  648 |   int64_t hit_start, max_hit_start, max_hit_end;
      |                      ^~~~~~~~~~~~~
In function 'FM_extendSeed',
    inlined from 'p7_SSVFM_longlarget' at fm_ssv.c:806:5:
fm_ssv.c:697:31: warning: 'max_hit_end' may be used uninitialized [-Wmaybe-uninitialized]
  697 |   diag->length  = max_hit_end - max_hit_start + 1;
      |                   ~~~~~~~~~~~~^~~~~~~~~~~~~~~
fm_ssv.c: In function 'p7_SSVFM_longlarget':
fm_ssv.c:648:37: note: 'max_hit_end' was declared here
  648 |   int64_t hit_start, max_hit_start, max_hit_end;
      |                                     ^~~~~~~~~~~
     CC hmmbuild.o
     CC hmmconvert.o
     CC hmmemit.o
     CC hmmfetch.o
     CC hmmpgmd.o
     CC hmmpgmd_shard.o
     CC hmmpress.o
     CC hmmscan.o
     CC hmmsearch.o
     CC hmmsim.o
In function 'output_filter_power',
    inlined from 'output_result' at hmmsim.c:756:38,
    inlined from 'serial_master' at hmmsim.c:384:11,
    inlined from 'main' at hmmsim.c:248:7:
hmmsim.c:902:25: warning: 'mu' may be used uninitialized [-Wmaybe-uninitialized]
  902 |                         esl_exp_surv   (scores[i], pmu, plambda));
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hmmsim.c: In function 'main':
hmmsim.c:360:15: note: 'mu' was declared here
  360 |   double      mu, lambda;
      |               ^~
In function 'output_filter_power',
    inlined from 'output_result' at hmmsim.c:756:38,
    inlined from 'serial_master' at hmmsim.c:384:11,
    inlined from 'main' at hmmsim.c:248:7:
hmmsim.c:902:25: warning: 'lambda' may be used uninitialized [-Wmaybe-uninitialized]
  902 |                         esl_exp_surv   (scores[i], pmu, plambda));
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hmmsim.c: In function 'main':
hmmsim.c:360:19: note: 'lambda' was declared here
  360 |   double      mu, lambda;
      |                   ^~~~~~
     CC hmmstat.o
     CC jackhmmer.o
     CC phmmer.o
     CC nhmmer.o
     CC nhmmscan.o
In function 'serial_loop',
    inlined from 'serial_master' at nhmmer.c:1071:35:
nhmmer.c:1386:6: warning: 'dbsq_revcmp' may be used uninitialized [-Wmaybe-uninitialized]
 1386 |   if (dbsq_revcmp) esl_sq_Destroy(dbsq_revcmp);
      |      ^
nhmmer.c: In function 'serial_master':
nhmmer.c:1338:13: note: 'dbsq_revcmp' was declared here
 1338 |   ESL_SQ   *dbsq_revcmp;
      |             ^~~~~~~~~~~
     CC makehmmerdb.o
     CC hmmc2.o
     CC hmmerfm-exactmatch.o
     AR libhmmer-src.stamp
     SUBDIR impl_sse
     CC decoding.o
In file included from /usr/include/stdio.h:906,
                 from ../easel/easel.h:22,
                 from hmmerfm-exactmatch.c:6:
In function 'fprintf',
    inlined from 'output_header' at hmmerfm-exactmatch.c:123:7,
    inlined from 'main' at hmmerfm-exactmatch.c:303:3:
/usr/include/bits/stdio2.h:79:10: warning: 'alph' may be used uninitialized [-Wmaybe-uninitialized]
   79 |   return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   80 |                         __va_arg_pack ());
      |                         ~~~~~~~~~~~~~~~~~
hmmerfm-exactmatch.c: In function 'main':
hmmerfm-exactmatch.c:94:9: note: 'alph' was declared here
   94 |   char *alph;
      |         ^~~~
     CC fwdback.o
     CC io.o
     CC ssvfilter.o
     CC msvfilter.o
     CC null2.o
     CC optacc.o
     CC stotrace.o
optacc.c: In function 'p7_OATrace':
optacc.c:255:21: warning: 'smax' may be used uninitialized [-Wmaybe-uninitialized]
  255 |       if ((status = p7_trace_AppendWithPP(tr, s1, k, i, postprob)) != eslOK) return status;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
optacc.c:398:10: note: 'smax' was declared here
  398 |   int    smax, kmax;
      |          ^~~~
In function 'get_postprob',
    inlined from 'p7_OATrace' at optacc.c:254:18:
optacc.c:269:21: warning: 'kmax' may be used uninitialized [-Wmaybe-uninitialized]
  269 |   int     q     = (k-1) % Q;            /* (q,r) is position of the current DP cell M(i,k) */
      |                   ~~^~~
optacc.c: In function 'p7_OATrace':
optacc.c:398:16: note: 'kmax' was declared here
  398 |   int    smax, kmax;
      |                ^~~~
     CC vitfilter.o
     CC p7_omx.o
     CC p7_oprofile.o
     CC mpi.o
     AR libhmmer-impl.stamp
     GEN alimask
     GEN hmmalign
     GEN hmmbuild
     GEN hmmconvert
     GEN hmmemit
     GEN hmmfetch
     GEN hmmlogo
     GEN hmmpgmd
     GEN hmmpgmd_shard
     GEN hmmpress
     GEN hmmscan
     GEN hmmsearch
     GEN hmmsim
     GEN hmmstat
     GEN jackhmmer
     GEN phmmer
     GEN nhmmer
     GEN nhmmscan
     GEN makehmmerdb
     GEN hmmc2
     GEN hmmerfm-exactmatch
     SUBDIR profmark
     CC create-profmark.o
     CC rocplot.o
In file included from /usr/include/stdio.h:906,
                 from create-profmark.c:18:
In function 'fprintf',
    inlined from 'main' at create-profmark.c:258:4:
/usr/include/bits/stdio2.h:79:10: warning: 'nfrags' may be used uninitialized [-Wmaybe-uninitialized]
   79 |   return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   80 |                         __va_arg_pack ());
      |                         ~~~~~~~~~~~~~~~~~
create-profmark.c: In function 'main':
create-profmark.c:167:17: note: 'nfrags' was declared here
  167 |   int           nfrags;         /* # of fragments removed          */
      |                 ^~~~~~
In function 'synthesize_positives',
    inlined from 'main' at create-profmark.c:253:4:
create-profmark.c:536:27: warning: 'j' may be used uninitialized [-Wmaybe-uninitialized]
  536 |           memcpy(sq->dsq+j+d1n+1, domain2->dsq+1, sizeof(ESL_DSQ) * d2n);
      |                           ^
create-profmark.c: In function 'main':
create-profmark.c:445:13: note: 'j' was declared here
  445 |   int     i,j;
      |             ^
     GEN rocplot
     GEN create-profmark
../easel/esl_ssi.h:115:13: warning: type of 'esl_ssi_FindNumber' does not match original declaration [-Wlto-type-mismatch]
  115 | extern int  esl_ssi_FindNumber(ESL_SSI *ssi, int64_t nkey,
      |             ^
../easel/esl_ssi.c:253:1: note: 'esl_ssi_FindNumber' was previously declared here
  253 | esl_ssi_FindNumber(ESL_SSI *ssi, int64_t nkey, uint16_t *opt_fh, off_t *opt_roff, off_t *opt_doff, int64_t *opt_L, char **opt_pkey)
      | ^
../easel/esl_ssi.c:253:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.U6tbqy
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386
++ dirname /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd hmmer-3.3.2
+ rm -rf /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386
+ make install DESTDIR=/builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386
     SUBDIR easel
     SUBDIR miniapps
     SUBDIR libdivsufsort
     SUBDIR src
     SUBDIR impl_sse
     SUBDIR profmark
/usr/bin/install -c -d /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin
/usr/bin/install -c -d /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/share/man/man1
make -C src install
make[1]: Entering directory '/builddir/build/BUILD/hmmer-3.3.2/src'
for file in alimask hmmalign hmmbuild hmmconvert hmmemit hmmfetch hmmlogo hmmpgmd hmmpgmd_shard hmmpress hmmscan hmmsearch hmmsim hmmstat jackhmmer phmmer nhmmer nhmmscan makehmmerdb; do \
   /usr/bin/install -c -m 0755 $file /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/ ;\
done
make[1]: Leaving directory '/builddir/build/BUILD/hmmer-3.3.2/src'
make -C documentation install
make[1]: Entering directory '/builddir/build/BUILD/hmmer-3.3.2/documentation'
make -C man install
make[2]: Entering directory '/builddir/build/BUILD/hmmer-3.3.2/documentation/man'
for file in hmmer hmmalign hmmbuild hmmc2 hmmconvert hmmemit hmmfetch hmmlogo hmmpgmd hmmpgmd_shard hmmpress hmmscan hmmsearch hmmsim hmmstat jackhmmer makehmmerdb phmmer nhmmer nhmmscan alimask; do \
   /usr/bin/install -c -m 0664 $file.man /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/share/man/man1/${file}.1 ;\
done
make[2]: Leaving directory '/builddir/build/BUILD/hmmer-3.3.2/documentation/man'
make[1]: Leaving directory '/builddir/build/BUILD/hmmer-3.3.2/documentation'
+ cd easel
+ make install DESTDIR=/builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386
/usr/bin/install -c -d /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin
/usr/bin/install -c -d /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/share/man/man1
make -C miniapps install
make[1]: Entering directory '/builddir/build/BUILD/hmmer-3.3.2/easel/miniapps'
/usr/bin/install -c -m 0755 easel /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/
for file in esl-afetch esl-alimanip esl-alimap esl-alimask esl-alimerge esl-alipid esl-alirev esl-alistat esl-compalign esl-compstruct esl-construct esl-histplot esl-mask esl-mixdchlet esl-reformat esl-selectn esl-seqrange esl-seqstat esl-sfetch esl-shuffle esl-ssdraw esl-translate esl-weight; do \
   /usr/bin/install -c -m 0755 $file /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/ ;\
done
for file in esl-afetch esl-alimanip esl-alimap esl-alimask esl-alimerge esl-alipid esl-alirev esl-alistat esl-compalign esl-compstruct esl-construct esl-histplot esl-mask esl-mixdchlet esl-reformat esl-selectn esl-seqrange esl-seqstat esl-sfetch esl-shuffle esl-ssdraw esl-translate esl-weight; do \
   /usr/bin/install -c -m 0644 $file.man /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/share/man/man1/${file}.1 ;\
done
make[1]: Leaving directory '/builddir/build/BUILD/hmmer-3.3.2/easel/miniapps'
+ /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 3.3.2-2.fc38 --unique-debug-suffix -3.3.2-2.fc38.i386 --unique-debug-src-base hmmer-3.3.2-2.fc38.i386 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/hmmer-3.3.2
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/alimask
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/easel
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-afetch
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-alimanip
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-alimap
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-alimask
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-alimerge
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-alipid
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-alirev
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-alistat
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-compalign
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-compstruct
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-construct
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-histplot
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-mask
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-mixdchlet
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-reformat
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-selectn
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-seqrange
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-seqstat
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-sfetch
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-shuffle
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-ssdraw
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-translate
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-weight
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/hmmalign
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/hmmbuild
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/hmmconvert
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/hmmemit
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/hmmfetch
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/hmmlogo
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/hmmpgmd
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/hmmpgmd_shard
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/hmmpress
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/hmmscan
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/hmmsearch
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/hmmsim
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/hmmstat
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/jackhmmer
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/makehmmerdb
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/nhmmer
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/nhmmscan
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/phmmer
original debug info size: 36644kB, size after compression: 27936kB
/usr/bin/sepdebugcrcfix: Updated 43 CRC32s, 0 CRC32s did match.
13596 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
+ /usr/lib/rpm/brp-remove-la-files
+ /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0
+ /usr/lib/rpm/redhat/brp-python-hardlink
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.5MT71l
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd hmmer-3.3.2
+ make check
     SUBDIR easel
     GEN easel_utest
./easel.c: In function 'esl_fail':
./easel.c:79:12: warning: 'ap' may be used uninitialized [-Wmaybe-uninitialized]
   79 |       else vsyslog(LOG_ERR, format, ap); // SRE: TODO: check this.
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
./easel.c:69:15: note: 'ap' was declared here
   69 |       va_list ap;
      |               ^~
./easel.c: In function 'esl_exception':
./easel.c:157:12: warning: 'argp' may be used uninitialized [-Wmaybe-uninitialized]
  157 |       else vsyslog(LOG_ERR, format, argp);
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./easel.c:131:11: note: 'argp' was declared here
  131 |   va_list argp;
      |           ^~~~
./easel.c: In function 'esl_fatal':
./easel.c:308:8: warning: 'argp' may be used uninitialized [-Wmaybe-uninitialized]
  308 |   else vsyslog(LOG_ERR, format, argp);
      |        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./easel.c:295:11: note: 'argp' was declared here
  295 |   va_list argp;
      |           ^~~~
     GEN esl_alloc_utest
     GEN esl_alphabet_utest
     GEN esl_bitfield_utest
     GEN esl_buffer_utest
     GEN esl_cluster_utest
     GEN esl_cpu_utest
     GEN esl_dirichlet_utest
     GEN esl_distance_utest
     GEN esl_dmatrix_utest
     GEN esl_dsqdata_utest
     GEN esl_exponential_utest
     GEN esl_fileparser_utest
     GEN esl_gamma_utest
     GEN esl_gencode_utest
     GEN esl_getopts_utest
     GEN esl_graph_utest
     GEN esl_gumbel_utest
     GEN esl_heap_utest
     GEN esl_histogram_utest
     GEN esl_hmm_utest
     GEN esl_huffman_utest
     GEN esl_hyperexp_utest
     GEN esl_json_utest
./esl_json.c: In function 'esl_json_Validate':
./esl_json.c:752:33: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  752 |           case eslJSON_BOOLEAN: if (! esl_memstrcmp(bf->mem + pos1, pos2-pos1+1, "true")  &&
      |                                 ^~
./esl_json.c:753:167: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  753 |                                     ! esl_memstrcmp(bf->mem + pos1, pos2-pos1+1, "false"))   ESL_FAIL(eslFAIL, errbuf, "boolean isn't a boolean, tok %d",         i); break;
      |                                                                                                                                                                       ^~~~~
     GEN esl_keyhash_utest
In function 'utest_stringkeys',
    inlined from 'main' at ./esl_keyhash.c:875:3:
./esl_keyhash.c:786:54: warning: 'h42' may be used uninitialized [-Wmaybe-uninitialized]
  786 |   if ( esl_keyhash_Lookup(kh, "XX", -1, &h) != eslOK || h != h42) esl_fatal(msg);
      |        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
./esl_keyhash.c: In function 'main':
./esl_keyhash.c:749:25: note: 'h42' was declared here
  749 |   int             i,j,h,h42;
      |                         ^~~
In function 'utest_memkeys',
    inlined from 'main' at ./esl_keyhash.c:876:3:
./esl_keyhash.c:835:62: warning: 'h42' may be used uninitialized [-Wmaybe-uninitialized]
  835 |   if ( esl_keyhash_Lookup(kh, keys[42], keylen, &h) != eslOK || h != h42) esl_fatal(msg);
      |        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
./esl_keyhash.c: In function 'main':
./esl_keyhash.c:812:23: note: 'h42' was declared here
  812 |   int             i,h,h42;
      |                       ^~~
     GEN esl_matrixops_utest
     GEN esl_mem_utest
     GEN esl_minimizer_utest
./esl_minimizer.c: In function 'esl_min_ConjugateGradientDescent':
./esl_minimizer.c:243:23: warning: 'fx' may be used uninitialized [-Wmaybe-uninitialized]
  243 |   if (opt_fx) *opt_fx = fx;
      |               ~~~~~~~~^~~~
./esl_minimizer.c:119:10: note: 'fx' was declared here
  119 |   double fx;
      |          ^~
In function 'brent',
    inlined from 'esl_min_ConjugateGradientDescent' at ./esl_minimizer.c:192:7:
./esl_minimizer.c:720:21: warning: 'ax' may be used uninitialized [-Wmaybe-uninitialized]
  720 |       m   = 0.5 * (a+b);
      |                   ~~^~~
./esl_minimizer.c: In function 'esl_min_ConjugateGradientDescent':
./esl_minimizer.c:118:10: note: 'ax' was declared here
  118 |   double ax,bx,cx;
      |          ^~
In function 'brent',
    inlined from 'esl_min_ConjugateGradientDescent' at ./esl_minimizer.c:192:7:
./esl_minimizer.c:720:21: warning: 'cx' may be used uninitialized [-Wmaybe-uninitialized]
  720 |       m   = 0.5 * (a+b);
      |                   ~~^~~
./esl_minimizer.c: In function 'esl_min_ConjugateGradientDescent':
./esl_minimizer.c:118:16: note: 'cx' was declared here
  118 |   double ax,bx,cx;
      |                ^~
     GEN esl_mixdchlet_utest
     GEN esl_msa_utest
     GEN esl_msacluster_utest
     GEN esl_msafile_utest
     GEN esl_msafile2_utest
     GEN esl_msafile_a2m_utest
     GEN esl_msafile_afa_utest
     GEN esl_msafile_clustal_utest
./esl_msafile_clustal.c: In function 'esl_msafile_clustal_Read':
./esl_msafile_clustal.c:247:12: warning: 'block_seq_start' may be used uninitialized [-Wmaybe-uninitialized]
  247 |         if (seq_start != block_seq_start) ESL_XFAIL(eslEFORMAT, afp->errmsg, "sequence start is misaligned");
      |            ^
./esl_msafile_clustal.c:203:13: note: 'block_seq_start' was declared here
  203 |   esl_pos_t block_seq_start, block_seq_len;
      |             ^~~~~~~~~~~~~~~
./esl_msafile_clustal.c:248:12: warning: 'block_seq_len' may be used uninitialized [-Wmaybe-uninitialized]
  248 |         if (seq_len   != block_seq_len)   ESL_XFAIL(eslEFORMAT, afp->errmsg, "sequence end is misaligned");
      |            ^
./esl_msafile_clustal.c:203:30: note: 'block_seq_len' was declared here
  203 |   esl_pos_t block_seq_start, block_seq_len;
      |                              ^~~~~~~~~~~~~
     GEN esl_msafile_phylip_utest
In function 'phylip_check_interleaved',
    inlined from 'esl_msafile_phylip_CheckFileFormat' at ./esl_msafile_phylip.c:389:13:
./esl_msafile_phylip.c:739:16: warning: 'nres1' may be used uninitialized [-Wmaybe-uninitialized]
  739 |       if (nres1+nres2 == alen) break;
      |           ~~~~~^~~~~~
./esl_msafile_phylip.c: In function 'esl_msafile_phylip_CheckFileFormat':
./esl_msafile_phylip.c:687:13: note: 'nres1' was declared here
  687 |   int       nres1;
      |             ^~~~~
In function 'phylip_deduce_namewidth',
    inlined from 'phylip_check_interleaved' at ./esl_msafile_phylip.c:747:22,
    inlined from 'esl_msafile_phylip_CheckFileFormat' at ./esl_msafile_phylip.c:389:13:
./esl_msafile_phylip.c:1048:10: warning: 'ncols0' may be used uninitialized [-Wmaybe-uninitialized]
 1048 |   for (c = ncols0-1; nres1 && c >= 0; c--)
      |        ~~^~~~~~~~~~
./esl_msafile_phylip.c: In function 'esl_msafile_phylip_CheckFileFormat':
./esl_msafile_phylip.c:683:20: note: 'ncols0' was declared here
  683 |   int       ncols, ncols0;
      |                    ^~~~~~
     GEN esl_msafile_psiblast_utest
./esl_msafile_psiblast.c: In function 'esl_msafile_psiblast_Read':
./esl_msafile_psiblast.c:228:12: warning: 'block_seq_start' may be used uninitialized [-Wmaybe-uninitialized]
  228 |         if (seq_start != block_seq_start) ESL_XFAIL(eslEFORMAT, afp->errmsg, "sequence start is misaligned");
      |            ^
./esl_msafile_psiblast.c:195:13: note: 'block_seq_start' was declared here
  195 |   esl_pos_t block_seq_start, block_seq_len;
      |             ^~~~~~~~~~~~~~~
./esl_msafile_psiblast.c:229:12: warning: 'block_seq_len' may be used uninitialized [-Wmaybe-uninitialized]
  229 |         if (seq_len   != block_seq_len)   ESL_XFAIL(eslEFORMAT, afp->errmsg, "sequence end is misaligned");
      |            ^
./esl_msafile_psiblast.c:195:30: note: 'block_seq_len' was declared here
  195 |   esl_pos_t block_seq_start, block_seq_len;
      |                              ^~~~~~~~~~~~~
     GEN esl_msafile_selex_utest
     GEN esl_msafile_stockholm_utest
     GEN esl_msaweight_utest
./esl_msaweight.c: In function 'esl_msaweight_IDFilter_adv':
./esl_msaweight.c:1035:9: warning: 'conscols_112' may be used uninitialized [-Wmaybe-uninitialized]
 1035 |         collect_counts(cfg, msa, conscols, ncons, ct, NULL);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./esl_msaweight.c:435:1: note: by argument 3 of type 'const int *' to 'collect_counts.isra.0' declared here
  435 | collect_counts(const ESL_MSAWEIGHT_CFG *cfg, const ESL_MSA *msa, const int *conscols, int ncons, int **ct, ESL_MSAWEIGHT_DAT *dat)
      | ^~~~~~~~~~~~~~
     GEN esl_normal_utest
     GEN esl_quicksort_utest
     GEN esl_random_utest
     GEN esl_rand64_utest
     GEN esl_randomseq_utest
     GEN esl_ratematrix_utest
     GEN esl_red_black_utest
In function 'esl_red_black_doublekey_linked_list_test',
    inlined from 'main' at ./esl_red_black.c:702:8:
./esl_red_black.c:563:5: warning: 'prev' may be used uninitialized [-Wmaybe-uninitialized]
  563 |   if(prev != head_ptr){
      |     ^
./esl_red_black.c: In function 'main':
./esl_red_black.c:546:28: note: 'prev' was declared here
  546 |   ESL_RED_BLACK_DOUBLEKEY *prev;
      |                            ^~~~
     GEN esl_recorder_utest
     GEN esl_regexp_utest
     GEN esl_rootfinder_utest
     GEN esl_scorematrix_utest
     GEN esl_sq_utest
     GEN esl_sqio_utest
     GEN esl_ssi_utest
     GEN esl_stack_utest
     GEN esl_stats_utest
     GEN esl_stretchexp_utest
     GEN esl_tree_utest
     GEN esl_varint_utest
./esl_varint.c: In function 'esl_varint_google_decode':
./esl_varint.c:474:11: warning: 'grp' may be used uninitialized [-Wmaybe-uninitialized]
  474 |   if (grp & cmask) { status = eslEOD; goto ERROR; }
      |       ~~~~^~~~~~~
./esl_varint.c:464:12: note: 'grp' was declared here
  464 |   uint64_t grp;                     // current k-bit code group
      |            ^~~
     GEN esl_vectorops_utest
     GEN esl_weibull_utest
     GEN esl_wuss_utest
./esl_wuss.c: In function 'esl_wuss2ct':
./esl_wuss.c:136:10: warning: 'status' may be used uninitialized [-Wmaybe-uninitialized]
  136 |   return status;
      |          ^~~~~~
./esl_wuss.c:56:14: note: 'status' was declared here
   56 |   int        status;      /* success or failure return status */
      |              ^~~~~~
     GEN esl_sse_utest
     GEN esl_avx_utest
     GEN esl_avx512_utest
     GEN esl_neon_utest
     GEN esl_vmx_utest
     SUBDIR miniapps
     SUBDIR libdivsufsort
     SUBDIR src
     SUBDIR impl_sse
     GEN build_utest
     GEN generic_fwdback_utest
     GEN generic_fwdback_chk_utest
     GEN generic_msv_utest
     GEN generic_stotrace_utest
./generic_stotrace.c: In function 'p7_GStochasticTrace':
./generic_stotrace.c:172:21: warning: 'scur' may be used uninitialized [-Wmaybe-uninitialized]
  172 |       if ((status = p7_trace_Append(tr, scur, k, i)) != eslOK) goto ERROR;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./generic_stotrace.c:57:11: note: 'scur' was declared here
   57 |   int     scur, sprv;
      |           ^~~~
     GEN generic_viterbi_utest
     GEN hmmer_utest
     GEN logsum_utest
     GEN modelconfig_utest
     GEN seqmodel_utest
     GEN p7_alidisplay_utest
     GEN p7_bg_utest
     GEN p7_domain_utest
./p7_domain.c: In function 'p7_domain_Serialize':
./p7_domain.c:191:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  191 |   network_32bit = esl_hton32(*((uint32_t *) &(obj->envsc)));  // ow, this hurts, but is probably the best way to get the
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_domain.c:198:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  198 |   network_32bit = esl_hton32(*((uint32_t *) &(obj->domcorrection)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_domain.c:203:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  203 |   network_32bit = esl_hton32(*((uint32_t *) &(obj->dombias)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_domain.c:208:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  208 |   network_32bit = esl_hton32(*((uint32_t *) &(obj->oasc)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_domain.c:213:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  213 |   network_32bit = esl_hton32(*((uint32_t *) &(obj->bitscore)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_domain.c:218:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  218 |   network_64bit = esl_hton64(*((uint64_t *) &(obj->lnP)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~
./p7_domain.c: In function 'p7_domain_Deserialize':
./p7_domain.c:341:22: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  341 |   ret_obj->envsc = *((float *) &host_32bit);
      |                     ~^~~~~~~~~~~~~~~~~~~~~~
./p7_domain.c:347:30: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  347 |   ret_obj->domcorrection = *((float *) &host_32bit);
      |                             ~^~~~~~~~~~~~~~~~~~~~~~
./p7_domain.c:353:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  353 |   ret_obj->dombias = *((float *) &host_32bit);
      |                       ~^~~~~~~~~~~~~~~~~~~~~~
./p7_domain.c:359:21: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  359 |   ret_obj->oasc = *((float *) &host_32bit);
      |                    ~^~~~~~~~~~~~~~~~~~~~~~
./p7_domain.c:365:25: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  365 |   ret_obj->bitscore = *((float *) &host_32bit);
      |                        ~^~~~~~~~~~~~~~~~~~~~~~
./p7_domain.c:371:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  371 |   ret_obj->lnP = *((double *) &host_64bit);
      |                   ~^~~~~~~~~~~~~~~~~~~~~~~
./p7_domain.c:398:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  398 |       ret_obj->scores_per_pos[i] = *((float *) &host_32bit);
      |                                     ~^~~~~~~~~~~~~~~~~~~~~~
     GEN p7_gmx_utest
     GEN p7_gmxchk_utest
     GEN p7_hit_utest
./p7_hit.c: In function 'p7_hit_Serialize':
./p7_hit.c:226:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  226 |   network_64bit = esl_hton64(*((uint64_t *) &(obj->sortkey)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c:231:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  231 |   network_32bit = esl_hton32(*((uint32_t *) &(obj->score)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c:236:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  236 |   network_32bit = esl_hton32(*((uint32_t *) &(obj->pre_score)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c:241:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  241 |   network_32bit = esl_hton32(*((uint32_t *) &(obj->sum_score)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c:246:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  246 |   network_64bit = esl_hton64(*((uint64_t *) &(obj->lnP)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c:251:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  251 |   network_64bit = esl_hton64(*((uint64_t *) &(obj->pre_lnP)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c:256:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  256 |   network_64bit = esl_hton64(*((uint64_t *) &(obj->sum_lnP)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c:261:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  261 |   network_32bit = esl_hton32(*((uint32_t *) &(obj->nexpected)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c: In function 'p7_hit_Deserialize':
./p7_hit.c:408:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  408 |   ret_obj->sortkey = *((double *) &host_64bit);
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c:414:22: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  414 |   ret_obj->score = *((float *) &host_32bit);
      |                     ~^~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c:420:26: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  420 |   ret_obj->pre_score = *((float *) &host_32bit);
      |                         ~^~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c:426:26: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  426 |   ret_obj->sum_score = *((float *) &host_32bit);
      |                         ~^~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c:432:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  432 |   ret_obj->lnP = *((double *) &host_64bit);
      |                   ~^~~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c:438:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  438 |   ret_obj->pre_lnP = *((double *) &host_64bit);
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c:444:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  444 |   ret_obj->sum_lnP = *((double *) &host_64bit);
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c:450:26: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  450 |   ret_obj->nexpected = *((float *) &host_32bit);
      |                         ~^~~~~~~~~~~~~~~~~~~~~~
     GEN p7_hmmd_search_stats_utest
./p7_hmmd_search_stats.c: In function 'p7_hmmd_search_stats_Serialize':
./p7_hmmd_search_stats.c:89:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   89 |   network_64bit = esl_hton64(*((uint64_t *) &(obj->elapsed)));  // ow, this hurts, but is probably the best way to get the
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_hmmd_search_stats.c:97:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   97 |   network_64bit = esl_hton64(*((uint64_t *) &(obj->user)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_hmmd_search_stats.c:103:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  103 |   network_64bit = esl_hton64(*((uint64_t *) &(obj->sys)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~
./p7_hmmd_search_stats.c:109:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  109 |   network_64bit = esl_hton64(*((uint64_t *) &(obj->Z)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~
./p7_hmmd_search_stats.c:115:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  115 |   network_64bit = esl_hton64(*((uint64_t *) &(obj->domZ)));
      |                               ~^~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_hmmd_search_stats.c: In function 'p7_hmmd_search_stats_Deserialize':
./p7_hmmd_search_stats.c:256:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  256 |   ret_obj->elapsed = *((double *) &host_64bit);
      |                       ~^~~~~~~~~~~~~~~~~~~~~~~
./p7_hmmd_search_stats.c:262:21: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  262 |   ret_obj->user = *((double *) &host_64bit);
      |                    ~^~~~~~~~~~~~~~~~~~~~~~~
./p7_hmmd_search_stats.c:268:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  268 |   ret_obj->sys = *((double *) &host_64bit);
      |                   ~^~~~~~~~~~~~~~~~~~~~~~~
./p7_hmmd_search_stats.c:274:18: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  274 |   ret_obj->Z = *((double *) &host_64bit);
      |                 ~^~~~~~~~~~~~~~~~~~~~~~~
./p7_hmmd_search_stats.c:280:21: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  280 |   ret_obj->domZ = *((double *) &host_64bit);
      |                    ~^~~~~~~~~~~~~~~~~~~~~~~
     GEN p7_hmm_utest
     GEN p7_hmmfile_utest
     GEN p7_profile_utest
     GEN p7_tophits_utest
In file included from /usr/include/stdio.h:906,
                 from ../easel/easel.h:22,
                 from ./p7_tophits.c:16:
In function 'fprintf',
    inlined from 'p7_tophits_Targets' at ./p7_tophits.c:1142:12:
/usr/include/bits/stdio2.h:79:10: warning: 'posw' may be used uninitialized [-Wmaybe-uninitialized]
   79 |   return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   80 |                         __va_arg_pack ());
      |                         ~~~~~~~~~~~~~~~~~
./p7_tophits.c: In function 'p7_tophits_Targets':
./p7_tophits.c:1068:10: note: 'posw' was declared here
 1068 |   int    posw;
      |          ^~~~
./p7_tophits.c: In function 'main':
./p7_tophits.c:2171:3: warning: 'key' may be used uninitialized [-Wmaybe-uninitialized]
 2171 |   p7_tophits_Add(h1, "last",  NULL, NULL, -1.0, (float) key, key, (float) key, key, i, i, N, i, i, N, 1, 1, NULL);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_tophits.c:2155:19: note: 'key' was declared here
 2155 |   double          key;
      |                   ^~~
     GEN p7_trace_utest
     GEN p7_scoredata_utest
     GEN hmmpgmd2msa_utest
     GEN hmmd_search_status_utest
     CC itest_brute.o
     GEN itest_brute
     SUBDIR impl_sse
     GEN decoding_utest
     GEN fwdback_utest
     GEN io_utest
     GEN msvfilter_utest
     GEN null2_utest
     GEN optacc_utest
./optacc.c: In function 'p7_OATrace':
./optacc.c:255:21: warning: 'smax' may be used uninitialized [-Wmaybe-uninitialized]
  255 |       if ((status = p7_trace_AppendWithPP(tr, s1, k, i, postprob)) != eslOK) return status;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./optacc.c:398:10: note: 'smax' was declared here
  398 |   int    smax, kmax;
      |          ^~~~
In function 'get_postprob',
    inlined from 'p7_OATrace' at ./optacc.c:254:18:
./optacc.c:269:21: warning: 'kmax' may be used uninitialized [-Wmaybe-uninitialized]
  269 |   int     q     = (k-1) % Q;            /* (q,r) is position of the current DP cell M(i,k) */
      |                   ~~^~~
./optacc.c: In function 'p7_OATrace':
./optacc.c:398:16: note: 'kmax' was declared here
  398 |   int    smax, kmax;
      |                ^~~~
     GEN stotrace_utest
     GEN vitfilter_utest
     SUBDIR easel
     SUBDIR miniapps
     SUBDIR testsuite
Running Easel test suite...
    exercise    1 [          easel-utest] ...     ok.
    exercise    2 [          alloc-utest] ...     ok.
    exercise    3 [       alphabet-utest] ...     ok.
    exercise    4 [            avx-utest] ...     ok.
    exercise    5 [         avx512-utest] ...     ok.
    exercise    6 [       bitfield-utest] ...     ok.
    exercise    7 [         buffer-utest] ...     ok.
    exercise    8 [        cluster-utest] ...     ok.
    exercise    9 [            cpu-utest] ...     ok.
    exercise   10 [      dirichlet-utest] ...     ok.
    exercise   11 [       distance-utest] ...     ok.
    exercise   12 [        dmatrix-utest] ...     ok.
    exercise   13 [        dsqdata-utest] ...     ok.
    exercise   14 [    exponential-utest] ...     ok.
    exercise   15 [     fileparser-utest] ...     ok.
    exercise   16 [          gamma-utest] ...     ok.
    exercise   17 [        gencode-utest] ...     ok.
    exercise   18 [        getopts-utest] ...     ok.
    exercise   19 [          graph-utest] ...     ok.
    exercise   20 [         gumbel-utest] ...     ok.
    exercise   21 [           heap-utest] ...     ok.
    exercise   22 [      histogram-utest] ...     ok.
    exercise   23 [        huffman-utest] ...     ok.
    exercise   24 [       hyperexp-utest] ...     ok.
    exercise   25 [           json-utest] ...     ok.
    exercise   26 [        keyhash-utest] ...     ok.
    exercise   27 [      matrixops-utest] ...     ok.
    exercise   28 [            mem-utest] ...     ok.
    exercise   29 [      minimizer-utest] ...     ok.
    exercise   30 [      mixdchlet-utest] ...     ok.
    exercise   31 [            msa-utest] ...     ok.
    exercise   32 [     msacluster-utest] ...     ok.
    exercise   33 [              msafile] ...     ok.
    exercise   34 [             msafile2] ...     ok.
    exercise   35 [          msafile-a2m] ...     ok.
    exercise   36 [          msafile-afa] ...     ok.
    exercise   37 [      msafile-clustal] ...     ok.
    exercise   38 [       msafile-phylip] ...     ok.
    exercise   39 [     msafile-psiblast] ...     ok.
    exercise   40 [        msafile-selex] ...     ok.
    exercise   41 [    msafile-stockholm] ...     ok.
    exercise   42 [      msaweight-utest] ...     ok.
    exercise   43 [           neon-utest] ...     ok.
    exercise   44 [         normal-utest] ...     ok.
    exercise   45 [      quicksort-utest] ...     ok.
    exercise   46 [         random-utest] ...     ok.
    exercise   47 [         rand64-utest] ...     ok.
    exercise   48 [      randomseq-utest] ...     ok.
    exercise   49 [     ratematrix-utest] ...     ok.
    exercise   50 [       recorder-utest] ...     ok.
    exercise   51 [      red_black-utest] ...     ok.
    exercise   52 [         regexp-utest] ...     ok.
    exercise   53 [     rootfinder-utest] ...     ok.
    exercise   54 [    scorematrix-utest] ...     ok.
    exercise   55 [             sq-utest] ...     ok.
    exercise   56 [           sqio-utest] ...     ok.
    exercise   57 [            sse-utest] ...     ok.
    exercise   58 [            ssi-utest] ...     ok.
    exercise   59 [          stack-utest] ...     ok.
    exercise   60 [          stats-utest] ...     ok.
    exercise   61 [     stretchexp-utest] ...     ok.
    exercise   62 [           tree-utest] ...     ok.
    exercise   63 [         varint-utest] ...     ok.
    exercise   64 [      vectorops-utest] ...     ok.
    exercise   65 [            vmx-utest] ...     ok.
    exercise   66 [        weibull-utest] ...     ok.
    exercise   67 [           wuss-utest] ...     ok.
    exercise   68 [                   e2] ...     ok.
    exercise   69 [       degen-residues] ...     ok.
    exercise   70 [         ncbi-indices] ...     ok.
    exercise   71 [             blank-gf] ...     ok.
    exercise   72 [        esl-translate] ...     ok.
    exercise   73 [           esl-afetch] ...     ok.
    exercise   74 [         esl-alimanip] ...     ok.
    exercise   75 [           esl-alimap] ...     ok.
    exercise   76 [          esl-alimask] ...     ok.
    exercise   77 [         esl-alimerge] ...     ok.
    exercise   78 [          esl-alistat] ...     ok.
    exercise   79 [        esl-compalign] ...     ok.
    exercise   80 [        esl-construct] ...     ok.
    exercise   81 [             esl-mask] ...     ok.
    exercise   82 [         esl-seqrange] ...     ok.
    exercise   83 [          esl-shuffle] ...     ok.
    exercise   84 [           esl-ssdraw] ...     ok.
All 84 exercises at level <= 2 passed.
System information:
Wed Dec 28 23:01:46 UTC 2022
Linux 94345065f58f4600a254cefdce73771a 6.0.8-300.fc37.x86_64 #1 SMP PREEMPT_DYNAMIC Fri Nov 11 15:09:04 UTC 2022 i686 GNU/Linux
     SUBDIR testsuite
Running HMMER test suite...
    exercise    1 [                hmmer] ...     ok.
    exercise    2 [                build] ...     ok.
    exercise    3 [      generic_fwdback] ...     ok.
    exercise    4 [          generic_msv] ...     ok.
    exercise    5 [     generic_stotrace] ...     ok.
    exercise    6 [      generic_viterbi] ...     ok.
    exercise    7 [   hmmd_search_status] ...     ok.
    exercise    8 [               logsum] ...     ok.
    exercise    9 [          modelconfig] ...     ok.
    exercise   10 [             seqmodel] ...     ok.
    exercise   11 [        p7_alidisplay] ...     ok.
    exercise   12 [                p7_bg] ...     ok.
    exercise   13 [            p7_domain] ...     ok.
    exercise   14 [               p7_gmx] ...     ok.
    exercise   15 [               p7_hit] ...     ok.
    exercise   16 [               p7_hmm] ...     ok.
    exercise   17 [           p7_hmmfile] ...     ok.
    exercise   18 [ p7_hmmd_search_stats] ...     ok.
    exercise   19 [           p7_profile] ...     ok.
    exercise   20 [           p7_tophits] ...     ok.
    exercise   21 [             p7_trace] ...     ok.
    exercise   22 [         p7_scoredata] ...     ok.
    exercise   23 [             decoding] ...     ok.
    exercise   24 [              fwdback] ...     ok.
    exercise   25 [                   io] ...     ok.
    exercise   26 [            msvfilter] ...     ok.
    exercise   27 [                null2] ...     ok.
    exercise   28 [               optacc] ...     ok.
    exercise   29 [             stotrace] ...     ok.
    exercise   30 [            vitfilter] ...     ok.
    exercise   31 [          hmmpgmd2msa] ...     ok.
    exercise   32 [             hmmalign] ...     ok.
    exercise   33 [          hmmalign/-h] ...     ok.
    exercise   34 [          hmmalign/-o] ...     ok.
    exercise   35 [    hmmalign/--mapali] ...     ok.
    exercise   36 [      hmmalign/--trim] ...     ok.
    exercise   37 [     hmmalign/--amino] ...     ok.
    exercise   38 [  hmmalign/--informat] ...     ok.
    exercise   39 [ hmmalign/--outformat] ...     ok.
    exercise   40 [             hmmbuild] ...     ok.
    exercise   41 [             build/-h] ...     ok.
    exercise   42 [             build/-n] ...     ok.
    exercise   43 [             build/-o] ...     ok.
    exercise   44 [             build/-O] ...     ok.
    exercise   45 [        build/--amino] ...     ok.
    exercise   46 [          build/--dna] ...     ok.
    exercise   47 [          build/--rna] ...     ok.
    exercise   48 [         build/--fast] ...     ok.
    exercise   49 [         build/--hand] ...     ok.
    exercise   50 [      build/--symfrac] ...     ok.
    exercise   51 [   build/--fragthresh] ...     ok.
    exercise   52 [          build/--wpb] ...     ok.
    exercise   53 [         build/--wgsc] ...     ok.
    exercise   54 [      build/--wblosum] ...     ok.
    exercise   55 [        build/--wnone] ...     ok.
    exercise   56 [          build/--wid] ...     ok.
    exercise   57 [         build/--eent] ...     ok.
    exercise   58 [       build/--eclust] ...     ok.
    exercise   59 [        build/--enone] ...     ok.
    exercise   60 [         build/--eset] ...     ok.
    exercise   61 [          build/--ere] ...     ok.
    exercise   62 [       build/--esigma] ...     ok.
    exercise   63 [          build/--eid] ...     ok.
    exercise   64 [        build/--pnone] ...     ok.
    exercise   65 [     build/--plaplace] ...     ok.
    exercise   66 [          build/--EmL] ...     ok.
    exercise   67 [          build/--EmN] ...     ok.
    exercise   68 [          build/--EvL] ...     ok.
    exercise   69 [          build/--EvN] ...     ok.
    exercise   70 [          build/--EfL] ...     ok.
    exercise   71 [          build/--EfN] ...     ok.
    exercise   72 [          build/--Eft] ...     ok.
    exercise   73 [     build/--informat] ...     ok.
    exercise   74 [         build/--seed] ...     ok.
    exercise   75 [               search] ...     ok.
    exercise   76 [            search/-h] ...     ok.
    exercise   77 [            search/-o] ...     ok.
    exercise   78 [            search/-A] ...     ok.
    exercise   79 [      search/--tblout] ...     ok.
    exercise   80 [   search/--domtblout] ...     ok.
    exercise   81 [  search/--pfamtblout] ...     ok.
    exercise   82 [         search/--acc] ...     ok.
    exercise   83 [       search/--noali] ...     ok.
    exercise   84 [     search/--notextw] ...     ok.
    exercise   85 [       search/--textw] ...     ok.
    exercise   86 [            search/-E] ...     ok.
    exercise   87 [            search/-T] ...     ok.
    exercise   88 [        search/--domE] ...     ok.
    exercise   89 [        search/--domT] ...     ok.
    exercise   90 [        search/--incE] ...     ok.
    exercise   91 [        search/--incT] ...     ok.
    exercise   92 [     search/--incdomE] ...     ok.
    exercise   93 [     search/--incdomT] ...     ok.
    exercise   94 [      search/--cut_ga] ...     ok.
    exercise   95 [      search/--cut_nc] ...     ok.
    exercise   96 [      search/--cut_tc] ...     ok.
    exercise   97 [         search/--max] ...     ok.
    exercise   98 [          search/--F1] ...     ok.
    exercise   99 [          search/--F2] ...     ok.
    exercise  100 [          search/--F3] ...     ok.
    exercise  101 [      search/--nobias] ...     ok.
    exercise  102 [     search/--nonull2] ...     ok.
    exercise  103 [            search/-Z] ...     ok.
    exercise  104 [        search/--domZ] ...     ok.
    exercise  105 [        search/--seed] ...     ok.
    exercise  106 [     search/--tformat] ...     ok.
    exercise  107 [              hmmscan] ...     ok.
    exercise  108 [              scan/-h] ...     ok.
    exercise  109 [              scan/-o] ...     ok.
    exercise  110 [        scan/--tblout] ...     ok.
    exercise  111 [     scan/--domtblout] ...     ok.
    exercise  112 [    scan/--pfamtblout] ...     ok.
    exercise  113 [           scan/--acc] ...     ok.
    exercise  114 [         scan/--noali] ...     ok.
    exercise  115 [       scan/--notextw] ...     ok.
    exercise  116 [         scan/--textw] ...     ok.
    exercise  117 [              scan/-E] ...     ok.
    exercise  118 [              scan/-T] ...     ok.
    exercise  119 [          scan/--domE] ...     ok.
    exercise  120 [          scan/--domT] ...     ok.
    exercise  121 [          scan/--incE] ...     ok.
    exercise  122 [          scan/--incT] ...     ok.
    exercise  123 [       scan/--incdomE] ...     ok.
    exercise  124 [       scan/--incdomT] ...     ok.
    exercise  125 [       scan/--incdomT] ...     ok.
    exercise  126 [        scan/--cut_ga] ...     ok.
    exercise  127 [        scan/--cut_nc] ...     ok.
    exercise  128 [        scan/--cut_tc] ...     ok.
    exercise  129 [           scan/--max] ...     ok.
    exercise  130 [            scan/--F1] ...     ok.
    exercise  131 [            scan/--F2] ...     ok.
    exercise  132 [            scan/--F3] ...     ok.
    exercise  133 [        scan/--nobias] ...     ok.
    exercise  134 [       scan/--nonull2] ...     ok.
    exercise  135 [              scan/-Z] ...     ok.
    exercise  136 [          scan/--domZ] ...     ok.
    exercise  137 [          scan/--seed] ...     ok.
    exercise  138 [       scan/--qformat] ...     ok.
    exercise  139 [           scan/--cpu] ...     ok.
    exercise  140 [            jackhmmer] ...     ok.
    exercise  141 [                 j/-h] ...     ok.
    exercise  142 [                 j/-N] ...     ok.
    exercise  143 [                 j/-o] ...     ok.
    exercise  144 [                 j/-A] ...     ok.
    exercise  145 [           j/--tblout] ...     ok.
    exercise  146 [        j/--domtblout] ...     ok.
    exercise  147 [           j/--chkhmm] ...     ok.
    exercise  148 [           j/--chkali] ...     ok.
    exercise  149 [              j/--acc] ...     ok.
    exercise  150 [            j/--noali] ...     ok.
    exercise  151 [          j/--notextw] ...     ok.
    exercise  152 [            j/--textw] ...     ok.
    exercise  153 [            j/--popen] ...     ok.
    exercise  154 [          j/--pextend] ...     ok.
    exercise  155 [           j/--mxfile] ...     ok.
    exercise  156 [                 j/-E] ...     ok.
    exercise  157 [                 j/-T] ...     ok.
    exercise  158 [             j/--domE] ...     ok.
    exercise  159 [             j/--domT] ...     ok.
    exercise  160 [             j/--incE] ...     ok.
    exercise  161 [             j/--incT] ...     ok.
    exercise  162 [          j/--incdomE] ...     ok.
    exercise  163 [          j/--incdomT] ...     ok.
    exercise  164 [              j/--max] ...     ok.
    exercise  165 [               j/--F1] ...     ok.
    exercise  166 [               j/--F2] ...     ok.
    exercise  167 [               j/--F3] ...     ok.
    exercise  168 [           j/--nobias] ...     ok.
    exercise  169 [              j/--EmL] ...     ok.
    exercise  170 [              j/--EmN] ...     ok.
    exercise  171 [              j/--EvL] ...     ok.
    exercise  172 [              j/--EvN] ...     ok.
    exercise  173 [              j/--EfL] ...     ok.
    exercise  174 [              j/--EfN] ...     ok.
    exercise  175 [              j/--Eft] ...     ok.
    exercise  176 [          j/--nonull2] ...     ok.
    exercise  177 [                 j/-Z] ...     ok.
    exercise  178 [             j/--domZ] ...     ok.
    exercise  179 [             j/--seed] ...     ok.
    exercise  180 [          j/--qformat] ...     ok.
    exercise  181 [          j/--tformat] ...     ok.
    exercise  182 [               phmmer] ...     ok.
    exercise  183 [            phmmer/-h] ...     ok.
    exercise  184 [            phmmer/-o] ...     ok.
    exercise  185 [            phmmer/-A] ...     ok.
    exercise  186 [      phmmer/--tblout] ...     ok.
    exercise  187 [   phmmer/--domtblout] ...     ok.
    exercise  188 [  phmmer/--pfamtblout] ...     ok.
    exercise  189 [         phmmer/--acc] ...     ok.
    exercise  190 [       phmmer/--noali] ...     ok.
    exercise  191 [     phmmer/--notextw] ...     ok.
    exercise  192 [       phmmer/--textw] ...     ok.
    exercise  193 [       phmmer/--popen] ...     ok.
    exercise  194 [     phmmer/--pextend] ...     ok.
    exercise  195 [      phmmer/--mxfile] ...     ok.
    exercise  196 [            phmmer/-E] ...     ok.
    exercise  197 [            phmmer/-T] ...     ok.
    exercise  198 [        phmmer/--domE] ...     ok.
    exercise  199 [        phmmer/--domT] ...     ok.
    exercise  200 [        phmmer/--incE] ...     ok.
    exercise  201 [        phmmer/--incT] ...     ok.
    exercise  202 [     phmmer/--incdomE] ...     ok.
    exercise  203 [     phmmer/--incdomT] ...     ok.
    exercise  204 [         phmmer/--max] ...     ok.
    exercise  205 [          phmmer/--F1] ...     ok.
    exercise  206 [          phmmer/--F2] ...     ok.
    exercise  207 [          phmmer/--F3] ...     ok.
    exercise  208 [      phmmer/--nobias] ...     ok.
    exercise  209 [         phmmer/--EmL] ...     ok.
    exercise  210 [         phmmer/--EmN] ...     ok.
    exercise  211 [         phmmer/--EvL] ...     ok.
    exercise  212 [         phmmer/--EvN] ...     ok.
    exercise  213 [         phmmer/--EfL] ...     ok.
    exercise  214 [         phmmer/--EfN] ...     ok.
    exercise  215 [         phmmer/--Eft] ...     ok.
    exercise  216 [     phmmer/--nonull2] ...     ok.
    exercise  217 [            phmmer/-Z] ...     ok.
    exercise  218 [        phmmer/--domZ] ...     ok.
    exercise  219 [        phmmer/--seed] ...     ok.
    exercise  220 [     phmmer/--qformat] ...     ok.
    exercise  221 [     phmmer/--tformat] ...     ok.
    exercise  222 [               nhmmer] ...     ok.
    exercise  223 [            nhmmer/-h] ...     ok.
    exercise  224 [            nhmmer/-o] ...     ok.
    exercise  225 [            nhmmer/-A] ...     ok.
    exercise  226 [      nhmmer/--tblout] ...     ok.
    exercise  227 [  nhmmer/--dfamtblout] ...     ok.
    exercise  228 [         nhmmer/--acc] ...     ok.
    exercise  229 [       nhmmer/--noali] ...     ok.
    exercise  230 [     nhmmer/--notextw] ...     ok.
    exercise  231 [       nhmmer/--textw] ...     ok.
    exercise  232 [            nhmmer/-E] ...     ok.
    exercise  233 [            nhmmer/-T] ...     ok.
    exercise  234 [        nhmmer/--incE] ...     ok.
    exercise  235 [        nhmmer/--incT] ...     ok.
    exercise  236 [         nhmmer/--max] ...     ok.
    exercise  237 [          nhmmer/--F1] ...     ok.
    exercise  238 [          nhmmer/--F2] ...     ok.
    exercise  239 [          nhmmer/--F3] ...     ok.
    exercise  240 [      nhmmer/--nobias] ...     ok.
    exercise  241 [     nhmmer/--nonull2] ...     ok.
    exercise  242 [            nhmmer/-Z] ...     ok.
    exercise  243 [        nhmmer/--seed] ...     ok.
    exercise  244 [             nhmmscan] ...     ok.
    exercise  245 [          nhmmscan/-h] ...     ok.
    exercise  246 [          nhmmscan/-o] ...     ok.
    exercise  247 [    nhmmscan/--tblout] ...     ok.
    exercise  248 [nhmmscan/--dfamtblout] ...     ok.
    exercise  249 [       nhmmscan/--acc] ...     ok.
    exercise  250 [     nhmmscan/--noali] ...     ok.
    exercise  251 [   nhmmscan/--notextw] ...     ok.
    exercise  252 [     nhmmscan/--textw] ...     ok.
    exercise  253 [          nhmmscan/-E] ...     ok.
    exercise  254 [          nhmmscan/-T] ...     ok.
    exercise  255 [      nhmmscan/--incE] ...     ok.
    exercise  256 [      nhmmscan/--incT] ...     ok.
    exercise  257 [       nhmmscan/--max] ...     ok.
    exercise  258 [        nhmmscan/--F1] ...     ok.
    exercise  259 [        nhmmscan/--F2] ...     ok.
    exercise  260 [        nhmmscan/--F3] ...     ok.
    exercise  261 [    nhmmscan/--nobias] ...     ok.
    exercise  262 [   nhmmscan/--nonull2] ...     ok.
    exercise  263 [          nhmmscan/-Z] ...     ok.
    exercise  264 [      nhmmscan/--seed] ...     ok.
    exercise  265 [              hmmemit] ...     ok.
    exercise  266 [           hmmemit/-h] ...     ok.
    exercise  267 [           hmmemit/-c] ...     ok.
    exercise  268 [           hmmemit/-o] ...     ok.
    exercise  269 [           hmmemit/-p] ...     ok.
    exercise  270 [           hmmemit/-N] ...     ok.
    exercise  271 [           hmmemit/-L] ...     ok.
    exercise  272 [      hmmemit/--local] ...     ok.
    exercise  273 [   hmmemit/--unilocal] ...     ok.
    exercise  274 [     hmmemit/--glocal] ...     ok.
    exercise  275 [  hmmemit/--uniglocal] ...     ok.
    exercise  276 [             hmmfetch] ...     ok.
    exercise  277 [              hmmstat] ...     ok.
    exercise  278 [              hmmlogo] ...     ok.
    exercise  279 [           hmmconvert] ...     ok.
    exercise  280 [               hmmsim] ...     ok.
    exercise  281 [   hmmbuild_variation] ...     ok.
    exercise  282 [    hmmscan_variation] ...     ok.
    exercise  283 [  hmmsearch_variation] ...     ok.
    exercise  284 [     phmmer_variation] ...     ok.
    exercise  285 [               mapali] ...     ok.
    exercise  286 [            fragments] ...     ok.
    exercise  287 [          nonresidues] ...     ok.
    exercise  288 [       opt-annotation] ...     ok.
    exercise  289 [            dup-names] ...     ok.
    exercise  290 [         mapali-again] ...     ok.
    exercise  291 [    delete-corruption] ...     ok.
    exercise  292 [        msa-integrity] ...     ok.
    exercise  293 [    hmmemit-consensus] ...     ok.
    exercise  294 [           hmmconvert] ...     ok.
    exercise  295 [          stdin_pipes] ...     ok.
    exercise  296 [       nhmmer_generic] ...     ok.
    exercise  297 [           hmmpgmd_ga] ...     ok.
    exercise  298 [               rewind] ...     ok.
    exercise  299 [     hmmpgmd_shard_ga] ...     ok.
    exercise  300 [            bad-fasta] ...     ok.
    exercise  301 [          brute-itest] ...     ok.
    exercise  302 [       hmmpress-itest] ...     ok.
    exercise  303 [                  h39] ...     ok.
    exercise  304 [                  h45] ...     ok.
    exercise  305 [                  h50] ...     ok.
    exercise  306 [                  h82] ...     ok.
    exercise  307 [               iss159] ...     ok.
All 307 exercises at level <= 2 passed.
System information:
Wed Dec 28 23:02:01 UTC 2022
Linux 94345065f58f4600a254cefdce73771a 6.0.8-300.fc37.x86_64 #1 SMP PREEMPT_DYNAMIC Fri Nov 11 15:09:04 UTC 2022 i686 GNU/Linux
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: hmmer-3.3.2-2.fc38.i686
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.rol7VO
+ umask 022
+ cd /builddir/build/BUILD
+ cd hmmer-3.3.2
+ LICENSEDIR=/builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/share/licenses/hmmer
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/share/licenses/hmmer
+ cp -pr LICENSE /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/share/licenses/hmmer
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: hmmer = 3.3.2-2.fc38 hmmer(x86-32) = 3.3.2-2.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libc.so.6 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1) libc.so.6(GLIBC_2.1.3) libc.so.6(GLIBC_2.11) libc.so.6(GLIBC_2.15) libc.so.6(GLIBC_2.17) libc.so.6(GLIBC_2.2) libc.so.6(GLIBC_2.3) libc.so.6(GLIBC_2.3.2) libc.so.6(GLIBC_2.3.4) libc.so.6(GLIBC_2.33) libc.so.6(GLIBC_2.34) libc.so.6(GLIBC_2.4) libm.so.6 libm.so.6(GLIBC_2.0) libm.so.6(GLIBC_2.1) libm.so.6(GLIBC_2.27) libm.so.6(GLIBC_2.29) rtld(GNU_HASH)
Processing files: hmmer-easel-3.3.2-2.fc38.i686
Provides: hmmer-easel = 3.3.2-2.fc38 hmmer-easel(x86-32) = 3.3.2-2.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libc.so.6 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1) libc.so.6(GLIBC_2.1.3) libc.so.6(GLIBC_2.17) libc.so.6(GLIBC_2.2) libc.so.6(GLIBC_2.3) libc.so.6(GLIBC_2.3.2) libc.so.6(GLIBC_2.3.4) libc.so.6(GLIBC_2.33) libc.so.6(GLIBC_2.34) libc.so.6(GLIBC_2.4) libm.so.6 libm.so.6(GLIBC_2.0) libm.so.6(GLIBC_2.1) libm.so.6(GLIBC_2.29) rtld(GNU_HASH)
Processing files: hmmer-doc-3.3.2-2.fc38.noarch
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.Cy3yyX
+ umask 022
+ cd /builddir/build/BUILD
+ cd hmmer-3.3.2
+ DOCDIR=/builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/share/doc/hmmer-doc
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/share/doc/hmmer-doc
+ cp -pr LICENSE /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/share/doc/hmmer-doc
+ cp -pr README.md /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/share/doc/hmmer-doc
+ cp -pr RELEASE-3.3.2.md /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/share/doc/hmmer-doc
+ cp -pr Userguide.pdf /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/share/doc/hmmer-doc
+ cp -pr tutorial/ /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/share/doc/hmmer-doc
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: hmmer-doc = 3.3.2-2.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: hmmer-debugsource-3.3.2-2.fc38.i686
Provides: hmmer-debugsource = 3.3.2-2.fc38 hmmer-debugsource(x86-32) = 3.3.2-2.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: hmmer-debuginfo-3.3.2-2.fc38.i686
Provides: debuginfo(build-id) = 0d5860dfca0dcc171da07ab96116994423bbf432 debuginfo(build-id) = 10bc3942c7030d5a4434034d68a368451872b5a6 debuginfo(build-id) = 180e4beb33d2c829737b78715f33df2d820c81bf debuginfo(build-id) = 256fa8c9205f1e05d00b75a9d27e7ac2666d8609 debuginfo(build-id) = 27f565309fd2180d06bef8a7f8b723cbcea80156 debuginfo(build-id) = 2d0b0922a3fdad9b3828ebf3f50cb7197d9a0096 debuginfo(build-id) = 33e799fac7f4e50a842ab1754cff2911fa7b24bb debuginfo(build-id) = 3b5bb9cc646652a0fdcbefe6f34c13c7b036a1b7 debuginfo(build-id) = 93a48862bfafa45803532f8cad4feebf1d1da072 debuginfo(build-id) = a9a94923042801a8f2b61fb4fa8caca335940524 debuginfo(build-id) = a9c4e712eb4d93e74c3e4ba4ae49550be2dfb022 debuginfo(build-id) = aee1edc1d758dd407b8c14805497ba0cd434213f debuginfo(build-id) = b8d310f4f7a002883fa24dcd4c49c0d84ed08be4 debuginfo(build-id) = ccc16726bc85b97abe017d216dea16725e1a1611 debuginfo(build-id) = d6dc551e0b493ac2b8b7f5ba6ed9e1e23d87cad2 debuginfo(build-id) = e0efc6e1f924b90206373a09931bc65d4ef9087d debuginfo(build-id) = e20e635545217df2330570f891d1bec3b71fc384 debuginfo(build-id) = e296f7ca7e8a95d25612c313233c5aaf9d4390ad debuginfo(build-id) = e91ee0ea1bad90cbfecb3d2b3148aa0cb0e48007 hmmer-debuginfo = 3.3.2-2.fc38 hmmer-debuginfo(x86-32) = 3.3.2-2.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: hmmer-debugsource(x86-32) = 3.3.2-2.fc38
Processing files: hmmer-easel-debuginfo-3.3.2-2.fc38.i686
Provides: debuginfo(build-id) = 0e62924f2a3b0ee11e4d4a57c04f9ca98eacbc58 debuginfo(build-id) = 1609cf9e9710b2eba826e866cc31570167d1a2ab debuginfo(build-id) = 342ad779d75224377c47e7cfe51dda25941915c6 debuginfo(build-id) = 4cbfb41f168636915ec5d6185367a7046fa29c54 debuginfo(build-id) = 51b635bae35993a95d76c1c64e02a8131ff4de0f debuginfo(build-id) = 5bce1313bea0090edcff6abc71d572cd8ac45d1e debuginfo(build-id) = 70147cdde2d2d5d49fdac040543f9ce93ad09553 debuginfo(build-id) = 72fddaf82dab9701e27557c8090f31db7824f30a debuginfo(build-id) = a5a392e7d77bba248bd9505133451370fd5142db debuginfo(build-id) = a651e086f05847120807fca865bfa6e000fa4c08 debuginfo(build-id) = ada1f8fff634468cd28b01770b015875e24d80c8 debuginfo(build-id) = ae39b40b59ed012d61cea58dae4303ee4827a39c debuginfo(build-id) = b882a88ea210cc18d3cf4b630023b5949e45e69c debuginfo(build-id) = ba278c5b6ec79b66e15ad21ee5e16aa63453d191 debuginfo(build-id) = c25d5aeb56d1295337535abbd36e76d46aa84e40 debuginfo(build-id) = c70937173c1d6b87a5e92dbacc166216a192597f debuginfo(build-id) = d7bb6e3acddeb5a39c2868bd3c7fbff6d16c509a debuginfo(build-id) = ea3219bba740cb595dfeb0d1d5bdfdf7e5ebc166 debuginfo(build-id) = ec21b32a87f4ec992ed679a8ddcd1a40640c39d1 debuginfo(build-id) = ee339731fbc6e3e3a134ac410029f8f99f8afd60 debuginfo(build-id) = f0c7f01f24c8f746a9759f11d8ddd8cf13f79976 debuginfo(build-id) = f6681a3bdb72a02d631c686e1b7ac94bb5e829a8 debuginfo(build-id) = fadef7d9d5d3a8b09345e2516bfade78d367f2d9 debuginfo(build-id) = fec7f1f4e5e6912c324b4e3f324a20e7582a6803 hmmer-easel-debuginfo = 3.3.2-2.fc38 hmmer-easel-debuginfo(x86-32) = 3.3.2-2.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: hmmer-debugsource(x86-32) = 3.3.2-2.fc38
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386
Wrote: /builddir/build/RPMS/hmmer-easel-debuginfo-3.3.2-2.fc38.i686.rpm
Wrote: /builddir/build/RPMS/hmmer-debuginfo-3.3.2-2.fc38.i686.rpm
Wrote: /builddir/build/RPMS/hmmer-debugsource-3.3.2-2.fc38.i686.rpm
Wrote: /builddir/build/RPMS/hmmer-3.3.2-2.fc38.i686.rpm
Wrote: /builddir/build/RPMS/hmmer-easel-3.3.2-2.fc38.i686.rpm
Wrote: /builddir/build/RPMS/hmmer-doc-3.3.2-2.fc38.noarch.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.dcqRRi
+ umask 022
+ cd /builddir/build/BUILD
+ cd hmmer-3.3.2
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.julfPh
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf hmmer-3.3.2 hmmer-3.3.2.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0
Child return code was: 0