Mock Version: 6.1
Mock Version: 6.1
Mock Version: 6.1
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target x86_64 --nodeps /builddir/build/SPECS/hmmer.spec'], chrootPath='/var/lib/mock/f43-build-59056405-6570729/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 0x7f969d2c1370>timeout=201600uid=1000gid=425user='mockbuild'unshare_net=TrueprintOutput=Falsenspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.82b2_1lr:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'])
Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.82b2_1lr:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']
Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', 'f097f1b73e8b4712bc90f49913fa0714', '-D', '/var/lib/mock/f43-build-59056405-6570729/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.82b2_1lr:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target x86_64 --nodeps /builddir/build/SPECS/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: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1737072000
Wrote: /builddir/build/SRPMS/hmmer-3.3.2-10.fc43.src.rpm
Child return code was: 0
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --noclean --target x86_64 --nodeps /builddir/build/SPECS/hmmer.spec'], chrootPath='/var/lib/mock/f43-build-59056405-6570729/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 0x7f969d2c1370>timeout=201600uid=1000gid=425user='mockbuild'unshare_net=TrueprintOutput=Falsenspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.82b2_1lr:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'])
Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.82b2_1lr:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']
Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', 'd785045fe79847cd8cfc4680c0a2ab6f', '-D', '/var/lib/mock/f43-build-59056405-6570729/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.82b2_1lr:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb --noclean --target x86_64 --nodeps /builddir/build/SPECS/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: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1737072000
Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.PtDxHl
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.BZpfTm
+ umask 022
+ cd /builddir/build/BUILD/hmmer-3.3.2-build
+ cd /builddir/build/BUILD/hmmer-3.3.2-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 .
+ echo 'Patch #0 (hmmer-3.3.2-chris.patch):'
Patch #0 (hmmer-3.3.2-chris.patch):
+ /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .chris --fuzz=0
patching file easel/esl_regexp.h
patching file src/hmmpgmd.h
patching file src/hmmpgmd_shard.h
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.Ai4u1J
+ umask 022
+ cd /builddir/build/BUILD/hmmer-3.3.2-build
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd hmmer-3.3.2
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ '[' '-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	2025-04-24 00:26:30.436897394 +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 -r --in-place=.backup '/lt_cv_sys_global_symbol_to_cdecl=/s#(".*"|'\''.*'\'')#"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 ./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'
+ 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 ./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 ./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'
+ '[' 1 = 1 ']'
+ '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors' ']'
++ find . -name ltmain.sh
++ grep -q runstatedir=DIR ./configure
+ ./configure --build=x86_64-redhat-linux-gnu --host=x86_64-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/bin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --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... x86_64-redhat-linux-gnu
checking host system type... x86_64-redhat-linux-gnu
checking whether to compile using MPI... no
checking for x86_64-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 x86_64-redhat-linux-gnu-strip... no
checking for strip... strip
checking for x86_64-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... no
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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer    -pthread 
   host:                 x86_64-redhat-linux-gnu
   linker:               -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 -j48
     SUBDIR easel
     CC easel.o
     CC esl_alloc.o
     CC esl_alphabet.o
     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_dirichlet.o
     CC esl_distance.o
     CC esl_dmatrix.o
     CC esl_cpu.o
     CC esl_exponential.o
     CC esl_dsqdata.o
     CC esl_fileparser.o
     CC esl_gamma.o
     CC esl_gencode.o
     CC esl_getopts.o
     CC esl_graph.o
     CC esl_gev.o
     CC esl_heap.o
     CC esl_gumbel.o
     CC esl_hmm.o
     CC esl_histogram.o
     CC esl_huffman.o
     CC esl_json.o
     CC esl_hyperexp.o
     CC esl_keyhash.o
     CC esl_matrixops.o
     CC esl_mem.o
     CC esl_minimizer.o
     CC esl_mixgev.o
     CC esl_mixdchlet.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
     CC esl_msafile_phylip.o
     CC esl_msafile_psiblast.o
     CC esl_msafile_selex.o
     CC esl_msaweight.o
     CC esl_msafile_stockholm.o
     CC esl_msashuffle.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_normal.o
     CC esl_paml.o
     CC esl_random.o
     CC esl_quicksort.o
     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_sq.o
     CC esl_scorematrix.o
     CC esl_sqio.o
     CC esl_sqio_ascii.o
     CC esl_sqio_ncbi.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_ssi.o
     CC esl_stack.o
     CC esl_stopwatch.o
     CC esl_stats.o
     CC esl_stretchexp.o
     CC esl_subcmd.o
In function ‘phylip_interleaved_Read’,
    inlined from ‘esl_msafile_phylip_Read’ at esl_msafile_phylip.c:284:56:
esl_msafile_phylip.c:452:15: warning: ‘block_alen’ may be used uninitialized [-Wmaybe-uninitialized]
  452 |       else if (cur_alen - alen != block_alen) ESL_XFAIL(eslEFORMAT, afp->errmsg, "number of residues on line differs from previous seqs in alignment block");
      |               ^
esl_msafile_phylip.c: In function ‘esl_msafile_phylip_Read’:
esl_msafile_phylip.c:422:13: note: ‘block_alen’ was declared here
  422 |   int64_t   block_alen;         /* # of residues being added by current block */
      |             ^~~~~~~~~~
     CC esl_threads.o
     CC esl_tree.o
     CC esl_varint.o
     CC esl_vectorops.o
     CC esl_weibull.o
     CC esl_workqueue.o
     CC esl_wuss.o
     CC esl_sse.o
     CC esl_avx.o
     CC esl_avx512.o
     CC esl_neon.o
     CC esl_vmx.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
      |            ^~~
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 */
      |              ^~~~~~
esl_msaweight.c: In function ‘esl_msaweight_IDFilter_adv’:
esl_msaweight.c:1035:9: warning: ‘conscols_103’ 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)
      | ^~~~~~~~~~~~~~
In file included from esl_scorematrix.c:22:
esl_scorematrix.c: In function ‘esl_scorematrix_Create’:
easel.h:164:17: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  164 |     if ( ((p) = malloc(size)) == NULL)  { \
      |                 ^~~~~~~~~~~~
In file included from easel.h:21:
/usr/include/stdlib.h:672:14: note: in a call to allocation function ‘malloc’ declared here
  672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__
      |              ^~~~~~
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;
      |                    ^~~~~~
In function ‘esl_sq_DestroyBlock’,
    inlined from ‘esl_sq_DestroyBlock’ at esl_sq.c:583:1,
    inlined from ‘sq_createblock’ at esl_sq.c:2152:3:
esl_sq.c:589:24: warning: ‘block_15->listSize’ may be used uninitialized [-Wmaybe-uninitialized]
  589 |   for (i = 0; i < block->listSize; ++i)
      |                   ~~~~~^~~~~~~~~~
esl_sq.c:589:24: warning: ‘block_15->listSize’ may be used uninitialized [-Wmaybe-uninitialized]
     AR libeasel.a
     SUBDIR miniapps
     GEN esl-afetch
     GEN esl-alimap
     GEN esl-alimanip
     GEN esl-alimask
     GEN esl-alipid
     GEN esl-alimerge
     GEN esl-alirev
     GEN esl-alistat
     GEN esl-compalign
     GEN esl-construct
     GEN esl-compstruct
     GEN esl-histplot
     GEN esl-mixdchlet
     GEN esl-selectn
     GEN esl-reformat
     GEN esl-seqrange
     GEN esl-mask
     GEN esl-seqstat
     GEN esl-sfetch
     GEN esl-shuffle
     GEN esl-ssdraw
     GEN esl-translate
     CC cmd_alistat.o
     GEN esl-weight
     CC cmd_downsample.o
     CC cmd_filter.o
     CC cmd_index.o
     GEN easel
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  */
      |          ^~~~~~~~~~~
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:322:45: warning: ‘ppidx’ may be used uninitialized [-Wmaybe-uninitialized]
  322 |               if(do_post_for_this_rfpos) ptm[ppidx]++;
      |                                             ^
esl-compalign.c:104:7: note: ‘ppidx’ was declared here
  104 |   int ppidx;           /* index of PP */
      |       ^~~~~
esl-alimask.c: In function ‘main’:
esl-alimask.c:1007:7: warning: ‘ppidx_thresh’ may be used uninitialized [-Wmaybe-uninitialized]
 1007 |   int ppidx_thresh;
      |       ^~~~~~~~~~~~
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;
      |         ^~~~
In file included from /usr/include/stdio.h:967,
                 from esl-alistat.c:6:
In function ‘printf’,
    inlined from ‘main’ at esl-alistat.c:293:6:
/usr/include/bits/stdio2.h:118:10: warning: ‘small’ may be used uninitialized [-Wmaybe-uninitialized]
  118 |   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:118:10: warning: ‘large’ may be used uninitialized [-Wmaybe-uninitialized]
  118 |   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      */
      |                        ^~~~~
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:967,
                 from esl-alimerge.c:26:
In function ‘fprintf’,
    inlined from ‘main’ at esl-alimerge.c:366:2:
/usr/include/bits/stdio2.h:111:10: warning: ‘namewidth’ may be used uninitialized [-Wmaybe-uninitialized]
  111 |   return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  112 |                         __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 */
      |                 ^~~~
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;
      |          ^~~~~~~~~
In file included from /usr/include/stdio.h:967,
                 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:111:10: warning: ‘namewidth’ may be used uninitialized [-Wmaybe-uninitialized]
  111 |   return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  112 |                         __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;
      |                   ^~
     SUBDIR libdivsufsort
     CC divsufsort.o
     AR libdivsufsort.a
     SUBDIR src
     CC alimask.o
     CC build.o
     CC cachedb.o
     CC cachedb_shard.o
     CC errors.o
     CC emit.o
     CC evalues.o
     CC eweight.o
     CC generic_decoding.o
     CC generic_fwdback_chk.o
     CC generic_fwdback_banded.o
     CC generic_fwdback.o
     CC generic_null2.o
     CC generic_optacc.o
     CC generic_msv.o
     CC generic_stotrace.o
     CC generic_vtrace.o
     CC generic_viterbi.o
     CC heatmap.o
     CC h2_io.o
     CC hmmdmstr.o
     CC hmmlogo.o
     CC hmmd_search_status.o
     CC hmmdmstr_shard.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
     CC p7_domaindef.o
     CC p7_gbands.o
     CC p7_gmx.o
     CC p7_gmxb.o
     CC p7_gmxchk.o
     CC p7_hit.o
     CC p7_hmm.o
     CC p7_hmmcache.o
     CC p7_hmmd_search_stats.o
     CC p7_hmmfile.o
     CC p7_hmmwindow.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;
      |                                                                                                                                                          ^~~~
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_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);
      |                         ~^~~~~~~~~~~~~~~~~~~~~~
p7_domain.c:365:25: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  365 |   ret_obj->bitscore = *((float *) &host_32bit);
      |                        ~^~~~~~~~~~~~~~~~~~~~~~
     CC p7_pipeline.o
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);
      |                                     ~^~~~~~~~~~~~~~~~~~~~~~
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_prior.o
     CC p7_profile.o
     CC p7_spensemble.o
     CC p7_tophits.o
     CC p7_trace.o
     CC p7_scoredata.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 hmmpgmd2msa.o
     CC fm_alphabet.o
     CC fm_general.o
     CC fm_sse.o
     CC fm_ssv.o
     CC hmmalign.o
     CC hmmbuild.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 hmmemit.o
     CC hmmconvert.o
     CC hmmfetch.o
     CC hmmpgmd_shard.o
     CC hmmpgmd.o
     CC hmmpress.o
     CC hmmscan.o
     CC hmmsearch.o
     CC hmmsim.o
     CC hmmstat.o
     CC jackhmmer.o
     CC phmmer.o
     CC nhmmer.o
     CC nhmmscan.o
     CC makehmmerdb.o
     CC hmmc2.o
     CC hmmerfm-exactmatch.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 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;
      |                         ^~~~
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;
      |                   ^~~~~~
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;
      |                                     ^~~~~~~~~~~
In file included from /usr/include/stdio.h:967,
                 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:111:10: warning: ‘alph’ may be used uninitialized [-Wmaybe-uninitialized]
  111 |   return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  112 |                         __va_arg_pack ());
      |                         ~~~~~~~~~~~~~~~~~
hmmerfm-exactmatch.c: In function ‘main’:
hmmerfm-exactmatch.c:94:9: note: ‘alph’ was declared here
   94 |   char *alph;
      |         ^~~~
In function ‘serial_loop’,
    inlined from ‘serial_master’ at nhmmer.c:1071:35:
nhmmer.c:1367:41: warning: ‘dbsq_revcmp’ may be used uninitialized [-Wmaybe-uninitialized]
 1367 |           info->pli->nres += dbsq_revcmp->W;
      |                              ~~~~~~~~~~~^~~
nhmmer.c: In function ‘serial_master’:
nhmmer.c:1338:13: note: ‘dbsq_revcmp’ was declared here
 1338 |   ESL_SQ   *dbsq_revcmp;
      |             ^~~~~~~~~~~
In file included from /usr/include/stdio.h:967,
                 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:111:10: warning: ‘posw’ may be used uninitialized [-Wmaybe-uninitialized]
  111 |   return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  112 |                         __va_arg_pack ());
      |                         ~~~~~~~~~~~~~~~~~
p7_tophits.c: In function ‘p7_tophits_Targets’:
p7_tophits.c:1068:10: note: ‘posw’ was declared here
 1068 |   int    posw;
      |          ^~~~
     AR libhmmer-src.stamp
     SUBDIR impl_sse
     CC decoding.o
     CC fwdback.o
     CC ssvfilter.o
     CC io.o
     CC msvfilter.o
     CC null2.o
     CC optacc.o
     CC vitfilter.o
     CC stotrace.o
     CC p7_omx.o
     CC p7_oprofile.o
     CC mpi.o
In function ‘get_postprob’,
    inlined from ‘p7_OATrace’ at optacc.c:254:18:
optacc.c:273:3: warning: ‘smax’ may be used uninitialized [-Wmaybe-uninitialized]
  273 |   switch (scur) {
      |   ^~~~~~
optacc.c: In function ‘p7_OATrace’:
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;
      |                ^~~~
     AR libhmmer-impl.stamp
     GEN hmmalign
     GEN alimask
     GEN hmmbuild
     GEN hmmconvert
     GEN hmmemit
     GEN hmmfetch
     GEN hmmlogo
     GEN hmmpgmd
     GEN hmmpress
     GEN hmmpgmd_shard
     GEN hmmscan
     GEN hmmsim
     GEN hmmstat
     GEN hmmsearch
     GEN nhmmer
     GEN phmmer
     GEN jackhmmer
     GEN nhmmscan
     GEN hmmc2
     GEN hmmerfm-exactmatch
     GEN makehmmerdb
../easel/esl_scorematrix.c: In function ‘esl_scorematrix_Create’:
../easel/esl_scorematrix.c:71:3: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
   71 |   ESL_ALLOC(S->outorder, sizeof(char) * (abc->Kp+1));
      |   ^
/usr/include/stdlib.h:672:14: note: in a call to allocation function ‘malloc’ declared here
  672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__
      |              ^
../easel/esl_scorematrix.c: In function ‘esl_scorematrix_Create’:
../easel/esl_scorematrix.c:71:3: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
   71 |   ESL_ALLOC(S->outorder, sizeof(char) * (abc->Kp+1));
      |   ^
/usr/include/stdlib.h:672:14: note: in a call to allocation function ‘malloc’ declared here
  672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__
      |              ^
../easel/esl_scorematrix.c: In function ‘esl_scorematrix_Create’:
../easel/esl_scorematrix.c:71:3: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
   71 |   ESL_ALLOC(S->outorder, sizeof(char) * (abc->Kp+1));
      |   ^
/usr/include/stdlib.h:672:14: note: in a call to allocation function ‘malloc’ declared here
  672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__
      |              ^
../easel/esl_scorematrix.c: In function ‘esl_scorematrix_Create’:
../easel/esl_scorematrix.c:71:3: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
   71 |   ESL_ALLOC(S->outorder, sizeof(char) * (abc->Kp+1));
      |   ^
/usr/include/stdlib.h:672:14: note: in a call to allocation function ‘malloc’ declared here
  672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__
      |              ^
../easel/esl_scorematrix.c: In function ‘esl_scorematrix_Create’:
../easel/esl_scorematrix.c:71:3: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
   71 |   ESL_ALLOC(S->outorder, sizeof(char) * (abc->Kp+1));
      |   ^
/usr/include/stdlib.h:672:14: note: in a call to allocation function ‘malloc’ declared here
  672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__
      |              ^
../easel/esl_scorematrix.c: In function ‘esl_scorematrix_Create’:
../easel/esl_scorematrix.c:71:3: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
   71 |   ESL_ALLOC(S->outorder, sizeof(char) * (abc->Kp+1));
      |   ^
/usr/include/stdlib.h:672:14: note: in a call to allocation function ‘malloc’ declared here
  672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__
      |              ^
     SUBDIR profmark
     CC create-profmark.o
     CC rocplot.o
In file included from /usr/include/stdio.h:967,
                 from create-profmark.c:18:
In function ‘fprintf’,
    inlined from ‘main’ at create-profmark.c:258:4:
/usr/include/bits/stdio2.h:111:10: warning: ‘nfrags’ may be used uninitialized [-Wmaybe-uninitialized]
  111 |   return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  112 |                         __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
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.Voh3H1
+ umask 022
+ cd /builddir/build/BUILD/hmmer-3.3.2-build
+ '[' /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT '!=' / ']'
+ rm -rf /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT
++ dirname /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT
+ mkdir -p /builddir/build/BUILD/hmmer-3.3.2-build
+ mkdir /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd hmmer-3.3.2
+ rm -rf /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT
+ make install DESTDIR=/builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT
     SUBDIR easel
     SUBDIR miniapps
     SUBDIR libdivsufsort
     SUBDIR src
     SUBDIR impl_sse
     SUBDIR profmark
/usr/bin/install -c -d /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/bin
/usr/bin/install -c -d /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/share/man/man1
make -C src install
make[1]: Entering directory '/builddir/build/BUILD/hmmer-3.3.2-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/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/bin/ ;\
done
make[1]: Leaving directory '/builddir/build/BUILD/hmmer-3.3.2-build/hmmer-3.3.2/src'
make -C documentation install
make[1]: Entering directory '/builddir/build/BUILD/hmmer-3.3.2-build/hmmer-3.3.2/documentation'
make -C man install
make[2]: Entering directory '/builddir/build/BUILD/hmmer-3.3.2-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 $file.man /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/share/man/man1/${file}.1 ;\
done
make[2]: Leaving directory '/builddir/build/BUILD/hmmer-3.3.2-build/hmmer-3.3.2/documentation/man'
make[1]: Leaving directory '/builddir/build/BUILD/hmmer-3.3.2-build/hmmer-3.3.2/documentation'
+ cd easel
+ make install DESTDIR=/builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT
/usr/bin/install -c -d /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/bin
/usr/bin/install -c -d /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/share/man/man1
make -C miniapps install
make[1]: Entering directory '/builddir/build/BUILD/hmmer-3.3.2-build/hmmer-3.3.2/easel/miniapps'
/usr/bin/install -c -m 0755 easel /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/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/BUILD/hmmer-3.3.2-build/BUILDROOT/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 $file.man /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/share/man/man1/${file}.1 ;\
done
make[1]: Leaving directory '/builddir/build/BUILD/hmmer-3.3.2-build/hmmer-3.3.2/easel/miniapps'
+ /usr/bin/find-debuginfo -j48 --strict-build-id -m -i --build-id-seed 3.3.2-10.fc43 --unique-debug-suffix -3.3.2-10.fc43.x86_64 --unique-debug-src-base hmmer-3.3.2-10.fc43.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/hmmer-3.3.2-build/hmmer-3.3.2
find-debuginfo: starting
Extracting debug info from 43 files
DWARF-compressing 43 files
sepdebugcrcfix: Updated 43 CRC32s, 0 CRC32s did match.
Creating .debug symlinks for symlinks to ELF files
Copying sources found by 'debugedit -l' to /usr/src/debug/hmmer-3.3.2-10.fc43.x86_64
find-debuginfo: done
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
+ /usr/lib/rpm/brp-remove-la-files
+ /usr/lib/rpm/redhat/brp-python-rpm-in-distinfo
+ env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j48
+ /usr/lib/rpm/redhat/brp-python-hardlink
+ /usr/bin/add-determinism --brp -j48 /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT
Scanned 19 directories and 371 files,
               processed 44 inodes,
               0 modified (0 replaced + 0 rewritten),
               0 unsupported format, 0 errors
Reading /builddir/build/BUILD/hmmer-3.3.2-build/SPECPARTS/rpm-debuginfo.specpart
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.Aon8sg
+ umask 022
+ cd /builddir/build/BUILD/hmmer-3.3.2-build
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd hmmer-3.3.2
+ make check
     SUBDIR easel
     GEN easel_utest
     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
     GEN esl_msafile_phylip_utest
In function ‘phylip_interleaved_Read’,
    inlined from ‘esl_msafile_phylip_Read’ at ./esl_msafile_phylip.c:284:56:
./esl_msafile_phylip.c:452:15: warning: ‘block_alen’ may be used uninitialized [-Wmaybe-uninitialized]
  452 |       else if (cur_alen - alen != block_alen) ESL_XFAIL(eslEFORMAT, afp->errmsg, "number of residues on line differs from previous seqs in alignment block");
      |               ^
./esl_msafile_phylip.c: In function ‘esl_msafile_phylip_Read’:
./esl_msafile_phylip.c:422:13: note: ‘block_alen’ was declared here
  422 |   int64_t   block_alen;         /* # of residues being added by current block */
      |             ^~~~~~~~~~
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
     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_103’ 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
In file included from ./esl_scorematrix.c:22:
./esl_scorematrix.c: In function ‘esl_scorematrix_Create’:
./easel.h:164:17: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  164 |     if ( ((p) = malloc(size)) == NULL)  { \
      |                 ^~~~~~~~~~~~
In file included from ./easel.h:21:
/usr/include/stdlib.h:672:14: note: in a call to allocation function ‘malloc’ declared here
  672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__
      |              ^~~~~~
./esl_scorematrix.c: In function ‘esl_scorematrix_Create’:
./esl_scorematrix.c:71:3: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
   71 |   ESL_ALLOC(S->outorder, sizeof(char) * (abc->Kp+1));
      |   ^
/usr/include/stdlib.h:672:14: note: in a call to allocation function ‘malloc’ declared here
  672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__
      |              ^
     GEN esl_sq_utest
In function ‘esl_sq_DestroyBlock’,
    inlined from ‘esl_sq_DestroyBlock’ at ./esl_sq.c:583:1,
    inlined from ‘sq_createblock’ at ./esl_sq.c:2152:3:
./esl_sq.c:589:24: warning: ‘block_15->listSize’ may be used uninitialized [-Wmaybe-uninitialized]
  589 |   for (i = 0; i < block->listSize; ++i)
      |                   ~~~~~^~~~~~~~~~
./esl_sq.c:589:24: warning: ‘block_15->listSize’ may be used uninitialized [-Wmaybe-uninitialized]
     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:967,
                 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:111:10: warning: ‘posw’ may be used uninitialized [-Wmaybe-uninitialized]
  111 |   return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  112 |                         __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
In function ‘get_postprob’,
    inlined from ‘p7_OATrace’ at ./optacc.c:254:18:
./optacc.c:273:3: warning: ‘smax’ may be used uninitialized [-Wmaybe-uninitialized]
  273 |   switch (scur) {
      |   ^~~~~~
./optacc.c: In function ‘p7_OATrace’:
./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:
Thu Apr 24 00:30:32 UTC 2025
Linux d785045fe79847cd8cfc4680c0a2ab6f 6.13.8-200.fc41.x86_64 #1 SMP PREEMPT_DYNAMIC Sun Mar 23 05:03:09 UTC 2025 x86_64 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:
Thu Apr 24 00:30:50 UTC 2025
Linux d785045fe79847cd8cfc4680c0a2ab6f 6.13.8-200.fc41.x86_64 #1 SMP PREEMPT_DYNAMIC Sun Mar 23 05:03:09 UTC 2025 x86_64 GNU/Linux
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: hmmer-3.3.2-10.fc43.x86_64
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.pEyjMB
+ umask 022
+ cd /builddir/build/BUILD/hmmer-3.3.2-build
+ cd hmmer-3.3.2
+ LICENSEDIR=/builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/share/licenses/hmmer
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/share/licenses/hmmer
+ cp -pr /builddir/build/BUILD/hmmer-3.3.2-build/hmmer-3.3.2/LICENSE /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/share/licenses/hmmer
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: hmmer = 3.3.2-10.fc43 hmmer(x86-64) = 3.3.2-10.fc43
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libc.so.6()(64bit) libc.so.6(GLIBC_2.11)(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.15)(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.27)(64bit) libm.so.6(GLIBC_2.29)(64bit) rtld(GNU_HASH)
Processing files: hmmer-easel-3.3.2-10.fc43.x86_64
Provides: hmmer-easel = 3.3.2-10.fc43 hmmer-easel(x86-64) = 3.3.2-10.fc43
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) rtld(GNU_HASH)
Processing files: hmmer-doc-3.3.2-10.fc43.noarch
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.G4dPat
+ umask 022
+ cd /builddir/build/BUILD/hmmer-3.3.2-build
+ cd hmmer-3.3.2
+ DOCDIR=/builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/share/doc/hmmer-doc
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/share/doc/hmmer-doc
+ cp -pr /builddir/build/BUILD/hmmer-3.3.2-build/hmmer-3.3.2/LICENSE /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/share/doc/hmmer-doc
+ cp -pr /builddir/build/BUILD/hmmer-3.3.2-build/hmmer-3.3.2/README.md /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/share/doc/hmmer-doc
+ cp -pr /builddir/build/BUILD/hmmer-3.3.2-build/hmmer-3.3.2/RELEASE-3.3.2.md /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/share/doc/hmmer-doc
+ cp -pr /builddir/build/BUILD/hmmer-3.3.2-build/hmmer-3.3.2/Userguide.pdf /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/share/doc/hmmer-doc
+ cp -pr /builddir/build/BUILD/hmmer-3.3.2-build/hmmer-3.3.2/tutorial /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/share/doc/hmmer-doc
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: hmmer-doc = 3.3.2-10.fc43
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: hmmer-debugsource-3.3.2-10.fc43.x86_64
Provides: hmmer-debugsource = 3.3.2-10.fc43 hmmer-debugsource(x86-64) = 3.3.2-10.fc43
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: hmmer-debuginfo-3.3.2-10.fc43.x86_64
Provides: debuginfo(build-id) = 068191114401539ce5f95e994b0c4efc91950e91 debuginfo(build-id) = 1dce20626fa8b9cad6f27a4d23788da803911163 debuginfo(build-id) = 22d5b2b1c77f0f0065a32655998b368fa44bd3ce debuginfo(build-id) = 259bbb4a014d58a10b88c2f0bfbd7c13e640465f debuginfo(build-id) = 41bb7a5ec2b16899c00cebca878aac1d916ea022 debuginfo(build-id) = 4879a3a50f6cc8fa806356b4a4f8de7ffb6c8bc3 debuginfo(build-id) = 5ba1e2a7b0da1ed92fb3c9778d8063b24aae9318 debuginfo(build-id) = 5cfae83614bd185f0141aee10efd90f77f86f2d4 debuginfo(build-id) = 65f674f15de200505bf4be912151471c64099d99 debuginfo(build-id) = 7e83423b7d1f10cd775dedf18db25fc879215330 debuginfo(build-id) = a21e70b087a372502c4f3d7bea2e7caa6162e494 debuginfo(build-id) = b56814288d1b60bd3a79d678b2af3a259f7db8fc debuginfo(build-id) = ba1d9460c8c204f7c4cc8c0da751610b0cd601b1 debuginfo(build-id) = bbafdbd997d42dbaebb5bf7b6698341976b33cc4 debuginfo(build-id) = c4ee9765cc582c5148c538b09c9119253c0bb896 debuginfo(build-id) = d18efbd8a35657f0e75d957216308cb1aec97f31 debuginfo(build-id) = e19da6605fb78359a3cde885a9c57c5c9a090fc7 debuginfo(build-id) = edee7680e6639eecb2fdfcfbcb0a4cd21e0abb49 debuginfo(build-id) = ee2c1471e779c971769bc2d31c8f5d25c71432ed hmmer-debuginfo = 3.3.2-10.fc43 hmmer-debuginfo(x86-64) = 3.3.2-10.fc43
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: hmmer-debugsource(x86-64) = 3.3.2-10.fc43
Processing files: hmmer-easel-debuginfo-3.3.2-10.fc43.x86_64
Provides: debuginfo(build-id) = 037966b9574072fa29801f80b6bd7be0b2fcdc4d debuginfo(build-id) = 07bb59c720555b8c4fde98985aaf98a268dd716e debuginfo(build-id) = 0db436e7fb95e352ffa142bd0941013e068d38d5 debuginfo(build-id) = 110411c72d9c7cdfbe853f18cad52ab85ab609e2 debuginfo(build-id) = 24fe1de92b3b91d7c17b16e419fa1d28fa174f73 debuginfo(build-id) = 392141194cb30d46a7812f7c783fc8fcf36f1f4e debuginfo(build-id) = 47a75e07a92109c674daf6844ff455fb7811b558 debuginfo(build-id) = 539943a6d3ec7c18f236e2090b6830cd88e689aa debuginfo(build-id) = 5df4187dcf313c45ba329ad86165807922f823cc debuginfo(build-id) = 61ca56d665ee2fd605c59f7d5bc875d6891d230c debuginfo(build-id) = 743892a01e36488b1af8da1a16da6e87fbe90d2a debuginfo(build-id) = 7618325268dd2d339ded340a54615f21ae214119 debuginfo(build-id) = 7f54abb78586d86a9b2cd1fc444a4fee1d719e31 debuginfo(build-id) = 923984219c25f1a5d0cd8edc22a1694f4c1cc540 debuginfo(build-id) = 95744938618a46a0d134292204fa938c2256eef5 debuginfo(build-id) = 9768ce419b5e9ce2106afaa49c8880d02a18d075 debuginfo(build-id) = 9e4b5e2e8e99c4612405f62dd6826420aa9bbde9 debuginfo(build-id) = a3594324c7602f774e8a13ef899d5516f1fd87cb debuginfo(build-id) = af1725458931b12b13e97e5fb7bda8751ec93608 debuginfo(build-id) = b436f886918ad415e404641120918e79c14d3e4d debuginfo(build-id) = bd6ea63693f8cf0182c90330f47452d20d9874f5 debuginfo(build-id) = cf836a179cca6ed9554715feb94b41fbde7414ea debuginfo(build-id) = d3c71373b45ee58d9456649ff82827471ef377d5 debuginfo(build-id) = fd107134bd1e2e9697f65f88a6fc50b6f1d3bbe8 hmmer-easel-debuginfo = 3.3.2-10.fc43 hmmer-easel-debuginfo(x86-64) = 3.3.2-10.fc43
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: hmmer-debugsource(x86-64) = 3.3.2-10.fc43
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT
Wrote: /builddir/build/RPMS/hmmer-doc-3.3.2-10.fc43.noarch.rpm
Wrote: /builddir/build/RPMS/hmmer-easel-3.3.2-10.fc43.x86_64.rpm
Wrote: /builddir/build/RPMS/hmmer-3.3.2-10.fc43.x86_64.rpm
Wrote: /builddir/build/RPMS/hmmer-debugsource-3.3.2-10.fc43.x86_64.rpm
Wrote: /builddir/build/RPMS/hmmer-easel-debuginfo-3.3.2-10.fc43.x86_64.rpm
Wrote: /builddir/build/RPMS/hmmer-debuginfo-3.3.2-10.fc43.x86_64.rpm
Child return code was: 0