Mock Version: 3.5
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target i686 --nodeps /builddir/build/SPECS/hmmer.spec'], chrootPath='/var/lib/mock/fedora-rawhide-i686-1671964767.188849/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 0x7f7e2c0b57d0>timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.92z986l8:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True)
Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.92z986l8:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']
Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '4a670d0b933e42de88a5c13a96a95adb', '-D', '/var/lib/mock/fedora-rawhide-i686-1671964767.188849/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.92z986l8:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target i686 --nodeps /builddir/build/SPECS/hmmer.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False
Building target platforms: i686
Building for target i686
setting SOURCE_DATE_EPOCH=1659312000
Wrote: /builddir/build/SRPMS/hmmer-3.3.2-2.fc38.src.rpm
Child return code was: 0
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target i686 --nodeps /builddir/build/SPECS/hmmer.spec'], chrootPath='/var/lib/mock/fedora-rawhide-i686-1671964767.188849/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 0x7f7e2c0b57d0>timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.92z986l8:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True)
Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.92z986l8:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']
Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', 'b4e97a6139ea47ee88390d7b5a67cf6e', '-D', '/var/lib/mock/fedora-rawhide-i686-1671964767.188849/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.92z986l8:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target i686 --nodeps /builddir/build/SPECS/hmmer.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False
Building target platforms: i686
Building for target i686
setting SOURCE_DATE_EPOCH=1659312000
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.cB99hG
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf hmmer-3.3.2
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/hmmer-3.3.2.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd hmmer-3.3.2
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.qi1dsR
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd hmmer-3.3.2
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']'
++ find . -type f -name configure -print
+ for file in $(find . -type f -name configure -print)
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure
+ diff -u ./configure.backup ./configure
--- ./configure.backup 2020-11-26 21:19:58.000000000 +0000
+++ ./configure 2022-12-25 10:40:40.286267882 +0000
@@ -1898,7 +1898,7 @@
#ifdef __cplusplus
extern "C"
#endif
-char $2 ();
+__attribute__ ((used)) char $2 ();
/* The GNU C library defines this for functions which it implements
to always fail with ENOSYS. Some functions are actually named
something starting with __ and the normal name is an alias. */
+ /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ '[' 1 = 1 ']'
+++ dirname ./configure
++ find . -name config.guess -o -name config.sub
+ for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub)
++ basename ./easel/config.sub
+ '[' -f /usr/lib/rpm/redhat/config.sub ']'
+ /usr/bin/rm -f ./easel/config.sub
++ basename ./easel/config.sub
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./easel/config.sub
'/usr/lib/rpm/redhat/config.sub' -> './easel/config.sub'
+ for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub)
++ basename ./easel/config.guess
+ '[' -f /usr/lib/rpm/redhat/config.guess ']'
+ /usr/bin/rm -f ./easel/config.guess
++ basename ./easel/config.guess
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./easel/config.guess
'/usr/lib/rpm/redhat/config.guess' -> './easel/config.guess'
+ for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub)
++ basename ./config.sub
+ '[' -f /usr/lib/rpm/redhat/config.sub ']'
+ /usr/bin/rm -f ./config.sub
++ basename ./config.sub
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./config.sub
'/usr/lib/rpm/redhat/config.sub' -> './config.sub'
+ for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub)
++ basename ./config.guess
+ '[' -f /usr/lib/rpm/redhat/config.guess ']'
+ /usr/bin/rm -f ./config.guess
++ basename ./config.guess
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./config.guess
'/usr/lib/rpm/redhat/config.guess' -> './config.guess'
+ '[' 1 = 1 ']'
+ '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']'
++ find . -name ltmain.sh
++ grep -q runstatedir=DIR ./configure
+ ./configure --build=i686-redhat-linux-gnu --host=i686-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info
configure: WARNING: unrecognized options: --disable-dependency-tracking
configure: Configuring HMMER3 for your system.
checking build system type... i686-redhat-linux-gnu
checking host system type... i686-redhat-linux-gnu
checking whether to compile using MPI... no
checking for i686-redhat-linux-gnu-gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gcc option to accept ISO C99... none needed
checking for gcc option to accept ISO Standard C... (cached) none needed
checking how to run the C preprocessor... gcc -E
checking for a BSD-compatible install... /usr/bin/install -c
checking for i686-redhat-linux-gnu-strip... no
checking for strip... strip
checking for i686-redhat-linux-gnu-ranlib... no
checking for ranlib... ranlib
checking for ar... /usr/bin/ar
checking whether ln -s works... yes
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking whether gcc is Clang... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking whether more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking whether gcc can compile our Altivec/VMX code... no
checking whether gcc can compile our SSE code... yes
configure: Activating Intel/AMD SSE vector DP implementation
checking whether _MM_SET_FLUSH_ZERO_MODE is supported... yes
checking compiler support --start-group... yes
checking for gzip... /usr/bin/gzip
checking for python3... yes
checking for library containing clock_gettime... none required
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking endian.h usability... yes
checking endian.h presence... yes
checking for endian.h... yes
checking for inttypes.h... (cached) yes
checking for stdint.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/types.h... (cached) yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking for sys/sysctl.h... no
checking for uint8_t... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking for off_t... yes
checking whether byte ordering is bigendian... no
checking for __attribute__((noreturn))... yes
checking for __attribute__((format))... yes
checking for mkstemp... yes
checking for popen... yes
checking for putenv... yes
checking for strcasecmp... yes
checking for strsep... yes
checking for times... yes
checking for getpid... yes
checking for sysctl... no
checking for sysconf... yes
checking for getcwd... yes
checking for chmod... yes
checking for stat... yes
checking for fstat... yes
checking for erfc... no
checking for library containing ntohs... none required
checking for library containing ntohl... none required
checking for library containing htons... none required
checking for library containing htonl... none required
checking for library containing socket... none required
checking for library containing inet_pton... none required
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating testsuite/Makefile
config.status: creating profmark/Makefile
config.status: creating src/impl_sse/Makefile
config.status: creating documentation/Makefile
config.status: creating documentation/man/Makefile
config.status: creating documentation/userguide/Makefile
config.status: creating documentation/userguide/inclusions/Makefile
config.status: creating libdivsufsort/Makefile
config.status: creating easel/Makefile
config.status: creating easel/miniapps/Makefile
config.status: creating easel/testsuite/Makefile
config.status: creating easel/documentation/Makefile
config.status: creating documentation/userguide/titlepage.tex
config.status: creating documentation/userguide/titlepage_daemon.tex
config.status: creating documentation/userguide/copyright.tex
config.status: creating documentation/man/alimask.man
config.status: creating documentation/man/hmmalign.man
config.status: creating documentation/man/hmmbuild.man
config.status: creating documentation/man/hmmc2.man
config.status: creating documentation/man/hmmconvert.man
config.status: creating documentation/man/hmmemit.man
config.status: creating documentation/man/hmmer.man
config.status: creating documentation/man/hmmfetch.man
config.status: creating documentation/man/hmmlogo.man
config.status: creating documentation/man/hmmpgmd.man
config.status: creating documentation/man/hmmpgmd_shard.man
config.status: creating documentation/man/hmmpress.man
config.status: creating documentation/man/hmmscan.man
config.status: creating documentation/man/hmmsearch.man
config.status: creating documentation/man/hmmsim.man
config.status: creating documentation/man/hmmstat.man
config.status: creating documentation/man/jackhmmer.man
config.status: creating documentation/man/makehmmerdb.man
config.status: creating documentation/man/nhmmer.man
config.status: creating documentation/man/nhmmscan.man
config.status: creating documentation/man/phmmer.man
config.status: creating easel/miniapps/esl-afetch.man
config.status: creating easel/miniapps/esl-alimanip.man
config.status: creating easel/miniapps/esl-alimap.man
config.status: creating easel/miniapps/esl-alimask.man
config.status: creating easel/miniapps/esl-alimerge.man
config.status: creating easel/miniapps/esl-alipid.man
config.status: creating easel/miniapps/esl-alirev.man
config.status: creating easel/miniapps/esl-alistat.man
config.status: creating easel/miniapps/esl-compalign.man
config.status: creating easel/miniapps/esl-compstruct.man
config.status: creating easel/miniapps/esl-construct.man
config.status: creating easel/miniapps/esl-histplot.man
config.status: creating easel/miniapps/esl-mask.man
config.status: creating easel/miniapps/esl-mixdchlet.man
config.status: creating easel/miniapps/esl-reformat.man
config.status: creating easel/miniapps/esl-selectn.man
config.status: creating easel/miniapps/esl-seqrange.man
config.status: creating easel/miniapps/esl-seqstat.man
config.status: creating easel/miniapps/esl-sfetch.man
config.status: creating easel/miniapps/esl-shuffle.man
config.status: creating easel/miniapps/esl-ssdraw.man
config.status: creating easel/miniapps/esl-translate.man
config.status: creating easel/miniapps/esl-weight.man
config.status: creating easel/decoy_config.h
config.status: creating src/p7_config.h
config.status: creating easel/esl_config.h
config.status: creating libdivsufsort/divsufsort.h
config.status: linking src/impl_sse to src/impl
configure: WARNING: unrecognized options: --disable-dependency-tracking
HMMER configuration:
compiler: gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -pthread
host: i686-redhat-linux-gnu
linker: -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes
libraries:
DP implementation: sse
Now do 'make' to build HMMER, and optionally:
'make check' to run self tests,
'make install' to install programs and man pages,
'(cd easel; make install)' to install Easel tools.
+ make -j2
SUBDIR easel
CC easel.o
CC esl_alloc.o
CC esl_alphabet.o
easel.c: In function 'esl_fail':
easel.c:79:12: warning: 'ap' may be used uninitialized [-Wmaybe-uninitialized]
79 | else vsyslog(LOG_ERR, format, ap); // SRE: TODO: check this.
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
easel.c:69:15: note: 'ap' was declared here
69 | va_list ap;
| ^~
easel.c: In function 'esl_exception':
easel.c:157:12: warning: 'argp' may be used uninitialized [-Wmaybe-uninitialized]
157 | else vsyslog(LOG_ERR, format, argp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
easel.c:131:11: note: 'argp' was declared here
131 | va_list argp;
| ^~~~
easel.c: In function 'esl_fatal':
easel.c:308:8: warning: 'argp' may be used uninitialized [-Wmaybe-uninitialized]
308 | else vsyslog(LOG_ERR, format, argp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
easel.c:295:11: note: 'argp' was declared here
295 | va_list argp;
| ^~~~
CC esl_arr2.o
CC esl_arr3.o
CC esl_bitfield.o
CC esl_buffer.o
CC esl_cluster.o
CC esl_composition.o
CC esl_cpu.o
CC esl_dirichlet.o
CC esl_distance.o
CC esl_dmatrix.o
CC esl_dsqdata.o
CC esl_exponential.o
CC esl_fileparser.o
CC esl_gamma.o
CC esl_gencode.o
CC esl_getopts.o
CC esl_gev.o
CC esl_graph.o
CC esl_gumbel.o
CC esl_heap.o
CC esl_histogram.o
CC esl_hmm.o
CC esl_huffman.o
CC esl_hyperexp.o
CC esl_json.o
esl_json.c: In function 'esl_json_Validate':
esl_json.c:752:33: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
752 | case eslJSON_BOOLEAN: if (! esl_memstrcmp(bf->mem + pos1, pos2-pos1+1, "true") &&
| ^~
esl_json.c:753:167: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
753 | ! esl_memstrcmp(bf->mem + pos1, pos2-pos1+1, "false")) ESL_FAIL(eslFAIL, errbuf, "boolean isn't a boolean, tok %d", i); break;
| ^~~~~
CC esl_keyhash.o
CC esl_matrixops.o
CC esl_mem.o
CC esl_minimizer.o
esl_minimizer.c: In function 'esl_min_ConjugateGradientDescent':
esl_minimizer.c:243:23: warning: 'fx' may be used uninitialized [-Wmaybe-uninitialized]
243 | if (opt_fx) *opt_fx = fx;
| ~~~~~~~~^~~~
esl_minimizer.c:119:10: note: 'fx' was declared here
119 | double fx;
| ^~
In function 'brent',
inlined from 'esl_min_ConjugateGradientDescent' at esl_minimizer.c:192:7:
esl_minimizer.c:720:21: warning: 'ax' may be used uninitialized [-Wmaybe-uninitialized]
720 | m = 0.5 * (a+b);
| ~~^~~
esl_minimizer.c: In function 'esl_min_ConjugateGradientDescent':
esl_minimizer.c:118:10: note: 'ax' was declared here
118 | double ax,bx,cx;
| ^~
In function 'brent',
inlined from 'esl_min_ConjugateGradientDescent' at esl_minimizer.c:192:7:
esl_minimizer.c:720:21: warning: 'cx' may be used uninitialized [-Wmaybe-uninitialized]
720 | m = 0.5 * (a+b);
| ~~^~~
esl_minimizer.c: In function 'esl_min_ConjugateGradientDescent':
esl_minimizer.c:118:16: note: 'cx' was declared here
118 | double ax,bx,cx;
| ^~
CC esl_mixdchlet.o
CC esl_mixgev.o
CC esl_mpi.o
CC esl_msa.o
CC esl_msacluster.o
CC esl_msafile.o
CC esl_msafile2.o
CC esl_msafile_a2m.o
CC esl_msafile_afa.o
CC esl_msafile_clustal.o
esl_msafile_clustal.c: In function 'esl_msafile_clustal_Read':
esl_msafile_clustal.c:247:12: warning: 'block_seq_start' may be used uninitialized [-Wmaybe-uninitialized]
247 | if (seq_start != block_seq_start) ESL_XFAIL(eslEFORMAT, afp->errmsg, "sequence start is misaligned");
| ^
esl_msafile_clustal.c:203:13: note: 'block_seq_start' was declared here
203 | esl_pos_t block_seq_start, block_seq_len;
| ^~~~~~~~~~~~~~~
esl_msafile_clustal.c:248:12: warning: 'block_seq_len' may be used uninitialized [-Wmaybe-uninitialized]
248 | if (seq_len != block_seq_len) ESL_XFAIL(eslEFORMAT, afp->errmsg, "sequence end is misaligned");
| ^
esl_msafile_clustal.c:203:30: note: 'block_seq_len' was declared here
203 | esl_pos_t block_seq_start, block_seq_len;
| ^~~~~~~~~~~~~
CC esl_msafile_phylip.o
CC esl_msafile_psiblast.o
esl_msafile_psiblast.c: In function 'esl_msafile_psiblast_Read':
esl_msafile_psiblast.c:228:12: warning: 'block_seq_start' may be used uninitialized [-Wmaybe-uninitialized]
228 | if (seq_start != block_seq_start) ESL_XFAIL(eslEFORMAT, afp->errmsg, "sequence start is misaligned");
| ^
esl_msafile_psiblast.c:195:13: note: 'block_seq_start' was declared here
195 | esl_pos_t block_seq_start, block_seq_len;
| ^~~~~~~~~~~~~~~
esl_msafile_psiblast.c:229:12: warning: 'block_seq_len' may be used uninitialized [-Wmaybe-uninitialized]
229 | if (seq_len != block_seq_len) ESL_XFAIL(eslEFORMAT, afp->errmsg, "sequence end is misaligned");
| ^
esl_msafile_psiblast.c:195:30: note: 'block_seq_len' was declared here
195 | esl_pos_t block_seq_start, block_seq_len;
| ^~~~~~~~~~~~~
In function 'phylip_check_interleaved',
inlined from 'esl_msafile_phylip_CheckFileFormat' at esl_msafile_phylip.c:389:13:
esl_msafile_phylip.c:739:16: warning: 'nres1' may be used uninitialized [-Wmaybe-uninitialized]
739 | if (nres1+nres2 == alen) break;
| ~~~~~^~~~~~
esl_msafile_phylip.c: In function 'esl_msafile_phylip_CheckFileFormat':
esl_msafile_phylip.c:687:13: note: 'nres1' was declared here
687 | int nres1;
| ^~~~~
In function 'phylip_deduce_namewidth',
inlined from 'phylip_check_interleaved' at esl_msafile_phylip.c:747:22,
inlined from 'esl_msafile_phylip_CheckFileFormat' at esl_msafile_phylip.c:389:13:
esl_msafile_phylip.c:1048:10: warning: 'ncols0' may be used uninitialized [-Wmaybe-uninitialized]
1048 | for (c = ncols0-1; nres1 && c >= 0; c--)
| ~~^~~~~~~~~~
esl_msafile_phylip.c: In function 'esl_msafile_phylip_CheckFileFormat':
esl_msafile_phylip.c:683:20: note: 'ncols0' was declared here
683 | int ncols, ncols0;
| ^~~~~~
CC esl_msafile_selex.o
CC esl_msafile_stockholm.o
CC esl_msashuffle.o
CC esl_msaweight.o
CC esl_normal.o
CC esl_paml.o
CC esl_quicksort.o
CC esl_random.o
esl_msaweight.c: In function 'esl_msaweight_IDFilter_adv':
esl_msaweight.c:1035:9: warning: 'conscols_112' may be used uninitialized [-Wmaybe-uninitialized]
1035 | collect_counts(cfg, msa, conscols, ncons, ct, NULL);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
esl_msaweight.c:435:1: note: by argument 3 of type 'const int *' to 'collect_counts.isra.0' declared here
435 | collect_counts(const ESL_MSAWEIGHT_CFG *cfg, const ESL_MSA *msa, const int *conscols, int ncons, int **ct, ESL_MSAWEIGHT_DAT *dat)
| ^~~~~~~~~~~~~~
CC esl_rand64.o
CC esl_randomseq.o
CC esl_ratematrix.o
CC esl_recorder.o
CC esl_red_black.o
CC esl_regexp.o
CC esl_rootfinder.o
CC esl_scorematrix.o
CC esl_sq.o
CC esl_sqio.o
CC esl_sqio_ascii.o
CC esl_sqio_ncbi.o
CC esl_ssi.o
CC esl_stack.o
CC esl_stats.o
CC esl_stopwatch.o
CC esl_stretchexp.o
CC esl_subcmd.o
CC esl_threads.o
CC esl_tree.o
CC esl_varint.o
esl_varint.c: In function 'esl_varint_google_decode':
esl_varint.c:474:11: warning: 'grp' may be used uninitialized [-Wmaybe-uninitialized]
474 | if (grp & cmask) { status = eslEOD; goto ERROR; }
| ~~~~^~~~~~~
esl_varint.c:464:12: note: 'grp' was declared here
464 | uint64_t grp; // current k-bit code group
| ^~~
CC esl_vectorops.o
CC esl_weibull.o
CC esl_workqueue.o
CC esl_wuss.o
CC esl_sse.o
esl_wuss.c: In function 'esl_wuss2ct':
esl_wuss.c:136:10: warning: 'status' may be used uninitialized [-Wmaybe-uninitialized]
136 | return status;
| ^~~~~~
esl_wuss.c:56:14: note: 'status' was declared here
56 | int status; /* success or failure return status */
| ^~~~~~
CC esl_avx.o
CC esl_avx512.o
CC esl_neon.o
CC esl_vmx.o
AR libeasel.a
SUBDIR miniapps
GEN esl-afetch
GEN esl-alimanip
GEN esl-alimap
GEN esl-alimask
In function 'mask_based_on_postprobs',
inlined from 'main' at esl-alimask.c:482:18:
esl-alimask.c:1085:33: warning: 'ppidx_thresh' may be used uninitialized [-Wmaybe-uninitialized]
1085 | for(ppidx = 10; ppidx >= ppidx_thresh; ppidx--) {
| ~~~~~~^~~~~~~~~~~~~~~
esl-alimask.c: In function 'main':
esl-alimask.c:1007:7: note: 'ppidx_thresh' was declared here
1007 | int ppidx_thresh;
| ^~~~~~~~~~~~
GEN esl-alimerge
esl-alimerge.c: In function 'validate_and_copy_msa_annotation':
esl-alimerge.c:732:7: warning: 'found_tag' may be used uninitialized [-Wmaybe-uninitialized]
732 | int found_tag;
| ^~~~~~~~~
In file included from /usr/include/stdio.h:906,
from esl-alimerge.c:26:
In function 'fprintf',
inlined from 'main' at esl-alimerge.c:366:2:
/usr/include/bits/stdio2.h:79:10: warning: 'namewidth' may be used uninitialized [-Wmaybe-uninitialized]
79 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
80 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
esl-alimerge.c: In function 'main':
esl-alimerge.c:136:14: note: 'namewidth' was declared here
136 | int namewidth; /* max width of file name */
| ^~~~~~~~~
esl-alimerge.c:412:16: warning: 'clen' may be used uninitialized [-Wmaybe-uninitialized]
412 | if((status = validate_and_copy_msa_annotation(go, outfmt, mmsa, msaA, nali_tot, clen, alen_mmsa, maxgap, maxmis, errbuf)) != eslOK)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
esl-alimerge.c:118:17: note: 'clen' was declared here
118 | int clen; /* consensus length (non-gap #=GC RF length) of all alignments */
| ^~~~
GEN esl-alipid
GEN esl-alirev
GEN esl-alistat
In file included from /usr/include/stdio.h:906,
from esl-alistat.c:6:
In function 'printf',
inlined from 'main' at esl-alistat.c:293:6:
/usr/include/bits/stdio2.h:86:10: warning: 'small' may be used uninitialized [-Wmaybe-uninitialized]
86 | return __printf_chk (__USE_FORTIFY_LEVEL - 1, __fmt, __va_arg_pack ());
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
esl-alistat.c: In function 'main':
esl-alistat.c:74:17: note: 'small' was declared here
74 | int64_t small, large; /* smallest, largest sequence */
| ^~~~~
In function 'printf',
inlined from 'main' at esl-alistat.c:294:6:
/usr/include/bits/stdio2.h:86:10: warning: 'large' may be used uninitialized [-Wmaybe-uninitialized]
86 | return __printf_chk (__USE_FORTIFY_LEVEL - 1, __fmt, __va_arg_pack ());
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
esl-alistat.c: In function 'main':
esl-alistat.c:74:24: note: 'large' was declared here
74 | int64_t small, large; /* smallest, largest sequence */
| ^~~~~
GEN esl-compalign
esl-compalign.c: In function 'main':
esl-compalign.c:231:13: warning: 'masklen' may be used uninitialized [-Wmaybe-uninitialized]
231 | if(masklen != rflen) {
| ^
esl-compalign.c:90:7: note: 'masklen' was declared here
90 | int masklen;
| ^~~~~~~
esl-compalign.c:326:30: warning: 'ppidx' may be used uninitialized [-Wmaybe-uninitialized]
326 | if(do_post) pti[ppidx]++;
| ^
esl-compalign.c:104:7: note: 'ppidx' was declared here
104 | int ppidx; /* index of PP */
| ^~~~~
GEN esl-compstruct
GEN esl-construct
esl-construct.c: In function 'main':
esl-construct.c:573:24: warning: 'fmin' may be used uninitialized [-Wmaybe-uninitialized]
573 | if(do_fmin) { printf("#\n# <x> determined to be %.3f\n", fthresh); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
esl-construct.c:129:9: note: 'fmin' was declared here
129 | float fmin;
| ^~~~
GEN esl-histplot
GEN esl-mask
GEN esl-mixdchlet
GEN esl-reformat
esl-reformat.c: In function 'main':
esl-reformat.c:416:9: warning: 'mapfp' may be used uninitialized [-Wmaybe-uninitialized]
416 | fclose(mapfp);
| ^~~~~~~~~~~~~
esl-reformat.c:304:20: note: 'mapfp' was declared here
304 | FILE *mapfp; /* output stream for the map file */
| ^~~~~
esl-reformat.c:212:13: warning: 'reached_eof' may be used uninitialized [-Wmaybe-uninitialized]
212 | if(! reached_eof) esl_fatal("Input file contains >1 alignments, but afa formatted output file can only contain 1");
| ^
esl-reformat.c:103:10: note: 'reached_eof' was declared here
103 | int reached_eof; /* reached EOF? used only in small mem mode */
| ^~~~~~~~~~~
GEN esl-selectn
GEN esl-seqrange
GEN esl-seqstat
GEN esl-sfetch
GEN esl-shuffle
GEN esl-ssdraw
esl-ssdraw.c: In function 'get_insert_info_from_ifile.constprop.0':
esl-ssdraw.c:6664:32: warning: 'rfpos' may be used uninitialized [-Wmaybe-uninitialized]
6664 | if(! seen_end_of_model_line) esl_fatal("Error reading insert file, didn't read the special '//' line at the end of file %s.\n", rfpos, efp->linenumber, ifile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
esl-ssdraw.c:6500:19: note: 'rfpos' was declared here
6500 | int rfpos; /* current nongap RF position */
| ^~~~~
In file included from esl-ssdraw.c:16:
In function 'draw_header_and_footer',
inlined from 'draw_sspostscript.isra.0' at esl-ssdraw.c:2491:18:
esl-ssdraw.c:6263:56: warning: 'split_idx' may be used uninitialized [-Wmaybe-uninitialized]
6263 | ESL_ALLOC(desc2print, sizeof(char) * (split_idx+1));
| ~~~~~~~~~~^~~
esl-ssdraw.c: In function 'draw_sspostscript.isra.0':
esl-ssdraw.c:6164:10: note: 'split_idx' was declared here
6164 | int i, split_idx;
| ^~~~~~~~~
GEN esl-translate
In file included from /usr/include/stdio.h:906,
from esl-ssdraw.c:10:
In function 'fprintf',
inlined from 'individuals_sspostscript.constprop.0' at esl-ssdraw.c:3663:7:
/usr/include/bits/stdio2.h:79:10: warning: 'namewidth' may be used uninitialized [-Wmaybe-uninitialized]
79 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
80 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
esl-ssdraw.c: In function 'individuals_sspostscript.constprop.0':
esl-ssdraw.c:3347:7: note: 'namewidth' was declared here
3347 | int namewidth; /* length in chars of longest seq name we'll print */
| ^~~~~~~~~
esl-ssdraw.c: In function 'parse_template_file.isra.0':
esl-ssdraw.c:2716:10: warning: 'ps' may be used uninitialized [-Wmaybe-uninitialized]
2716 | if(ps->rflen == msa_rflen) { found_match = TRUE; }
| ~~^~~~~~~
esl-ssdraw.c:2703:19: note: 'ps' was declared here
2703 | SSPostscript_t *ps;
| ^~
GEN esl-weight
CC cmd_alistat.o
CC cmd_downsample.o
CC cmd_filter.o
CC cmd_index.o
GEN easel
SUBDIR libdivsufsort
CC divsufsort.o
AR libdivsufsort.a
SUBDIR src
CC alimask.o
CC build.o
alimask.c: In function 'main':
alimask.c:313:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
313 | if (puts("Must specify mask range with --modelrange, --alirange, --model2ali, or --ali2model\n") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto ERROR;
| ^~
alimask.c:313:154: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
313 | if (puts("Must specify mask range with --modelrange, --alirange, --model2ali, or --ali2model\n") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto ERROR;
| ^~~~
CC cachedb.o
CC cachedb_shard.o
CC emit.o
CC errors.o
CC evalues.o
CC eweight.o
CC generic_decoding.o
CC generic_fwdback.o
CC generic_fwdback_chk.o
CC generic_fwdback_banded.o
CC generic_null2.o
CC generic_msv.o
CC generic_optacc.o
CC generic_stotrace.o
generic_stotrace.c: In function 'p7_GStochasticTrace':
generic_stotrace.c:172:21: warning: 'scur' may be used uninitialized [-Wmaybe-uninitialized]
172 | if ((status = p7_trace_Append(tr, scur, k, i)) != eslOK) goto ERROR;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
generic_stotrace.c:57:11: note: 'scur' was declared here
57 | int scur, sprv;
| ^~~~
CC generic_viterbi.o
CC generic_vtrace.o
CC h2_io.o
CC heatmap.o
CC hmmlogo.o
CC hmmdmstr.o
CC hmmdmstr_shard.o
In function 'process_ServerCmd',
inlined from 'clientside_loop' at hmmdmstr.c:1134:5:
hmmdmstr.c:1020:24: warning: array subscript 'struct HMMD_COMMAND[0]' is partly outside array bounds of 'unsigned char[12]' [-Warray-bounds=]
1020 | cmd->hdr.command = HMMD_CMD_SHUTDOWN;
hmmdmstr.c:1017:18: note: object of size 12 allocated by 'malloc'
1017 | if ((cmd = malloc(sizeof(HMMD_HEADER))) == NULL) LOG_FATAL_MSG("malloc", errno);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
hmmdmstr.c:1046:3: warning: array subscript 'struct HMMD_COMMAND[0]' is partly outside array bounds of 'unsigned char[12]' [-Warray-bounds=]
1046 | printf("Queuing command %d from %s (%d)\n", cmd->hdr.command, parms->ip_addr, parms->sock);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hmmdmstr.c:1017:18: note: object of size 12 allocated by 'malloc'
1017 | if ((cmd = malloc(sizeof(HMMD_HEADER))) == NULL) LOG_FATAL_MSG("malloc", errno);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'process_ServerCmd',
inlined from 'clientside_loop' at hmmdmstr_shard.c:1173:5:
hmmdmstr_shard.c:1059:24: warning: array subscript 'struct HMMD_COMMAND_SHARD[0]' is partly outside array bounds of 'unsigned char[12]' [-Warray-bounds=]
1059 | cmd->hdr.command = HMMD_CMD_SHUTDOWN;
hmmdmstr_shard.c:1056:18: note: object of size 12 allocated by 'malloc'
1056 | if ((cmd = malloc(sizeof(HMMD_HEADER))) == NULL) LOG_FATAL_MSG("malloc", errno);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
hmmdmstr_shard.c:1085:3: warning: array subscript 'struct HMMD_COMMAND_SHARD[0]' is partly outside array bounds of 'unsigned char[12]' [-Warray-bounds=]
1085 | printf("Queuing command %d from %s (%d)\n", cmd->hdr.command, parms->ip_addr, parms->sock);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hmmdmstr_shard.c:1056:18: note: object of size 12 allocated by 'malloc'
1056 | if ((cmd = malloc(sizeof(HMMD_HEADER))) == NULL) LOG_FATAL_MSG("malloc", errno);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:535,
from hmmdmstr.c:10:
In function 'memset',
inlined from 'destroy_worker' at hmmdmstr.c:948:5,
inlined from 'update_workers.part.0' at hmmdmstr.c:285:7:
/usr/include/bits/string_fortified.h:59:10: warning: argument 1 null where non-null expected [-Wnonnull]
59 | return __builtin___memset_chk (__dest, __ch, __len,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
60 | __glibc_objsize0 (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/bits/string_fortified.h:59:10: note: in a call to built-in function 'memset'
In file included from /usr/include/string.h:535,
from hmmdmstr_shard.c:10:
In function 'memset',
inlined from 'destroy_worker' at hmmdmstr_shard.c:987:5,
inlined from 'update_workers.part.0' at hmmdmstr_shard.c:306:7:
/usr/include/bits/string_fortified.h:59:10: warning: argument 1 null where non-null expected [-Wnonnull]
59 | return __builtin___memset_chk (__dest, __ch, __len,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
60 | __glibc_objsize0 (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/bits/string_fortified.h:59:10: note: in a call to built-in function 'memset'
CC hmmd_search_status.o
CC hmmdwrkr.o
CC hmmdwrkr_shard.o
CC hmmdutils.o
CC hmmer.o
CC logsum.o
CC modelconfig.o
CC modelstats.o
CC mpisupport.o
CC seqmodel.o
CC tracealign.o
CC p7_alidisplay.o
CC p7_bg.o
CC p7_builder.o
CC p7_domain.o
p7_domain.c: In function 'p7_domain_Serialize':
p7_domain.c:191:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
191 | network_32bit = esl_hton32(*((uint32_t *) &(obj->envsc))); // ow, this hurts, but is probably the best way to get the
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~
p7_domain.c:198:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
198 | network_32bit = esl_hton32(*((uint32_t *) &(obj->domcorrection)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
p7_domain.c:203:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
203 | network_32bit = esl_hton32(*((uint32_t *) &(obj->dombias)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
p7_domain.c:208:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
208 | network_32bit = esl_hton32(*((uint32_t *) &(obj->oasc)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~
p7_domain.c:213:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
213 | network_32bit = esl_hton32(*((uint32_t *) &(obj->bitscore)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
p7_domain.c:218:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
218 | network_64bit = esl_hton64(*((uint64_t *) &(obj->lnP)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~
p7_domain.c: In function 'p7_domain_Deserialize':
p7_domain.c:341:22: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
341 | ret_obj->envsc = *((float *) &host_32bit);
| ~^~~~~~~~~~~~~~~~~~~~~~
p7_domain.c:347:30: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
347 | ret_obj->domcorrection = *((float *) &host_32bit);
| ~^~~~~~~~~~~~~~~~~~~~~~
p7_domain.c:353:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
353 | ret_obj->dombias = *((float *) &host_32bit);
| ~^~~~~~~~~~~~~~~~~~~~~~
p7_domain.c:359:21: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
359 | ret_obj->oasc = *((float *) &host_32bit);
| ~^~~~~~~~~~~~~~~~~~~~~~
p7_domain.c:365:25: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
365 | ret_obj->bitscore = *((float *) &host_32bit);
| ~^~~~~~~~~~~~~~~~~~~~~~
p7_domain.c:371:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
371 | ret_obj->lnP = *((double *) &host_64bit);
| ~^~~~~~~~~~~~~~~~~~~~~~~
p7_domain.c:398:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
398 | ret_obj->scores_per_pos[i] = *((float *) &host_32bit);
| ~^~~~~~~~~~~~~~~~~~~~~~
CC p7_domaindef.o
CC p7_gbands.o
p7_domaindef.c: In function 'rescore_isolated_domain':
p7_domaindef.c:932:5: warning: 'orig_L' may be used uninitialized [-Wmaybe-uninitialized]
932 | p7_oprofile_ReconfigRestLength(om, orig_L);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
p7_domaindef.c:827:18: note: 'orig_L' was declared here
827 | int orig_L;
| ^~~~~~
CC p7_gmx.o
CC p7_gmxb.o
CC p7_gmxchk.o
CC p7_hit.o
CC p7_hmm.o
p7_hit.c: In function 'p7_hit_Serialize':
p7_hit.c:226:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
226 | network_64bit = esl_hton64(*((uint64_t *) &(obj->sortkey)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
p7_hit.c:231:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
231 | network_32bit = esl_hton32(*((uint32_t *) &(obj->score)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~
p7_hit.c:236:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
236 | network_32bit = esl_hton32(*((uint32_t *) &(obj->pre_score)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
p7_hit.c:241:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
241 | network_32bit = esl_hton32(*((uint32_t *) &(obj->sum_score)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
p7_hit.c:246:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
246 | network_64bit = esl_hton64(*((uint64_t *) &(obj->lnP)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~
p7_hit.c:251:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
251 | network_64bit = esl_hton64(*((uint64_t *) &(obj->pre_lnP)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
p7_hit.c:256:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
256 | network_64bit = esl_hton64(*((uint64_t *) &(obj->sum_lnP)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
p7_hit.c:261:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
261 | network_32bit = esl_hton32(*((uint32_t *) &(obj->nexpected)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
p7_hit.c: In function 'p7_hit_Deserialize':
p7_hit.c:408:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
408 | ret_obj->sortkey = *((double *) &host_64bit);
| ~^~~~~~~~~~~~~~~~~~~~~~~
p7_hit.c:414:22: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
414 | ret_obj->score = *((float *) &host_32bit);
| ~^~~~~~~~~~~~~~~~~~~~~~
p7_hit.c:420:26: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
420 | ret_obj->pre_score = *((float *) &host_32bit);
| ~^~~~~~~~~~~~~~~~~~~~~~
p7_hit.c:426:26: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
426 | ret_obj->sum_score = *((float *) &host_32bit);
| ~^~~~~~~~~~~~~~~~~~~~~~
p7_hit.c:432:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
432 | ret_obj->lnP = *((double *) &host_64bit);
| ~^~~~~~~~~~~~~~~~~~~~~~~
p7_hit.c:438:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
438 | ret_obj->pre_lnP = *((double *) &host_64bit);
| ~^~~~~~~~~~~~~~~~~~~~~~~
p7_hit.c:444:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
444 | ret_obj->sum_lnP = *((double *) &host_64bit);
| ~^~~~~~~~~~~~~~~~~~~~~~~
p7_hit.c:450:26: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
450 | ret_obj->nexpected = *((float *) &host_32bit);
| ~^~~~~~~~~~~~~~~~~~~~~~
CC p7_hmmcache.o
CC p7_hmmd_search_stats.o
p7_hmmd_search_stats.c: In function 'p7_hmmd_search_stats_Serialize':
p7_hmmd_search_stats.c:89:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
89 | network_64bit = esl_hton64(*((uint64_t *) &(obj->elapsed))); // ow, this hurts, but is probably the best way to get the
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
p7_hmmd_search_stats.c:97:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
97 | network_64bit = esl_hton64(*((uint64_t *) &(obj->user)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~
p7_hmmd_search_stats.c:103:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
103 | network_64bit = esl_hton64(*((uint64_t *) &(obj->sys)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~
p7_hmmd_search_stats.c:109:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
109 | network_64bit = esl_hton64(*((uint64_t *) &(obj->Z)));
| ~^~~~~~~~~~~~~~~~~~~~~~~
p7_hmmd_search_stats.c:115:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
115 | network_64bit = esl_hton64(*((uint64_t *) &(obj->domZ)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~
p7_hmmd_search_stats.c: In function 'p7_hmmd_search_stats_Deserialize':
p7_hmmd_search_stats.c:256:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
256 | ret_obj->elapsed = *((double *) &host_64bit);
| ~^~~~~~~~~~~~~~~~~~~~~~~
p7_hmmd_search_stats.c:262:21: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
262 | ret_obj->user = *((double *) &host_64bit);
| ~^~~~~~~~~~~~~~~~~~~~~~~
p7_hmmd_search_stats.c:268:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
268 | ret_obj->sys = *((double *) &host_64bit);
| ~^~~~~~~~~~~~~~~~~~~~~~~
p7_hmmd_search_stats.c:274:18: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
274 | ret_obj->Z = *((double *) &host_64bit);
| ~^~~~~~~~~~~~~~~~~~~~~~~
p7_hmmd_search_stats.c:280:21: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
280 | ret_obj->domZ = *((double *) &host_64bit);
| ~^~~~~~~~~~~~~~~~~~~~~~~
CC p7_hmmfile.o
CC p7_hmmwindow.o
CC p7_pipeline.o
CC p7_prior.o
CC p7_profile.o
CC p7_spensemble.o
CC p7_tophits.o
In file included from p7_spensemble.c:7:
p7_spensemble.c: In function 'p7_spensemble_Cluster':
p7_spensemble.c:344:43: warning: 'imax' may be used uninitialized [-Wmaybe-uninitialized]
344 | cwindow_width = ESL_MAX(ESL_MAX(imax-imin+1, jmax-jmin+1),
| ~~~~^~~~~
p7_spensemble.c:294:7: note: 'imax' was declared here
294 | int imax, jmax, kmax, mmax;
| ^~~~
p7_spensemble.c:344:56: warning: 'jmin' may be used uninitialized [-Wmaybe-uninitialized]
344 | cwindow_width = ESL_MAX(ESL_MAX(imax-imin+1, jmax-jmin+1),
| ~~~~^~~~~
p7_spensemble.c:293:13: note: 'jmin' was declared here
293 | int imin, jmin, kmin, mmin;
| ^~~~
p7_spensemble.c:345:43: warning: 'kmin' may be used uninitialized [-Wmaybe-uninitialized]
345 | ESL_MAX(kmax-kmin+1, mmax-mmin+1));
| ~~~~^~~~~
p7_spensemble.c:293:19: note: 'kmin' was declared here
293 | int imin, jmin, kmin, mmin;
| ^~~~
p7_spensemble.c:345:56: warning: 'mmin' may be used uninitialized [-Wmaybe-uninitialized]
345 | ESL_MAX(kmax-kmin+1, mmax-mmin+1));
| ~~~~^~~~~
p7_spensemble.c:293:25: note: 'mmin' was declared here
293 | int imin, jmin, kmin, mmin;
| ^~~~
p7_spensemble.c:344:56: warning: 'jmax' may be used uninitialized [-Wmaybe-uninitialized]
344 | cwindow_width = ESL_MAX(ESL_MAX(imax-imin+1, jmax-jmin+1),
| ~~~~^~~~~
p7_spensemble.c:294:13: note: 'jmax' was declared here
294 | int imax, jmax, kmax, mmax;
| ^~~~
p7_spensemble.c:345:43: warning: 'kmax' may be used uninitialized [-Wmaybe-uninitialized]
345 | ESL_MAX(kmax-kmin+1, mmax-mmin+1));
| ~~~~^~~~~
p7_spensemble.c:294:19: note: 'kmax' was declared here
294 | int imax, jmax, kmax, mmax;
| ^~~~
p7_spensemble.c:345:56: warning: 'mmax' may be used uninitialized [-Wmaybe-uninitialized]
345 | ESL_MAX(kmax-kmin+1, mmax-mmin+1));
| ~~~~^~~~~
p7_spensemble.c:294:25: note: 'mmax' was declared here
294 | int imax, jmax, kmax, mmax;
| ^~~~
CC p7_trace.o
In file included from /usr/include/stdio.h:906,
from ../easel/easel.h:22,
from p7_tophits.c:16:
In function 'fprintf',
inlined from 'p7_tophits_Targets' at p7_tophits.c:1142:12:
/usr/include/bits/stdio2.h:79:10: warning: 'posw' may be used uninitialized [-Wmaybe-uninitialized]
79 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
80 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
p7_tophits.c: In function 'p7_tophits_Targets':
p7_tophits.c:1068:10: note: 'posw' was declared here
1068 | int posw;
| ^~~~
CC p7_scoredata.o
CC hmmpgmd2msa.o
CC fm_alphabet.o
CC fm_general.o
CC fm_sse.o
CC fm_ssv.o
CC hmmalign.o
In function 'FM_extendSeed',
inlined from 'p7_SSVFM_longlarget' at fm_ssv.c:806:5:
fm_ssv.c:696:32: warning: 'max_hit_start' may be used uninitialized [-Wmaybe-uninitialized]
696 | diag->k = model_start + max_hit_start - 1;
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~
fm_ssv.c: In function 'p7_SSVFM_longlarget':
fm_ssv.c:648:22: note: 'max_hit_start' was declared here
648 | int64_t hit_start, max_hit_start, max_hit_end;
| ^~~~~~~~~~~~~
In function 'FM_extendSeed',
inlined from 'p7_SSVFM_longlarget' at fm_ssv.c:806:5:
fm_ssv.c:697:31: warning: 'max_hit_end' may be used uninitialized [-Wmaybe-uninitialized]
697 | diag->length = max_hit_end - max_hit_start + 1;
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~
fm_ssv.c: In function 'p7_SSVFM_longlarget':
fm_ssv.c:648:37: note: 'max_hit_end' was declared here
648 | int64_t hit_start, max_hit_start, max_hit_end;
| ^~~~~~~~~~~
CC hmmbuild.o
CC hmmconvert.o
CC hmmemit.o
CC hmmfetch.o
CC hmmpgmd.o
CC hmmpgmd_shard.o
CC hmmpress.o
CC hmmscan.o
CC hmmsearch.o
CC hmmsim.o
In function 'output_filter_power',
inlined from 'output_result' at hmmsim.c:756:38,
inlined from 'serial_master' at hmmsim.c:384:11,
inlined from 'main' at hmmsim.c:248:7:
hmmsim.c:902:25: warning: 'mu' may be used uninitialized [-Wmaybe-uninitialized]
902 | esl_exp_surv (scores[i], pmu, plambda));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hmmsim.c: In function 'main':
hmmsim.c:360:15: note: 'mu' was declared here
360 | double mu, lambda;
| ^~
In function 'output_filter_power',
inlined from 'output_result' at hmmsim.c:756:38,
inlined from 'serial_master' at hmmsim.c:384:11,
inlined from 'main' at hmmsim.c:248:7:
hmmsim.c:902:25: warning: 'lambda' may be used uninitialized [-Wmaybe-uninitialized]
902 | esl_exp_surv (scores[i], pmu, plambda));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hmmsim.c: In function 'main':
hmmsim.c:360:19: note: 'lambda' was declared here
360 | double mu, lambda;
| ^~~~~~
CC hmmstat.o
CC jackhmmer.o
CC phmmer.o
CC nhmmer.o
CC nhmmscan.o
In function 'serial_loop',
inlined from 'serial_master' at nhmmer.c:1071:35:
nhmmer.c:1386:6: warning: 'dbsq_revcmp' may be used uninitialized [-Wmaybe-uninitialized]
1386 | if (dbsq_revcmp) esl_sq_Destroy(dbsq_revcmp);
| ^
nhmmer.c: In function 'serial_master':
nhmmer.c:1338:13: note: 'dbsq_revcmp' was declared here
1338 | ESL_SQ *dbsq_revcmp;
| ^~~~~~~~~~~
CC makehmmerdb.o
CC hmmc2.o
CC hmmerfm-exactmatch.o
AR libhmmer-src.stamp
SUBDIR impl_sse
CC decoding.o
In file included from /usr/include/stdio.h:906,
from ../easel/easel.h:22,
from hmmerfm-exactmatch.c:6:
In function 'fprintf',
inlined from 'output_header' at hmmerfm-exactmatch.c:123:7,
inlined from 'main' at hmmerfm-exactmatch.c:303:3:
/usr/include/bits/stdio2.h:79:10: warning: 'alph' may be used uninitialized [-Wmaybe-uninitialized]
79 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
80 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
hmmerfm-exactmatch.c: In function 'main':
hmmerfm-exactmatch.c:94:9: note: 'alph' was declared here
94 | char *alph;
| ^~~~
CC fwdback.o
CC io.o
CC ssvfilter.o
CC msvfilter.o
CC null2.o
CC optacc.o
CC stotrace.o
optacc.c: In function 'p7_OATrace':
optacc.c:255:21: warning: 'smax' may be used uninitialized [-Wmaybe-uninitialized]
255 | if ((status = p7_trace_AppendWithPP(tr, s1, k, i, postprob)) != eslOK) return status;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
optacc.c:398:10: note: 'smax' was declared here
398 | int smax, kmax;
| ^~~~
In function 'get_postprob',
inlined from 'p7_OATrace' at optacc.c:254:18:
optacc.c:269:21: warning: 'kmax' may be used uninitialized [-Wmaybe-uninitialized]
269 | int q = (k-1) % Q; /* (q,r) is position of the current DP cell M(i,k) */
| ~~^~~
optacc.c: In function 'p7_OATrace':
optacc.c:398:16: note: 'kmax' was declared here
398 | int smax, kmax;
| ^~~~
CC vitfilter.o
CC p7_omx.o
CC p7_oprofile.o
CC mpi.o
AR libhmmer-impl.stamp
GEN alimask
GEN hmmalign
GEN hmmbuild
GEN hmmconvert
GEN hmmemit
GEN hmmfetch
GEN hmmlogo
GEN hmmpgmd
GEN hmmpgmd_shard
GEN hmmpress
GEN hmmscan
GEN hmmsearch
GEN hmmsim
GEN hmmstat
GEN jackhmmer
GEN phmmer
GEN nhmmer
GEN nhmmscan
GEN makehmmerdb
GEN hmmc2
GEN hmmerfm-exactmatch
SUBDIR profmark
CC create-profmark.o
CC rocplot.o
In file included from /usr/include/stdio.h:906,
from create-profmark.c:18:
In function 'fprintf',
inlined from 'main' at create-profmark.c:258:4:
/usr/include/bits/stdio2.h:79:10: warning: 'nfrags' may be used uninitialized [-Wmaybe-uninitialized]
79 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
80 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
create-profmark.c: In function 'main':
create-profmark.c:167:17: note: 'nfrags' was declared here
167 | int nfrags; /* # of fragments removed */
| ^~~~~~
In function 'synthesize_positives',
inlined from 'main' at create-profmark.c:253:4:
create-profmark.c:536:27: warning: 'j' may be used uninitialized [-Wmaybe-uninitialized]
536 | memcpy(sq->dsq+j+d1n+1, domain2->dsq+1, sizeof(ESL_DSQ) * d2n);
| ^
create-profmark.c: In function 'main':
create-profmark.c:445:13: note: 'j' was declared here
445 | int i,j;
| ^
GEN rocplot
GEN create-profmark
../easel/esl_ssi.h:115:13: warning: type of 'esl_ssi_FindNumber' does not match original declaration [-Wlto-type-mismatch]
115 | extern int esl_ssi_FindNumber(ESL_SSI *ssi, int64_t nkey,
| ^
../easel/esl_ssi.c:253:1: note: 'esl_ssi_FindNumber' was previously declared here
253 | esl_ssi_FindNumber(ESL_SSI *ssi, int64_t nkey, uint16_t *opt_fh, off_t *opt_roff, off_t *opt_doff, int64_t *opt_L, char **opt_pkey)
| ^
../easel/esl_ssi.c:253:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.Rl1RtF
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386
++ dirname /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd hmmer-3.3.2
+ rm -rf /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386
+ make install DESTDIR=/builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386
SUBDIR easel
SUBDIR miniapps
SUBDIR libdivsufsort
SUBDIR src
SUBDIR impl_sse
SUBDIR profmark
/usr/bin/install -c -d /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin
/usr/bin/install -c -d /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/share/man/man1
make -C src install
make[1]: Entering directory '/builddir/build/BUILD/hmmer-3.3.2/src'
for file in alimask hmmalign hmmbuild hmmconvert hmmemit hmmfetch hmmlogo hmmpgmd hmmpgmd_shard hmmpress hmmscan hmmsearch hmmsim hmmstat jackhmmer phmmer nhmmer nhmmscan makehmmerdb; do \
/usr/bin/install -c -m 0755 $file /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/ ;\
done
make[1]: Leaving directory '/builddir/build/BUILD/hmmer-3.3.2/src'
make -C documentation install
make[1]: Entering directory '/builddir/build/BUILD/hmmer-3.3.2/documentation'
make -C man install
make[2]: Entering directory '/builddir/build/BUILD/hmmer-3.3.2/documentation/man'
for file in hmmer hmmalign hmmbuild hmmc2 hmmconvert hmmemit hmmfetch hmmlogo hmmpgmd hmmpgmd_shard hmmpress hmmscan hmmsearch hmmsim hmmstat jackhmmer makehmmerdb phmmer nhmmer nhmmscan alimask; do \
/usr/bin/install -c -m 0664 $file.man /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/share/man/man1/${file}.1 ;\
done
make[2]: Leaving directory '/builddir/build/BUILD/hmmer-3.3.2/documentation/man'
make[1]: Leaving directory '/builddir/build/BUILD/hmmer-3.3.2/documentation'
+ cd easel
+ make install DESTDIR=/builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386
/usr/bin/install -c -d /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin
/usr/bin/install -c -d /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/share/man/man1
make -C miniapps install
make[1]: Entering directory '/builddir/build/BUILD/hmmer-3.3.2/easel/miniapps'
/usr/bin/install -c -m 0755 easel /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/
for file in esl-afetch esl-alimanip esl-alimap esl-alimask esl-alimerge esl-alipid esl-alirev esl-alistat esl-compalign esl-compstruct esl-construct esl-histplot esl-mask esl-mixdchlet esl-reformat esl-selectn esl-seqrange esl-seqstat esl-sfetch esl-shuffle esl-ssdraw esl-translate esl-weight; do \
/usr/bin/install -c -m 0755 $file /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/ ;\
done
for file in esl-afetch esl-alimanip esl-alimap esl-alimask esl-alimerge esl-alipid esl-alirev esl-alistat esl-compalign esl-compstruct esl-construct esl-histplot esl-mask esl-mixdchlet esl-reformat esl-selectn esl-seqrange esl-seqstat esl-sfetch esl-shuffle esl-ssdraw esl-translate esl-weight; do \
/usr/bin/install -c -m 0644 $file.man /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/share/man/man1/${file}.1 ;\
done
make[1]: Leaving directory '/builddir/build/BUILD/hmmer-3.3.2/easel/miniapps'
+ /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 3.3.2-2.fc38 --unique-debug-suffix -3.3.2-2.fc38.i386 --unique-debug-src-base hmmer-3.3.2-2.fc38.i386 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/hmmer-3.3.2
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/easel
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/alimask
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-afetch
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-alimanip
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-alimap
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-alimask
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-alimerge
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-alipid
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extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-compstruct
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extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-mask
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-mixdchlet
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extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-selectn
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-seqrange
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-seqstat
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-sfetch
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extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-translate
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/esl-weight
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/hmmalign
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/hmmbuild
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/hmmconvert
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/hmmemit
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/hmmfetch
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/hmmlogo
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/hmmpgmd
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/hmmpgmd_shard
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extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/hmmsearch
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extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/hmmstat
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/jackhmmer
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/makehmmerdb
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/nhmmer
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/nhmmscan
extracting debug info from /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/bin/phmmer
original debug info size: 36644kB, size after compression: 27936kB
/usr/bin/sepdebugcrcfix: Updated 43 CRC32s, 0 CRC32s did match.
13596 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
+ /usr/lib/rpm/brp-remove-la-files
+ /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0
+ /usr/lib/rpm/redhat/brp-python-hardlink
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.lSswc3
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd hmmer-3.3.2
+ make check
SUBDIR easel
GEN easel_utest
./easel.c: In function 'esl_fail':
./easel.c:79:12: warning: 'ap' may be used uninitialized [-Wmaybe-uninitialized]
79 | else vsyslog(LOG_ERR, format, ap); // SRE: TODO: check this.
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
./easel.c:69:15: note: 'ap' was declared here
69 | va_list ap;
| ^~
./easel.c: In function 'esl_exception':
./easel.c:157:12: warning: 'argp' may be used uninitialized [-Wmaybe-uninitialized]
157 | else vsyslog(LOG_ERR, format, argp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./easel.c:131:11: note: 'argp' was declared here
131 | va_list argp;
| ^~~~
./easel.c: In function 'esl_fatal':
./easel.c:308:8: warning: 'argp' may be used uninitialized [-Wmaybe-uninitialized]
308 | else vsyslog(LOG_ERR, format, argp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./easel.c:295:11: note: 'argp' was declared here
295 | va_list argp;
| ^~~~
GEN esl_alloc_utest
GEN esl_alphabet_utest
GEN esl_bitfield_utest
GEN esl_buffer_utest
GEN esl_cluster_utest
GEN esl_cpu_utest
GEN esl_dirichlet_utest
GEN esl_distance_utest
GEN esl_dmatrix_utest
GEN esl_dsqdata_utest
GEN esl_exponential_utest
GEN esl_fileparser_utest
GEN esl_gamma_utest
GEN esl_gencode_utest
GEN esl_getopts_utest
GEN esl_graph_utest
GEN esl_gumbel_utest
GEN esl_heap_utest
GEN esl_histogram_utest
GEN esl_hmm_utest
GEN esl_huffman_utest
GEN esl_hyperexp_utest
GEN esl_json_utest
./esl_json.c: In function 'esl_json_Validate':
./esl_json.c:752:33: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
752 | case eslJSON_BOOLEAN: if (! esl_memstrcmp(bf->mem + pos1, pos2-pos1+1, "true") &&
| ^~
./esl_json.c:753:167: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
753 | ! esl_memstrcmp(bf->mem + pos1, pos2-pos1+1, "false")) ESL_FAIL(eslFAIL, errbuf, "boolean isn't a boolean, tok %d", i); break;
| ^~~~~
GEN esl_keyhash_utest
In function 'utest_stringkeys',
inlined from 'main' at ./esl_keyhash.c:875:3:
./esl_keyhash.c:786:54: warning: 'h42' may be used uninitialized [-Wmaybe-uninitialized]
786 | if ( esl_keyhash_Lookup(kh, "XX", -1, &h) != eslOK || h != h42) esl_fatal(msg);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
./esl_keyhash.c: In function 'main':
./esl_keyhash.c:749:25: note: 'h42' was declared here
749 | int i,j,h,h42;
| ^~~
In function 'utest_memkeys',
inlined from 'main' at ./esl_keyhash.c:876:3:
./esl_keyhash.c:835:62: warning: 'h42' may be used uninitialized [-Wmaybe-uninitialized]
835 | if ( esl_keyhash_Lookup(kh, keys[42], keylen, &h) != eslOK || h != h42) esl_fatal(msg);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
./esl_keyhash.c: In function 'main':
./esl_keyhash.c:812:23: note: 'h42' was declared here
812 | int i,h,h42;
| ^~~
GEN esl_matrixops_utest
GEN esl_mem_utest
GEN esl_minimizer_utest
./esl_minimizer.c: In function 'esl_min_ConjugateGradientDescent':
./esl_minimizer.c:243:23: warning: 'fx' may be used uninitialized [-Wmaybe-uninitialized]
243 | if (opt_fx) *opt_fx = fx;
| ~~~~~~~~^~~~
./esl_minimizer.c:119:10: note: 'fx' was declared here
119 | double fx;
| ^~
In function 'brent',
inlined from 'esl_min_ConjugateGradientDescent' at ./esl_minimizer.c:192:7:
./esl_minimizer.c:720:21: warning: 'ax' may be used uninitialized [-Wmaybe-uninitialized]
720 | m = 0.5 * (a+b);
| ~~^~~
./esl_minimizer.c: In function 'esl_min_ConjugateGradientDescent':
./esl_minimizer.c:118:10: note: 'ax' was declared here
118 | double ax,bx,cx;
| ^~
In function 'brent',
inlined from 'esl_min_ConjugateGradientDescent' at ./esl_minimizer.c:192:7:
./esl_minimizer.c:720:21: warning: 'cx' may be used uninitialized [-Wmaybe-uninitialized]
720 | m = 0.5 * (a+b);
| ~~^~~
./esl_minimizer.c: In function 'esl_min_ConjugateGradientDescent':
./esl_minimizer.c:118:16: note: 'cx' was declared here
118 | double ax,bx,cx;
| ^~
GEN esl_mixdchlet_utest
GEN esl_msa_utest
GEN esl_msacluster_utest
GEN esl_msafile_utest
GEN esl_msafile2_utest
GEN esl_msafile_a2m_utest
GEN esl_msafile_afa_utest
GEN esl_msafile_clustal_utest
./esl_msafile_clustal.c: In function 'esl_msafile_clustal_Read':
./esl_msafile_clustal.c:247:12: warning: 'block_seq_start' may be used uninitialized [-Wmaybe-uninitialized]
247 | if (seq_start != block_seq_start) ESL_XFAIL(eslEFORMAT, afp->errmsg, "sequence start is misaligned");
| ^
./esl_msafile_clustal.c:203:13: note: 'block_seq_start' was declared here
203 | esl_pos_t block_seq_start, block_seq_len;
| ^~~~~~~~~~~~~~~
./esl_msafile_clustal.c:248:12: warning: 'block_seq_len' may be used uninitialized [-Wmaybe-uninitialized]
248 | if (seq_len != block_seq_len) ESL_XFAIL(eslEFORMAT, afp->errmsg, "sequence end is misaligned");
| ^
./esl_msafile_clustal.c:203:30: note: 'block_seq_len' was declared here
203 | esl_pos_t block_seq_start, block_seq_len;
| ^~~~~~~~~~~~~
GEN esl_msafile_phylip_utest
In function 'phylip_check_interleaved',
inlined from 'esl_msafile_phylip_CheckFileFormat' at ./esl_msafile_phylip.c:389:13:
./esl_msafile_phylip.c:739:16: warning: 'nres1' may be used uninitialized [-Wmaybe-uninitialized]
739 | if (nres1+nres2 == alen) break;
| ~~~~~^~~~~~
./esl_msafile_phylip.c: In function 'esl_msafile_phylip_CheckFileFormat':
./esl_msafile_phylip.c:687:13: note: 'nres1' was declared here
687 | int nres1;
| ^~~~~
In function 'phylip_deduce_namewidth',
inlined from 'phylip_check_interleaved' at ./esl_msafile_phylip.c:747:22,
inlined from 'esl_msafile_phylip_CheckFileFormat' at ./esl_msafile_phylip.c:389:13:
./esl_msafile_phylip.c:1048:10: warning: 'ncols0' may be used uninitialized [-Wmaybe-uninitialized]
1048 | for (c = ncols0-1; nres1 && c >= 0; c--)
| ~~^~~~~~~~~~
./esl_msafile_phylip.c: In function 'esl_msafile_phylip_CheckFileFormat':
./esl_msafile_phylip.c:683:20: note: 'ncols0' was declared here
683 | int ncols, ncols0;
| ^~~~~~
GEN esl_msafile_psiblast_utest
./esl_msafile_psiblast.c: In function 'esl_msafile_psiblast_Read':
./esl_msafile_psiblast.c:228:12: warning: 'block_seq_start' may be used uninitialized [-Wmaybe-uninitialized]
228 | if (seq_start != block_seq_start) ESL_XFAIL(eslEFORMAT, afp->errmsg, "sequence start is misaligned");
| ^
./esl_msafile_psiblast.c:195:13: note: 'block_seq_start' was declared here
195 | esl_pos_t block_seq_start, block_seq_len;
| ^~~~~~~~~~~~~~~
./esl_msafile_psiblast.c:229:12: warning: 'block_seq_len' may be used uninitialized [-Wmaybe-uninitialized]
229 | if (seq_len != block_seq_len) ESL_XFAIL(eslEFORMAT, afp->errmsg, "sequence end is misaligned");
| ^
./esl_msafile_psiblast.c:195:30: note: 'block_seq_len' was declared here
195 | esl_pos_t block_seq_start, block_seq_len;
| ^~~~~~~~~~~~~
GEN esl_msafile_selex_utest
GEN esl_msafile_stockholm_utest
GEN esl_msaweight_utest
./esl_msaweight.c: In function 'esl_msaweight_IDFilter_adv':
./esl_msaweight.c:1035:9: warning: 'conscols_112' may be used uninitialized [-Wmaybe-uninitialized]
1035 | collect_counts(cfg, msa, conscols, ncons, ct, NULL);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./esl_msaweight.c:435:1: note: by argument 3 of type 'const int *' to 'collect_counts.isra.0' declared here
435 | collect_counts(const ESL_MSAWEIGHT_CFG *cfg, const ESL_MSA *msa, const int *conscols, int ncons, int **ct, ESL_MSAWEIGHT_DAT *dat)
| ^~~~~~~~~~~~~~
GEN esl_normal_utest
GEN esl_quicksort_utest
GEN esl_random_utest
GEN esl_rand64_utest
GEN esl_randomseq_utest
GEN esl_ratematrix_utest
GEN esl_red_black_utest
In function 'esl_red_black_doublekey_linked_list_test',
inlined from 'main' at ./esl_red_black.c:702:8:
./esl_red_black.c:563:5: warning: 'prev' may be used uninitialized [-Wmaybe-uninitialized]
563 | if(prev != head_ptr){
| ^
./esl_red_black.c: In function 'main':
./esl_red_black.c:546:28: note: 'prev' was declared here
546 | ESL_RED_BLACK_DOUBLEKEY *prev;
| ^~~~
GEN esl_recorder_utest
GEN esl_regexp_utest
GEN esl_rootfinder_utest
GEN esl_scorematrix_utest
GEN esl_sq_utest
GEN esl_sqio_utest
GEN esl_ssi_utest
GEN esl_stack_utest
GEN esl_stats_utest
GEN esl_stretchexp_utest
GEN esl_tree_utest
GEN esl_varint_utest
./esl_varint.c: In function 'esl_varint_google_decode':
./esl_varint.c:474:11: warning: 'grp' may be used uninitialized [-Wmaybe-uninitialized]
474 | if (grp & cmask) { status = eslEOD; goto ERROR; }
| ~~~~^~~~~~~
./esl_varint.c:464:12: note: 'grp' was declared here
464 | uint64_t grp; // current k-bit code group
| ^~~
GEN esl_vectorops_utest
GEN esl_weibull_utest
GEN esl_wuss_utest
./esl_wuss.c: In function 'esl_wuss2ct':
./esl_wuss.c:136:10: warning: 'status' may be used uninitialized [-Wmaybe-uninitialized]
136 | return status;
| ^~~~~~
./esl_wuss.c:56:14: note: 'status' was declared here
56 | int status; /* success or failure return status */
| ^~~~~~
GEN esl_sse_utest
GEN esl_avx_utest
GEN esl_avx512_utest
GEN esl_neon_utest
GEN esl_vmx_utest
SUBDIR miniapps
SUBDIR libdivsufsort
SUBDIR src
SUBDIR impl_sse
GEN build_utest
GEN generic_fwdback_utest
GEN generic_fwdback_chk_utest
GEN generic_msv_utest
GEN generic_stotrace_utest
./generic_stotrace.c: In function 'p7_GStochasticTrace':
./generic_stotrace.c:172:21: warning: 'scur' may be used uninitialized [-Wmaybe-uninitialized]
172 | if ((status = p7_trace_Append(tr, scur, k, i)) != eslOK) goto ERROR;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./generic_stotrace.c:57:11: note: 'scur' was declared here
57 | int scur, sprv;
| ^~~~
GEN generic_viterbi_utest
GEN hmmer_utest
GEN logsum_utest
GEN modelconfig_utest
GEN seqmodel_utest
GEN p7_alidisplay_utest
GEN p7_bg_utest
GEN p7_domain_utest
./p7_domain.c: In function 'p7_domain_Serialize':
./p7_domain.c:191:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
191 | network_32bit = esl_hton32(*((uint32_t *) &(obj->envsc))); // ow, this hurts, but is probably the best way to get the
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_domain.c:198:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
198 | network_32bit = esl_hton32(*((uint32_t *) &(obj->domcorrection)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_domain.c:203:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
203 | network_32bit = esl_hton32(*((uint32_t *) &(obj->dombias)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_domain.c:208:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
208 | network_32bit = esl_hton32(*((uint32_t *) &(obj->oasc)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_domain.c:213:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
213 | network_32bit = esl_hton32(*((uint32_t *) &(obj->bitscore)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_domain.c:218:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
218 | network_64bit = esl_hton64(*((uint64_t *) &(obj->lnP)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~
./p7_domain.c: In function 'p7_domain_Deserialize':
./p7_domain.c:341:22: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
341 | ret_obj->envsc = *((float *) &host_32bit);
| ~^~~~~~~~~~~~~~~~~~~~~~
./p7_domain.c:347:30: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
347 | ret_obj->domcorrection = *((float *) &host_32bit);
| ~^~~~~~~~~~~~~~~~~~~~~~
./p7_domain.c:353:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
353 | ret_obj->dombias = *((float *) &host_32bit);
| ~^~~~~~~~~~~~~~~~~~~~~~
./p7_domain.c:359:21: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
359 | ret_obj->oasc = *((float *) &host_32bit);
| ~^~~~~~~~~~~~~~~~~~~~~~
./p7_domain.c:365:25: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
365 | ret_obj->bitscore = *((float *) &host_32bit);
| ~^~~~~~~~~~~~~~~~~~~~~~
./p7_domain.c:371:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
371 | ret_obj->lnP = *((double *) &host_64bit);
| ~^~~~~~~~~~~~~~~~~~~~~~~
./p7_domain.c:398:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
398 | ret_obj->scores_per_pos[i] = *((float *) &host_32bit);
| ~^~~~~~~~~~~~~~~~~~~~~~
GEN p7_gmx_utest
GEN p7_gmxchk_utest
GEN p7_hit_utest
./p7_hit.c: In function 'p7_hit_Serialize':
./p7_hit.c:226:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
226 | network_64bit = esl_hton64(*((uint64_t *) &(obj->sortkey)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c:231:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
231 | network_32bit = esl_hton32(*((uint32_t *) &(obj->score)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c:236:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
236 | network_32bit = esl_hton32(*((uint32_t *) &(obj->pre_score)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c:241:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
241 | network_32bit = esl_hton32(*((uint32_t *) &(obj->sum_score)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c:246:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
246 | network_64bit = esl_hton64(*((uint64_t *) &(obj->lnP)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c:251:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
251 | network_64bit = esl_hton64(*((uint64_t *) &(obj->pre_lnP)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c:256:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
256 | network_64bit = esl_hton64(*((uint64_t *) &(obj->sum_lnP)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c:261:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
261 | network_32bit = esl_hton32(*((uint32_t *) &(obj->nexpected)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c: In function 'p7_hit_Deserialize':
./p7_hit.c:408:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
408 | ret_obj->sortkey = *((double *) &host_64bit);
| ~^~~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c:414:22: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
414 | ret_obj->score = *((float *) &host_32bit);
| ~^~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c:420:26: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
420 | ret_obj->pre_score = *((float *) &host_32bit);
| ~^~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c:426:26: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
426 | ret_obj->sum_score = *((float *) &host_32bit);
| ~^~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c:432:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
432 | ret_obj->lnP = *((double *) &host_64bit);
| ~^~~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c:438:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
438 | ret_obj->pre_lnP = *((double *) &host_64bit);
| ~^~~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c:444:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
444 | ret_obj->sum_lnP = *((double *) &host_64bit);
| ~^~~~~~~~~~~~~~~~~~~~~~~
./p7_hit.c:450:26: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
450 | ret_obj->nexpected = *((float *) &host_32bit);
| ~^~~~~~~~~~~~~~~~~~~~~~
GEN p7_hmmd_search_stats_utest
./p7_hmmd_search_stats.c: In function 'p7_hmmd_search_stats_Serialize':
./p7_hmmd_search_stats.c:89:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
89 | network_64bit = esl_hton64(*((uint64_t *) &(obj->elapsed))); // ow, this hurts, but is probably the best way to get the
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_hmmd_search_stats.c:97:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
97 | network_64bit = esl_hton64(*((uint64_t *) &(obj->user)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_hmmd_search_stats.c:103:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
103 | network_64bit = esl_hton64(*((uint64_t *) &(obj->sys)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~
./p7_hmmd_search_stats.c:109:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
109 | network_64bit = esl_hton64(*((uint64_t *) &(obj->Z)));
| ~^~~~~~~~~~~~~~~~~~~~~~~
./p7_hmmd_search_stats.c:115:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
115 | network_64bit = esl_hton64(*((uint64_t *) &(obj->domZ)));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_hmmd_search_stats.c: In function 'p7_hmmd_search_stats_Deserialize':
./p7_hmmd_search_stats.c:256:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
256 | ret_obj->elapsed = *((double *) &host_64bit);
| ~^~~~~~~~~~~~~~~~~~~~~~~
./p7_hmmd_search_stats.c:262:21: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
262 | ret_obj->user = *((double *) &host_64bit);
| ~^~~~~~~~~~~~~~~~~~~~~~~
./p7_hmmd_search_stats.c:268:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
268 | ret_obj->sys = *((double *) &host_64bit);
| ~^~~~~~~~~~~~~~~~~~~~~~~
./p7_hmmd_search_stats.c:274:18: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
274 | ret_obj->Z = *((double *) &host_64bit);
| ~^~~~~~~~~~~~~~~~~~~~~~~
./p7_hmmd_search_stats.c:280:21: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
280 | ret_obj->domZ = *((double *) &host_64bit);
| ~^~~~~~~~~~~~~~~~~~~~~~~
GEN p7_hmm_utest
GEN p7_hmmfile_utest
GEN p7_profile_utest
GEN p7_tophits_utest
In file included from /usr/include/stdio.h:906,
from ../easel/easel.h:22,
from ./p7_tophits.c:16:
In function 'fprintf',
inlined from 'p7_tophits_Targets' at ./p7_tophits.c:1142:12:
/usr/include/bits/stdio2.h:79:10: warning: 'posw' may be used uninitialized [-Wmaybe-uninitialized]
79 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
80 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
./p7_tophits.c: In function 'p7_tophits_Targets':
./p7_tophits.c:1068:10: note: 'posw' was declared here
1068 | int posw;
| ^~~~
./p7_tophits.c: In function 'main':
./p7_tophits.c:2171:3: warning: 'key' may be used uninitialized [-Wmaybe-uninitialized]
2171 | p7_tophits_Add(h1, "last", NULL, NULL, -1.0, (float) key, key, (float) key, key, i, i, N, i, i, N, 1, 1, NULL);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./p7_tophits.c:2155:19: note: 'key' was declared here
2155 | double key;
| ^~~
GEN p7_trace_utest
GEN p7_scoredata_utest
GEN hmmpgmd2msa_utest
GEN hmmd_search_status_utest
CC itest_brute.o
GEN itest_brute
SUBDIR impl_sse
GEN decoding_utest
GEN fwdback_utest
GEN io_utest
GEN msvfilter_utest
GEN null2_utest
GEN optacc_utest
./optacc.c: In function 'p7_OATrace':
./optacc.c:255:21: warning: 'smax' may be used uninitialized [-Wmaybe-uninitialized]
255 | if ((status = p7_trace_AppendWithPP(tr, s1, k, i, postprob)) != eslOK) return status;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./optacc.c:398:10: note: 'smax' was declared here
398 | int smax, kmax;
| ^~~~
In function 'get_postprob',
inlined from 'p7_OATrace' at ./optacc.c:254:18:
./optacc.c:269:21: warning: 'kmax' may be used uninitialized [-Wmaybe-uninitialized]
269 | int q = (k-1) % Q; /* (q,r) is position of the current DP cell M(i,k) */
| ~~^~~
./optacc.c: In function 'p7_OATrace':
./optacc.c:398:16: note: 'kmax' was declared here
398 | int smax, kmax;
| ^~~~
GEN stotrace_utest
GEN vitfilter_utest
SUBDIR easel
SUBDIR miniapps
SUBDIR testsuite
Running Easel test suite...
exercise 1 [ easel-utest] ... ok.
exercise 2 [ alloc-utest] ... ok.
exercise 3 [ alphabet-utest] ... ok.
exercise 4 [ avx-utest] ... ok.
exercise 5 [ avx512-utest] ... ok.
exercise 6 [ bitfield-utest] ... ok.
exercise 7 [ buffer-utest] ... ok.
exercise 8 [ cluster-utest] ... ok.
exercise 9 [ cpu-utest] ... ok.
exercise 10 [ dirichlet-utest] ... ok.
exercise 11 [ distance-utest] ... ok.
exercise 12 [ dmatrix-utest] ... ok.
exercise 13 [ dsqdata-utest] ... ok.
exercise 14 [ exponential-utest] ... ok.
exercise 15 [ fileparser-utest] ... ok.
exercise 16 [ gamma-utest] ... ok.
exercise 17 [ gencode-utest] ... ok.
exercise 18 [ getopts-utest] ... ok.
exercise 19 [ graph-utest] ... ok.
exercise 20 [ gumbel-utest] ... ok.
exercise 21 [ heap-utest] ... ok.
exercise 22 [ histogram-utest] ... ok.
exercise 23 [ huffman-utest] ... ok.
exercise 24 [ hyperexp-utest] ... ok.
exercise 25 [ json-utest] ... ok.
exercise 26 [ keyhash-utest] ... ok.
exercise 27 [ matrixops-utest] ... ok.
exercise 28 [ mem-utest] ... ok.
exercise 29 [ minimizer-utest] ... ok.
exercise 30 [ mixdchlet-utest] ... ok.
exercise 31 [ msa-utest] ... ok.
exercise 32 [ msacluster-utest] ... ok.
exercise 33 [ msafile] ... ok.
exercise 34 [ msafile2] ... ok.
exercise 35 [ msafile-a2m] ... ok.
exercise 36 [ msafile-afa] ... ok.
exercise 37 [ msafile-clustal] ... ok.
exercise 38 [ msafile-phylip] ... ok.
exercise 39 [ msafile-psiblast] ... ok.
exercise 40 [ msafile-selex] ... ok.
exercise 41 [ msafile-stockholm] ... ok.
exercise 42 [ msaweight-utest] ... ok.
exercise 43 [ neon-utest] ... ok.
exercise 44 [ normal-utest] ... ok.
exercise 45 [ quicksort-utest] ... ok.
exercise 46 [ random-utest] ... ok.
exercise 47 [ rand64-utest] ... ok.
exercise 48 [ randomseq-utest] ... ok.
exercise 49 [ ratematrix-utest] ... ok.
exercise 50 [ recorder-utest] ... ok.
exercise 51 [ red_black-utest] ... ok.
exercise 52 [ regexp-utest] ... ok.
exercise 53 [ rootfinder-utest] ... ok.
exercise 54 [ scorematrix-utest] ... ok.
exercise 55 [ sq-utest] ... ok.
exercise 56 [ sqio-utest] ... ok.
exercise 57 [ sse-utest] ... ok.
exercise 58 [ ssi-utest] ... ok.
exercise 59 [ stack-utest] ... ok.
exercise 60 [ stats-utest] ... ok.
exercise 61 [ stretchexp-utest] ... ok.
exercise 62 [ tree-utest] ... ok.
exercise 63 [ varint-utest] ... ok.
exercise 64 [ vectorops-utest] ... ok.
exercise 65 [ vmx-utest] ... ok.
exercise 66 [ weibull-utest] ... ok.
exercise 67 [ wuss-utest] ... ok.
exercise 68 [ e2] ... ok.
exercise 69 [ degen-residues] ... ok.
exercise 70 [ ncbi-indices] ... ok.
exercise 71 [ blank-gf] ... ok.
exercise 72 [ esl-translate] ... ok.
exercise 73 [ esl-afetch] ... ok.
exercise 74 [ esl-alimanip] ... ok.
exercise 75 [ esl-alimap] ... ok.
exercise 76 [ esl-alimask] ... ok.
exercise 77 [ esl-alimerge] ... ok.
exercise 78 [ esl-alistat] ... ok.
exercise 79 [ esl-compalign] ... ok.
exercise 80 [ esl-construct] ... ok.
exercise 81 [ esl-mask] ... ok.
exercise 82 [ esl-seqrange] ... ok.
exercise 83 [ esl-shuffle] ... ok.
exercise 84 [ esl-ssdraw] ... ok.
All 84 exercises at level <= 2 passed.
System information:
Sun Dec 25 10:47:28 UTC 2022
Linux b4e97a6139ea47ee88390d7b5a67cf6e 6.0.7-301.fc37.x86_64 #1 SMP PREEMPT_DYNAMIC Fri Nov 4 18:35:48 UTC 2022 i686 GNU/Linux
SUBDIR testsuite
Running HMMER test suite...
exercise 1 [ hmmer] ... ok.
exercise 2 [ build] ... ok.
exercise 3 [ generic_fwdback] ... ok.
exercise 4 [ generic_msv] ... ok.
exercise 5 [ generic_stotrace] ... ok.
exercise 6 [ generic_viterbi] ... ok.
exercise 7 [ hmmd_search_status] ... ok.
exercise 8 [ logsum] ... ok.
exercise 9 [ modelconfig] ... ok.
exercise 10 [ seqmodel] ... ok.
exercise 11 [ p7_alidisplay] ... ok.
exercise 12 [ p7_bg] ... ok.
exercise 13 [ p7_domain] ... ok.
exercise 14 [ p7_gmx] ... ok.
exercise 15 [ p7_hit] ... ok.
exercise 16 [ p7_hmm] ... ok.
exercise 17 [ p7_hmmfile] ... ok.
exercise 18 [ p7_hmmd_search_stats] ... ok.
exercise 19 [ p7_profile] ... ok.
exercise 20 [ p7_tophits] ... ok.
exercise 21 [ p7_trace] ... ok.
exercise 22 [ p7_scoredata] ... ok.
exercise 23 [ decoding] ... ok.
exercise 24 [ fwdback] ... ok.
exercise 25 [ io] ... ok.
exercise 26 [ msvfilter] ... ok.
exercise 27 [ null2] ... ok.
exercise 28 [ optacc] ... ok.
exercise 29 [ stotrace] ... ok.
exercise 30 [ vitfilter] ... ok.
exercise 31 [ hmmpgmd2msa] ... ok.
exercise 32 [ hmmalign] ... ok.
exercise 33 [ hmmalign/-h] ... ok.
exercise 34 [ hmmalign/-o] ... ok.
exercise 35 [ hmmalign/--mapali] ... ok.
exercise 36 [ hmmalign/--trim] ... ok.
exercise 37 [ hmmalign/--amino] ... ok.
exercise 38 [ hmmalign/--informat] ... ok.
exercise 39 [ hmmalign/--outformat] ... ok.
exercise 40 [ hmmbuild] ... ok.
exercise 41 [ build/-h] ... ok.
exercise 42 [ build/-n] ... ok.
exercise 43 [ build/-o] ... ok.
exercise 44 [ build/-O] ... ok.
exercise 45 [ build/--amino] ... ok.
exercise 46 [ build/--dna] ... ok.
exercise 47 [ build/--rna] ... ok.
exercise 48 [ build/--fast] ... ok.
exercise 49 [ build/--hand] ... ok.
exercise 50 [ build/--symfrac] ... ok.
exercise 51 [ build/--fragthresh] ... ok.
exercise 52 [ build/--wpb] ... ok.
exercise 53 [ build/--wgsc] ... ok.
exercise 54 [ build/--wblosum] ... ok.
exercise 55 [ build/--wnone] ... ok.
exercise 56 [ build/--wid] ... ok.
exercise 57 [ build/--eent] ... ok.
exercise 58 [ build/--eclust] ... ok.
exercise 59 [ build/--enone] ... ok.
exercise 60 [ build/--eset] ... ok.
exercise 61 [ build/--ere] ... ok.
exercise 62 [ build/--esigma] ... ok.
exercise 63 [ build/--eid] ... ok.
exercise 64 [ build/--pnone] ... ok.
exercise 65 [ build/--plaplace] ... ok.
exercise 66 [ build/--EmL] ... ok.
exercise 67 [ build/--EmN] ... ok.
exercise 68 [ build/--EvL] ... ok.
exercise 69 [ build/--EvN] ... ok.
exercise 70 [ build/--EfL] ... ok.
exercise 71 [ build/--EfN] ... ok.
exercise 72 [ build/--Eft] ... ok.
exercise 73 [ build/--informat] ... ok.
exercise 74 [ build/--seed] ... ok.
exercise 75 [ search] ... ok.
exercise 76 [ search/-h] ... ok.
exercise 77 [ search/-o] ... ok.
exercise 78 [ search/-A] ... ok.
exercise 79 [ search/--tblout] ... ok.
exercise 80 [ search/--domtblout] ... ok.
exercise 81 [ search/--pfamtblout] ... ok.
exercise 82 [ search/--acc] ... ok.
exercise 83 [ search/--noali] ... ok.
exercise 84 [ search/--notextw] ... ok.
exercise 85 [ search/--textw] ... ok.
exercise 86 [ search/-E] ... ok.
exercise 87 [ search/-T] ... ok.
exercise 88 [ search/--domE] ... ok.
exercise 89 [ search/--domT] ... ok.
exercise 90 [ search/--incE] ... ok.
exercise 91 [ search/--incT] ... ok.
exercise 92 [ search/--incdomE] ... ok.
exercise 93 [ search/--incdomT] ... ok.
exercise 94 [ search/--cut_ga] ... ok.
exercise 95 [ search/--cut_nc] ... ok.
exercise 96 [ search/--cut_tc] ... ok.
exercise 97 [ search/--max] ... ok.
exercise 98 [ search/--F1] ... ok.
exercise 99 [ search/--F2] ... ok.
exercise 100 [ search/--F3] ... ok.
exercise 101 [ search/--nobias] ... ok.
exercise 102 [ search/--nonull2] ... ok.
exercise 103 [ search/-Z] ... ok.
exercise 104 [ search/--domZ] ... ok.
exercise 105 [ search/--seed] ... ok.
exercise 106 [ search/--tformat] ... ok.
exercise 107 [ hmmscan] ... ok.
exercise 108 [ scan/-h] ... ok.
exercise 109 [ scan/-o] ... ok.
exercise 110 [ scan/--tblout] ... ok.
exercise 111 [ scan/--domtblout] ... ok.
exercise 112 [ scan/--pfamtblout] ... ok.
exercise 113 [ scan/--acc] ... ok.
exercise 114 [ scan/--noali] ... ok.
exercise 115 [ scan/--notextw] ... ok.
exercise 116 [ scan/--textw] ... ok.
exercise 117 [ scan/-E] ... ok.
exercise 118 [ scan/-T] ... ok.
exercise 119 [ scan/--domE] ... ok.
exercise 120 [ scan/--domT] ... ok.
exercise 121 [ scan/--incE] ... ok.
exercise 122 [ scan/--incT] ... ok.
exercise 123 [ scan/--incdomE] ... ok.
exercise 124 [ scan/--incdomT] ... ok.
exercise 125 [ scan/--incdomT] ... ok.
exercise 126 [ scan/--cut_ga] ... ok.
exercise 127 [ scan/--cut_nc] ... ok.
exercise 128 [ scan/--cut_tc] ... ok.
exercise 129 [ scan/--max] ... ok.
exercise 130 [ scan/--F1] ... ok.
exercise 131 [ scan/--F2] ... ok.
exercise 132 [ scan/--F3] ... ok.
exercise 133 [ scan/--nobias] ... ok.
exercise 134 [ scan/--nonull2] ... ok.
exercise 135 [ scan/-Z] ... ok.
exercise 136 [ scan/--domZ] ... ok.
exercise 137 [ scan/--seed] ... ok.
exercise 138 [ scan/--qformat] ... ok.
exercise 139 [ scan/--cpu] ... ok.
exercise 140 [ jackhmmer] ... ok.
exercise 141 [ j/-h] ... ok.
exercise 142 [ j/-N] ... ok.
exercise 143 [ j/-o] ... ok.
exercise 144 [ j/-A] ... ok.
exercise 145 [ j/--tblout] ... ok.
exercise 146 [ j/--domtblout] ... ok.
exercise 147 [ j/--chkhmm] ... ok.
exercise 148 [ j/--chkali] ... ok.
exercise 149 [ j/--acc] ... ok.
exercise 150 [ j/--noali] ... ok.
exercise 151 [ j/--notextw] ... ok.
exercise 152 [ j/--textw] ... ok.
exercise 153 [ j/--popen] ... ok.
exercise 154 [ j/--pextend] ... ok.
exercise 155 [ j/--mxfile] ... ok.
exercise 156 [ j/-E] ... ok.
exercise 157 [ j/-T] ... ok.
exercise 158 [ j/--domE] ... ok.
exercise 159 [ j/--domT] ... ok.
exercise 160 [ j/--incE] ... ok.
exercise 161 [ j/--incT] ... ok.
exercise 162 [ j/--incdomE] ... ok.
exercise 163 [ j/--incdomT] ... ok.
exercise 164 [ j/--max] ... ok.
exercise 165 [ j/--F1] ... ok.
exercise 166 [ j/--F2] ... ok.
exercise 167 [ j/--F3] ... ok.
exercise 168 [ j/--nobias] ... ok.
exercise 169 [ j/--EmL] ... ok.
exercise 170 [ j/--EmN] ... ok.
exercise 171 [ j/--EvL] ... ok.
exercise 172 [ j/--EvN] ... ok.
exercise 173 [ j/--EfL] ... ok.
exercise 174 [ j/--EfN] ... ok.
exercise 175 [ j/--Eft] ... ok.
exercise 176 [ j/--nonull2] ... ok.
exercise 177 [ j/-Z] ... ok.
exercise 178 [ j/--domZ] ... ok.
exercise 179 [ j/--seed] ... ok.
exercise 180 [ j/--qformat] ... ok.
exercise 181 [ j/--tformat] ... ok.
exercise 182 [ phmmer] ... ok.
exercise 183 [ phmmer/-h] ... ok.
exercise 184 [ phmmer/-o] ... ok.
exercise 185 [ phmmer/-A] ... ok.
exercise 186 [ phmmer/--tblout] ... ok.
exercise 187 [ phmmer/--domtblout] ... ok.
exercise 188 [ phmmer/--pfamtblout] ... ok.
exercise 189 [ phmmer/--acc] ... ok.
exercise 190 [ phmmer/--noali] ... ok.
exercise 191 [ phmmer/--notextw] ... ok.
exercise 192 [ phmmer/--textw] ... ok.
exercise 193 [ phmmer/--popen] ... ok.
exercise 194 [ phmmer/--pextend] ... ok.
exercise 195 [ phmmer/--mxfile] ... ok.
exercise 196 [ phmmer/-E] ... ok.
exercise 197 [ phmmer/-T] ... ok.
exercise 198 [ phmmer/--domE] ... ok.
exercise 199 [ phmmer/--domT] ... ok.
exercise 200 [ phmmer/--incE] ... ok.
exercise 201 [ phmmer/--incT] ... ok.
exercise 202 [ phmmer/--incdomE] ... ok.
exercise 203 [ phmmer/--incdomT] ... ok.
exercise 204 [ phmmer/--max] ... ok.
exercise 205 [ phmmer/--F1] ... ok.
exercise 206 [ phmmer/--F2] ... ok.
exercise 207 [ phmmer/--F3] ... ok.
exercise 208 [ phmmer/--nobias] ... ok.
exercise 209 [ phmmer/--EmL] ... ok.
exercise 210 [ phmmer/--EmN] ... ok.
exercise 211 [ phmmer/--EvL] ... ok.
exercise 212 [ phmmer/--EvN] ... ok.
exercise 213 [ phmmer/--EfL] ... ok.
exercise 214 [ phmmer/--EfN] ... ok.
exercise 215 [ phmmer/--Eft] ... ok.
exercise 216 [ phmmer/--nonull2] ... ok.
exercise 217 [ phmmer/-Z] ... ok.
exercise 218 [ phmmer/--domZ] ... ok.
exercise 219 [ phmmer/--seed] ... ok.
exercise 220 [ phmmer/--qformat] ... ok.
exercise 221 [ phmmer/--tformat] ... ok.
exercise 222 [ nhmmer] ... ok.
exercise 223 [ nhmmer/-h] ... ok.
exercise 224 [ nhmmer/-o] ... ok.
exercise 225 [ nhmmer/-A] ... ok.
exercise 226 [ nhmmer/--tblout] ... ok.
exercise 227 [ nhmmer/--dfamtblout] ... ok.
exercise 228 [ nhmmer/--acc] ... ok.
exercise 229 [ nhmmer/--noali] ... ok.
exercise 230 [ nhmmer/--notextw] ... ok.
exercise 231 [ nhmmer/--textw] ... ok.
exercise 232 [ nhmmer/-E] ... ok.
exercise 233 [ nhmmer/-T] ... ok.
exercise 234 [ nhmmer/--incE] ... ok.
exercise 235 [ nhmmer/--incT] ... ok.
exercise 236 [ nhmmer/--max] ... ok.
exercise 237 [ nhmmer/--F1] ... ok.
exercise 238 [ nhmmer/--F2] ... ok.
exercise 239 [ nhmmer/--F3] ... ok.
exercise 240 [ nhmmer/--nobias] ... ok.
exercise 241 [ nhmmer/--nonull2] ... ok.
exercise 242 [ nhmmer/-Z] ... ok.
exercise 243 [ nhmmer/--seed] ... ok.
exercise 244 [ nhmmscan] ... ok.
exercise 245 [ nhmmscan/-h] ... ok.
exercise 246 [ nhmmscan/-o] ... ok.
exercise 247 [ nhmmscan/--tblout] ... ok.
exercise 248 [nhmmscan/--dfamtblout] ... ok.
exercise 249 [ nhmmscan/--acc] ... ok.
exercise 250 [ nhmmscan/--noali] ... ok.
exercise 251 [ nhmmscan/--notextw] ... ok.
exercise 252 [ nhmmscan/--textw] ... ok.
exercise 253 [ nhmmscan/-E] ... ok.
exercise 254 [ nhmmscan/-T] ... ok.
exercise 255 [ nhmmscan/--incE] ... ok.
exercise 256 [ nhmmscan/--incT] ... ok.
exercise 257 [ nhmmscan/--max] ... ok.
exercise 258 [ nhmmscan/--F1] ... ok.
exercise 259 [ nhmmscan/--F2] ... ok.
exercise 260 [ nhmmscan/--F3] ... ok.
exercise 261 [ nhmmscan/--nobias] ... ok.
exercise 262 [ nhmmscan/--nonull2] ... ok.
exercise 263 [ nhmmscan/-Z] ... ok.
exercise 264 [ nhmmscan/--seed] ... ok.
exercise 265 [ hmmemit] ... ok.
exercise 266 [ hmmemit/-h] ... ok.
exercise 267 [ hmmemit/-c] ... ok.
exercise 268 [ hmmemit/-o] ... ok.
exercise 269 [ hmmemit/-p] ... ok.
exercise 270 [ hmmemit/-N] ... ok.
exercise 271 [ hmmemit/-L] ... ok.
exercise 272 [ hmmemit/--local] ... ok.
exercise 273 [ hmmemit/--unilocal] ... ok.
exercise 274 [ hmmemit/--glocal] ... ok.
exercise 275 [ hmmemit/--uniglocal] ... ok.
exercise 276 [ hmmfetch] ... ok.
exercise 277 [ hmmstat] ... ok.
exercise 278 [ hmmlogo] ... ok.
exercise 279 [ hmmconvert] ... ok.
exercise 280 [ hmmsim] ... ok.
exercise 281 [ hmmbuild_variation] ... ok.
exercise 282 [ hmmscan_variation] ... ok.
exercise 283 [ hmmsearch_variation] ... ok.
exercise 284 [ phmmer_variation] ... ok.
exercise 285 [ mapali] ... ok.
exercise 286 [ fragments] ... ok.
exercise 287 [ nonresidues] ... ok.
exercise 288 [ opt-annotation] ... ok.
exercise 289 [ dup-names] ... ok.
exercise 290 [ mapali-again] ... ok.
exercise 291 [ delete-corruption] ... ok.
exercise 292 [ msa-integrity] ... ok.
exercise 293 [ hmmemit-consensus] ... ok.
exercise 294 [ hmmconvert] ... ok.
exercise 295 [ stdin_pipes] ... ok.
exercise 296 [ nhmmer_generic] ... ok.
exercise 297 [ hmmpgmd_ga] ... ok.
exercise 298 [ rewind] ... ok.
exercise 299 [ hmmpgmd_shard_ga] ... ok.
exercise 300 [ bad-fasta] ... ok.
exercise 301 [ brute-itest] ... ok.
exercise 302 [ hmmpress-itest] ... ok.
exercise 303 [ h39] ... ok.
exercise 304 [ h45] ... ok.
exercise 305 [ h50] ... ok.
exercise 306 [ h82] ... ok.
exercise 307 [ iss159] ... ok.
All 307 exercises at level <= 2 passed.
System information:
Sun Dec 25 10:47:43 UTC 2022
Linux b4e97a6139ea47ee88390d7b5a67cf6e 6.0.7-301.fc37.x86_64 #1 SMP PREEMPT_DYNAMIC Fri Nov 4 18:35:48 UTC 2022 i686 GNU/Linux
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: hmmer-3.3.2-2.fc38.i686
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.rtkO3W
+ umask 022
+ cd /builddir/build/BUILD
+ cd hmmer-3.3.2
+ LICENSEDIR=/builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/share/licenses/hmmer
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/share/licenses/hmmer
+ cp -pr LICENSE /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/share/licenses/hmmer
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: hmmer = 3.3.2-2.fc38 hmmer(x86-32) = 3.3.2-2.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libc.so.6 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1) libc.so.6(GLIBC_2.1.3) libc.so.6(GLIBC_2.11) libc.so.6(GLIBC_2.15) libc.so.6(GLIBC_2.17) libc.so.6(GLIBC_2.2) libc.so.6(GLIBC_2.3) libc.so.6(GLIBC_2.3.2) libc.so.6(GLIBC_2.3.4) libc.so.6(GLIBC_2.33) libc.so.6(GLIBC_2.34) libc.so.6(GLIBC_2.4) libm.so.6 libm.so.6(GLIBC_2.0) libm.so.6(GLIBC_2.1) libm.so.6(GLIBC_2.27) libm.so.6(GLIBC_2.29) rtld(GNU_HASH)
Processing files: hmmer-easel-3.3.2-2.fc38.i686
Provides: hmmer-easel = 3.3.2-2.fc38 hmmer-easel(x86-32) = 3.3.2-2.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libc.so.6 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1) libc.so.6(GLIBC_2.1.3) libc.so.6(GLIBC_2.17) libc.so.6(GLIBC_2.2) libc.so.6(GLIBC_2.3) libc.so.6(GLIBC_2.3.2) libc.so.6(GLIBC_2.3.4) libc.so.6(GLIBC_2.33) libc.so.6(GLIBC_2.34) libc.so.6(GLIBC_2.4) libm.so.6 libm.so.6(GLIBC_2.0) libm.so.6(GLIBC_2.1) libm.so.6(GLIBC_2.29) rtld(GNU_HASH)
Processing files: hmmer-doc-3.3.2-2.fc38.noarch
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.Z2yoh0
+ umask 022
+ cd /builddir/build/BUILD
+ cd hmmer-3.3.2
+ DOCDIR=/builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/share/doc/hmmer-doc
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/share/doc/hmmer-doc
+ cp -pr LICENSE /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/share/doc/hmmer-doc
+ cp -pr README.md /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/share/doc/hmmer-doc
+ cp -pr RELEASE-3.3.2.md /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/share/doc/hmmer-doc
+ cp -pr Userguide.pdf /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/share/doc/hmmer-doc
+ cp -pr tutorial/ /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386/usr/share/doc/hmmer-doc
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: hmmer-doc = 3.3.2-2.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: hmmer-debugsource-3.3.2-2.fc38.i686
Provides: hmmer-debugsource = 3.3.2-2.fc38 hmmer-debugsource(x86-32) = 3.3.2-2.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: hmmer-debuginfo-3.3.2-2.fc38.i686
Provides: debuginfo(build-id) = 0d5860dfca0dcc171da07ab96116994423bbf432 debuginfo(build-id) = 10bc3942c7030d5a4434034d68a368451872b5a6 debuginfo(build-id) = 180e4beb33d2c829737b78715f33df2d820c81bf debuginfo(build-id) = 256fa8c9205f1e05d00b75a9d27e7ac2666d8609 debuginfo(build-id) = 27f565309fd2180d06bef8a7f8b723cbcea80156 debuginfo(build-id) = 2d0b0922a3fdad9b3828ebf3f50cb7197d9a0096 debuginfo(build-id) = 33e799fac7f4e50a842ab1754cff2911fa7b24bb debuginfo(build-id) = 3b5bb9cc646652a0fdcbefe6f34c13c7b036a1b7 debuginfo(build-id) = 93a48862bfafa45803532f8cad4feebf1d1da072 debuginfo(build-id) = a9a94923042801a8f2b61fb4fa8caca335940524 debuginfo(build-id) = a9c4e712eb4d93e74c3e4ba4ae49550be2dfb022 debuginfo(build-id) = aee1edc1d758dd407b8c14805497ba0cd434213f debuginfo(build-id) = b8d310f4f7a002883fa24dcd4c49c0d84ed08be4 debuginfo(build-id) = ccc16726bc85b97abe017d216dea16725e1a1611 debuginfo(build-id) = d6dc551e0b493ac2b8b7f5ba6ed9e1e23d87cad2 debuginfo(build-id) = e0efc6e1f924b90206373a09931bc65d4ef9087d debuginfo(build-id) = e20e635545217df2330570f891d1bec3b71fc384 debuginfo(build-id) = e296f7ca7e8a95d25612c313233c5aaf9d4390ad debuginfo(build-id) = e91ee0ea1bad90cbfecb3d2b3148aa0cb0e48007 hmmer-debuginfo = 3.3.2-2.fc38 hmmer-debuginfo(x86-32) = 3.3.2-2.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: hmmer-debugsource(x86-32) = 3.3.2-2.fc38
Processing files: hmmer-easel-debuginfo-3.3.2-2.fc38.i686
Provides: debuginfo(build-id) = 0e62924f2a3b0ee11e4d4a57c04f9ca98eacbc58 debuginfo(build-id) = 1609cf9e9710b2eba826e866cc31570167d1a2ab debuginfo(build-id) = 342ad779d75224377c47e7cfe51dda25941915c6 debuginfo(build-id) = 4cbfb41f168636915ec5d6185367a7046fa29c54 debuginfo(build-id) = 51b635bae35993a95d76c1c64e02a8131ff4de0f debuginfo(build-id) = 5bce1313bea0090edcff6abc71d572cd8ac45d1e debuginfo(build-id) = 70147cdde2d2d5d49fdac040543f9ce93ad09553 debuginfo(build-id) = 72fddaf82dab9701e27557c8090f31db7824f30a debuginfo(build-id) = a5a392e7d77bba248bd9505133451370fd5142db debuginfo(build-id) = a651e086f05847120807fca865bfa6e000fa4c08 debuginfo(build-id) = ada1f8fff634468cd28b01770b015875e24d80c8 debuginfo(build-id) = ae39b40b59ed012d61cea58dae4303ee4827a39c debuginfo(build-id) = b882a88ea210cc18d3cf4b630023b5949e45e69c debuginfo(build-id) = ba278c5b6ec79b66e15ad21ee5e16aa63453d191 debuginfo(build-id) = c25d5aeb56d1295337535abbd36e76d46aa84e40 debuginfo(build-id) = c70937173c1d6b87a5e92dbacc166216a192597f debuginfo(build-id) = d7bb6e3acddeb5a39c2868bd3c7fbff6d16c509a debuginfo(build-id) = ea3219bba740cb595dfeb0d1d5bdfdf7e5ebc166 debuginfo(build-id) = ec21b32a87f4ec992ed679a8ddcd1a40640c39d1 debuginfo(build-id) = ee339731fbc6e3e3a134ac410029f8f99f8afd60 debuginfo(build-id) = f0c7f01f24c8f746a9759f11d8ddd8cf13f79976 debuginfo(build-id) = f6681a3bdb72a02d631c686e1b7ac94bb5e829a8 debuginfo(build-id) = fadef7d9d5d3a8b09345e2516bfade78d367f2d9 debuginfo(build-id) = fec7f1f4e5e6912c324b4e3f324a20e7582a6803 hmmer-easel-debuginfo = 3.3.2-2.fc38 hmmer-easel-debuginfo(x86-32) = 3.3.2-2.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: hmmer-debugsource(x86-32) = 3.3.2-2.fc38
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386
Wrote: /builddir/build/RPMS/hmmer-easel-debuginfo-3.3.2-2.fc38.i686.rpm
Wrote: /builddir/build/RPMS/hmmer-debuginfo-3.3.2-2.fc38.i686.rpm
Wrote: /builddir/build/RPMS/hmmer-debugsource-3.3.2-2.fc38.i686.rpm
Wrote: /builddir/build/RPMS/hmmer-3.3.2-2.fc38.i686.rpm
Wrote: /builddir/build/RPMS/hmmer-doc-3.3.2-2.fc38.noarch.rpm
Wrote: /builddir/build/RPMS/hmmer-easel-3.3.2-2.fc38.i686.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.9STEHR
+ umask 022
+ cd /builddir/build/BUILD
+ cd hmmer-3.3.2
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/hmmer-3.3.2-2.fc38.i386
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.F7Bulv
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf hmmer-3.3.2 hmmer-3.3.2.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0
Child return code was: 0