Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/k/kalign/kalign_3.3-1+b3_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/kalign-3.3-1+b3839ozb5d/kalign_3.3-1+b3_amd64.buildinfo Get source package info: kalign=1:3.3-1 Source URL: http://snapshot.notset.fr/mr/package/kalign/1:3.3-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-14 automake=1:1.16.3-2 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=11 base-passwd=3.5.49 bash=5.1-2+b1 binutils=2.35.2-2 binutils-common=2.35.2-2 binutils-x86-64-linux-gnu=2.35.2-2 bsdextrautils=2.36.1-7 bsdutils=1:2.36.1-7 build-essential=12.9 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.2.1-6 dash=0.5.11+git20210120+802ebd4-1 debconf=1.5.75 debhelper=13.3.4 debianutils=4.11.2 dh-autoreconf=20 dh-strip-nondeterminism=1.11.0-1 diffutils=1:3.7-5 dpkg=1.20.7.1 dpkg-dev=1.20.7.1 dwz=0.14-1 file=1:5.39-3 findutils=4.8.0-1 g++=4:10.2.1-1 g++-10=10.2.1-6 gcc=4:10.2.1-1 gcc-10=10.2.1-6 gcc-10-base=10.2.1-6 gettext=0.21-4 gettext-base=0.21-4 grep=3.6-1 groff-base=1.22.4-6 gzip=1.10-4 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-10 libarchive-zip-perl=1.68-1 libasan6=10.2.1-6 libatomic1=10.2.1-6 libattr1=1:2.4.48-6 libaudit-common=1:3.0-2 libaudit1=1:3.0-2 libbinutils=2.35.2-2 libblkid1=2.36.1-7 libbz2-1.0=1.0.8-4 libc-bin=2.31-9 libc-dev-bin=2.31-9 libc6=2.31-9 libc6-dev=2.31-9 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-6 libcom-err2=1.46.2-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.2-2 libctf0=2.35.2-2 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.256 libdebhelper-perl=13.3.4 libdpkg-perl=1.20.7.1 libelf1=0.183-3 libfile-stripnondeterminism-perl=1.11.0-1 libgcc-10-dev=10.2.1-6 libgcc-s1=10.2.1-6 libgcrypt20=1.8.7-3 libgdbm-compat4=1.19-2 libgdbm6=1.19-2 libgmp10=2:6.2.1+dfsg-1 libgomp1=10.2.1-6 libgpg-error0=1.38-2 libgssapi-krb5-2=1.18.3-4 libicu67=67.1-6 libisl23=0.23-1 libitm1=10.2.1-6 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 liblsan0=10.2.1-6 liblz4-1=1.9.3-1 liblzma5=5.2.5-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.36.1-7 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libpam-modules=1.4.0-6 libpam-modules-bin=1.4.0-6 libpam-runtime=1.4.0-6 libpam0g=1.4.0-6 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.1-3 libpipeline1=1.5.3-1 libquadmath0=10.2.1-6 libseccomp2=2.5.1-1 libselinux1=3.1-3 libsigsegv2=2.13-1 libsimde-dev=0.7.2-4 libsmartcols1=2.36.1-7 libssl1.1=1.1.1j-1 libstdc++-10-dev=10.2.1-6 libstdc++6=10.2.1-6 libsub-override-perl=0.09-2 libsystemd0=247.3-2 libtinfo6=6.2+20201114-2 libtirpc-common=1.3.1-1 libtirpc-dev=1.3.1-1 libtirpc3=1.3.1-1 libtool=2.4.6-15 libtsan0=10.2.1-6 libubsan1=10.2.1-6 libuchardet0=0.0.7-1 libudev1=247.3-2 libunistring2=0.9.10-4 libuuid1=2.36.1-7 libxml2=2.9.10+dfsg-6.3+b1 libzstd1=1.4.8+dfsg-2.1 linux-libc-dev=5.10.19-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4 man-db=2.9.4-2 mawk=1.3.4.20200120-2 ncurses-base=6.2+20201114-2 ncurses-bin=6.2+20201114-2 patch=2.7.6-7 perl=5.32.1-3 perl-base=5.32.1-3 perl-modules-5.32=5.32.1-3 po-debconf=1.0.21+nmu1 sed=4.7-1 sensible-utils=0.0.14 sysvinit-utils=2.96-6 tar=1.34+dfsg-1 util-linux=2.36.1-7 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210311T143034Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d kalign=1:3.3-1 && mkdir -p /build/kalign-V8kuw9 && dpkg-source --no-check -x /*.dsc /build/kalign-V8kuw9/kalign-3.3 && cd /build/kalign-V8kuw9/kalign-3.3 && { printf '%s' 'kalign (1:3.3-1+b3) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * rebuild for outdated built-using -- all / amd64 / i386 Build Daemon (x86-conova-01) Thu, 11 Mar 2021 23:06:02 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/kalign-V8kuw9" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/kalign-V8kuw9/kalign-3.3 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1615503962" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/kalign-V8kuw9 /tmp/kalign-3.3-1+b3839ozb5d bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20210311T143034Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.bTqD9H0hZk as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.bTqD9H0hZk Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-7). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20210311T143034Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210311T143034Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (425 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4663 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-9) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210311T143034Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.bTqD9H0hZk Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20210311T143034Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 21s (1099 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.bTqD9H0hZk I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d kalign=1:3.3-1 && mkdir -p /build/kalign-V8kuw9 && dpkg-source --no-check -x /*.dsc /build/kalign-V8kuw9/kalign-3.3 && cd /build/kalign-V8kuw9/kalign-3.3 && { printf '%s' 'kalign (1:3.3-1+b3) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * rebuild for outdated built-using -- all / amd64 / i386 Build Daemon (x86-conova-01) Thu, 11 Mar 2021 23:06:02 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/kalign-V8kuw9"' exec /tmp/mmdebstrap.bTqD9H0hZk Reading package lists... NOTICE: 'kalign' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/kalign.git Please use: git clone https://salsa.debian.org/med-team/kalign.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 956 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main kalign 1:3.3-1 (dsc) [1941 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main kalign 1:3.3-1 (tar) [940 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main kalign 1:3.3-1 (diff) [14.0 kB] Fetched 956 kB in 1s (1120 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'kalign_3.3-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting kalign in /build/kalign-V8kuw9/kalign-3.3 dpkg-source: info: unpacking kalign_3.3.orig.tar.gz dpkg-source: info: unpacking kalign_3.3-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying simde dpkg-source: info: applying no-native-build dpkg-source: info: applying keep-debugging I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/kalign-V8kuw9/kalign-3.3 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1615503962" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.bTqD9H0hZk dpkg-buildpackage: info: source package kalign dpkg-buildpackage: info: source version 1:3.3-1+b3 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by all / amd64 / i386 Build Daemon (x86-conova-01) dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' libtoolize: 'AC_PROG_RANLIB' is rendered obsolete by 'LT_INIT' configure.ac:5: installing './compile' configure.ac:16: installing './config.guess' configure.ac:16: installing './config.sub' configure.ac:6: installing './install-sh' configure.ac:6: installing './missing' src/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' dh_auto_configure -a ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for 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 whether gcc understands -c and -o together... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E 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 minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking dependency style of gcc... none checking for gawk... (cached) mawk checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking for ranlib... ranlib checking whether make supports nested variables... (cached) yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... (cached) ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether C compiler accepts -D_FORTIFY_SOURCE=2... yes checking whether C compiler accepts -ffunction-sections... yes checking whether C compiler accepts -fdata-sections... yes checking whether C compiler accepts --gc-sections... no checking for OpenMP flag of C compiler... -fopenmp checking for _Generic... yes checking for sqrt in -lm... yes checking for main in -lpthread... yes checking for library containing clock_gettime... none required checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking mach/mach.h usability... no checking mach/mach.h presence... no checking for mach/mach.h... no checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for inline... inline checking for size_t... yes checking for ssize_t... yes checking for int8_t... yes checking for int32_t... yes checking for int16_t... yes checking for int64_t... yes checking for uint8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for working strnlen... yes checking for error_at_line... yes checking for gettimeofday... yes checking for pow... yes checking for realpath... yes checking for sqrt... yes checking for strstr... yes checking for memset... yes checking for clock_gettime... yes checking for gethrtime... no checking for gettimeofday... (cached) yes checking for localtime_r... yes checking for strcspn... yes checking for valgrind... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating dev/Makefile config.status: creating src/config.h config.status: executing depfiles commands config.status: executing libtool commands configure: --------------------------------------------------------- configure: Configuration complete - kalign-3.3 configure: configure: General Information: configure: Version: 3.3 configure: Configured on: configure: Configured by: builduser configure: Host system: x86_64-pc-linux-gnu configure: Uname information: configure: Installation point: /usr configure: CFLAGS: -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd configure: CPFLAGS: -Wdate-time -D_FORTIFY_SOURCE=2 configure: LDFLAGS: -Wl,-z,relro -Wl,-z,now configure: SIMD flags: configure: --------------------------------------------------------- debian/rules override_dh_auto_build make[1]: Entering directory '/build/kalign-V8kuw9/kalign-3.3' mkdir -p /build/kalign-V8kuw9/kalign-3.3/debian/kalign/usr mkdir -p /build/kalign-V8kuw9/kalign-3.3/debian/kalign/usr/lib/kalign make clean ; dh_auto_configure -- CFLAGS="-g -O2 -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2" && dh_auto_build && cp src/kalign src/kalign-avx2 && cp src/timescorealn src/timescorealn-avx2 && make clean ; dh_auto_configure -- CFLAGS="-g -O2 -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx" && dh_auto_build && cp src/kalign src/kalign-avx && cp src/timescorealn src/timescorealn-avx && make clean ; dh_auto_configure -- CFLAGS="-g -O2 -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1" && dh_auto_build && cp src/kalign src/kalign-sse4.1 && cp src/timescorealn src/timescorealn-sse4.1 && make clean ; dh_auto_configure -- CFLAGS="-g -O2 -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3" && dh_auto_build && cp src/kalign src/kalign-ssse3 && cp src/timescorealn src/timescorealn-ssse3 && make clean ; dh_auto_configure -- CFLAGS="-g -O2 -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3" && dh_auto_build && cp src/kalign src/kalign-sse3 && cp src/timescorealn src/timescorealn-sse3 && true make[2]: Entering directory '/build/kalign-V8kuw9/kalign-3.3' Making clean in src make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/src' rm -f kalign kchaos rm -f edist alphabet misc_test bpm_test rwaln rstdin_test test -z "ihmm_seq_itest_read_test.fa test_model_file.txt test.lfa test_dna.lfa libhdf5gluetest_exp.h5 libhdf5gluetest.h5 model_at_*h5 test1.h5 test2.h5" || rm -f ihmm_seq_itest_read_test.fa test_model_file.txt test.lfa test_dna.lfa libhdf5gluetest_exp.h5 libhdf5gluetest.h5 model_at_*h5 test1.h5 test2.h5 rm -rf .libs _libs rm -f timescorealn benchrunner genruncmds genkaligndiffcmds rm -f *.o test -z "edist.log alphabet.log misc_test.log bpm_test.log rstdin_test.log" || rm -f edist.log alphabet.log misc_test.log bpm_test.log rstdin_test.log test -z "edist.trs alphabet.trs misc_test.trs bpm_test.trs rstdin_test.trs" || rm -f edist.trs alphabet.trs misc_test.trs bpm_test.trs rstdin_test.trs test -z "test-suite.log" || rm -f test-suite.log rm -f *.lo make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/src' Making clean in dev make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/dev' test -z "rwtest.clu rwtest.fasta rwtest.msf test.afa" || rm -f rwtest.clu rwtest.fasta rwtest.msf test.afa rm -rf .libs _libs rm -f *.lo make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/dev' make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3' rm -rf .libs _libs rm -f *.lo make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3' make[2]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3' ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking "CFLAGS=-g -O2 -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2" checking for 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 whether gcc understands -c and -o together... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E 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 minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking dependency style of gcc... none checking for gawk... (cached) mawk checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking for ranlib... ranlib checking whether make supports nested variables... (cached) yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... (cached) ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether C compiler accepts -D_FORTIFY_SOURCE=2... yes checking whether C compiler accepts -ffunction-sections... yes checking whether C compiler accepts -fdata-sections... yes checking whether C compiler accepts --gc-sections... no checking for OpenMP flag of C compiler... -fopenmp checking for _Generic... yes checking for sqrt in -lm... yes checking for main in -lpthread... yes checking for library containing clock_gettime... none required checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking mach/mach.h usability... no checking mach/mach.h presence... no checking for mach/mach.h... no checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for inline... inline checking for size_t... yes checking for ssize_t... yes checking for int8_t... yes checking for int32_t... yes checking for int16_t... yes checking for int64_t... yes checking for uint8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for working strnlen... yes checking for error_at_line... yes checking for gettimeofday... yes checking for pow... yes checking for realpath... yes checking for sqrt... yes checking for strstr... yes checking for memset... yes checking for clock_gettime... yes checking for gethrtime... no checking for gettimeofday... (cached) yes checking for localtime_r... yes checking for strcspn... yes checking for valgrind... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating dev/Makefile config.status: creating src/config.h config.status: src/config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands configure: --------------------------------------------------------- configure: Configuration complete - kalign-3.3 configure: configure: General Information: configure: Version: 3.3 configure: Configured on: configure: Configured by: builduser configure: Host system: x86_64-pc-linux-gnu configure: Uname information: configure: Installation point: /usr configure: CFLAGS: -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 configure: CPFLAGS: -Wdate-time -D_FORTIFY_SOURCE=2 configure: LDFLAGS: -Wl,-z,relro -Wl,-z,now configure: SIMD flags: configure: --------------------------------------------------------- make -j4 make[2]: Entering directory '/build/kalign-V8kuw9/kalign-3.3' Making all in src make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/src' make all-am make[4]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/src' gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o run_kalign.o run_kalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o idata.o idata.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o tldevel.o tldevel.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o tlmisc.o tlmisc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o esl_stopwatch.o esl_stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o tlrng.o tlrng.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o alphabet.o alphabet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o alignment_parameters.o alignment_parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o pick_anchor.o pick_anchor.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o bisectingKmeans.o bisectingKmeans.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o sequence_distance.o sequence_distance.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o euclidean_dist.o euclidean_dist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o weave_alignment.o weave_alignment.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o rwalign.o rwalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o misc.o misc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o bpm.o bpm.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o aln_task.o aln_task.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o aln_mem.o aln_mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o aln_setup.o aln_setup.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o aln_run.o aln_run.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o aln_controller.o aln_controller.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o aln_seqseq.o aln_seqseq.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o aln_seqprofile.o aln_seqprofile.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o aln_profileprofile.o aln_profileprofile.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o queue.o queue.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o kchaos.o kchaos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o time_and_score_aln.o time_and_score_aln.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o benchrunner.o benchrunner.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o create_run_cmds.o create_run_cmds.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o create_run_kalign_diff_cmds.o create_run_kalign_diff_cmds.c create_run_cmds.c: In function ‘main’: create_run_cmds.c:54:164: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 6845 and 8101 [-Wformat-truncation=] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~ ~~~ create_run_cmds.c:54:76: note: directive argument in the range [0, 65535] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output between 124 and 17766 bytes into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm create_run_kalign_diff_cmds.c: In function ‘main’: create_run_kalign_diff_cmds.c:158:42: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size 512 [-Wformat-truncation=] 158 | snprintf(filename, 512, "%s", ret); | ^~ ~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin_snprintf’ output between 1 and 8192 bytes into a destination of size 512 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:181:113: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:181:52: note: directive argument in the range [1, 2147483647] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:185:113: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:185:52: note: directive argument in the range [2, 2147483647] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:189:120: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 7618 and 8129 [-Wformat-truncation=] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:189:52: note: directive argument in the range [3, 2147483647] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output 81 or more bytes (assuming 8792) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:193:122: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 7616 and 8127 [-Wformat-truncation=] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:193:52: note: directive argument in the range [4, 2147483647] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output 83 or more bytes (assuming 8794) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm -fopenmp /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm -fopenmp make[4]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/src' make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/src' Making all in dev make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/dev' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/dev' make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3' make[2]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3' make[2]: Entering directory '/build/kalign-V8kuw9/kalign-3.3' Making clean in src make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/src' rm -f kalign kchaos rm -f edist alphabet misc_test bpm_test rwaln rstdin_test test -z "ihmm_seq_itest_read_test.fa test_model_file.txt test.lfa test_dna.lfa libhdf5gluetest_exp.h5 libhdf5gluetest.h5 model_at_*h5 test1.h5 test2.h5" || rm -f ihmm_seq_itest_read_test.fa test_model_file.txt test.lfa test_dna.lfa libhdf5gluetest_exp.h5 libhdf5gluetest.h5 model_at_*h5 test1.h5 test2.h5 rm -rf .libs _libs rm -f timescorealn benchrunner genruncmds genkaligndiffcmds rm -f *.o test -z "edist.log alphabet.log misc_test.log bpm_test.log rstdin_test.log" || rm -f edist.log alphabet.log misc_test.log bpm_test.log rstdin_test.log test -z "edist.trs alphabet.trs misc_test.trs bpm_test.trs rstdin_test.trs" || rm -f edist.trs alphabet.trs misc_test.trs bpm_test.trs rstdin_test.trs test -z "test-suite.log" || rm -f test-suite.log rm -f *.lo make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/src' Making clean in dev make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/dev' test -z "rwtest.clu rwtest.fasta rwtest.msf test.afa" || rm -f rwtest.clu rwtest.fasta rwtest.msf test.afa rm -rf .libs _libs rm -f *.lo make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/dev' make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3' rm -rf .libs _libs rm -f *.lo make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3' make[2]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3' ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking "CFLAGS=-g -O2 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BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... (cached) ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether C compiler accepts -D_FORTIFY_SOURCE=2... yes checking whether C compiler accepts -ffunction-sections... yes checking whether C compiler accepts -fdata-sections... yes checking whether C compiler accepts --gc-sections... no checking for OpenMP flag of C compiler... -fopenmp checking for _Generic... yes checking for sqrt in -lm... yes checking for main in -lpthread... yes checking for library containing clock_gettime... none required checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking mach/mach.h usability... no checking mach/mach.h presence... no checking for mach/mach.h... no checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for inline... inline checking for size_t... yes checking for ssize_t... yes checking for int8_t... yes checking for int32_t... yes checking for int16_t... yes checking for int64_t... yes checking for uint8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for working strnlen... yes checking for error_at_line... yes checking for gettimeofday... yes checking for pow... yes checking for realpath... yes checking for sqrt... yes checking for strstr... yes checking for memset... yes checking for clock_gettime... yes checking for gethrtime... no checking for gettimeofday... (cached) yes checking for localtime_r... yes checking for strcspn... yes checking for valgrind... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating dev/Makefile config.status: creating src/config.h config.status: src/config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands configure: --------------------------------------------------------- configure: Configuration complete - kalign-3.3 configure: configure: General Information: configure: Version: 3.3 configure: Configured on: configure: Configured by: builduser configure: Host system: x86_64-pc-linux-gnu configure: Uname information: configure: Installation point: /usr configure: CFLAGS: -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx configure: CPFLAGS: -Wdate-time -D_FORTIFY_SOURCE=2 configure: LDFLAGS: -Wl,-z,relro -Wl,-z,now configure: SIMD flags: configure: --------------------------------------------------------- make -j4 make[2]: Entering directory '/build/kalign-V8kuw9/kalign-3.3' Making all in src make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/src' make all-am make[4]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/src' gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o run_kalign.o run_kalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o idata.o idata.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o tldevel.o tldevel.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o tlmisc.o tlmisc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o esl_stopwatch.o esl_stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o tlrng.o tlrng.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o alphabet.o alphabet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o alignment_parameters.o alignment_parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o pick_anchor.o pick_anchor.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o bisectingKmeans.o bisectingKmeans.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o sequence_distance.o sequence_distance.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o euclidean_dist.o euclidean_dist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o weave_alignment.o weave_alignment.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o rwalign.o rwalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o misc.o misc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o bpm.o bpm.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o aln_task.o aln_task.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o aln_mem.o aln_mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o aln_setup.o aln_setup.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o aln_run.o aln_run.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o aln_controller.o aln_controller.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o aln_seqseq.o aln_seqseq.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o aln_seqprofile.o aln_seqprofile.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o aln_profileprofile.o aln_profileprofile.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o queue.o queue.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o kchaos.o kchaos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o time_and_score_aln.o time_and_score_aln.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o benchrunner.o benchrunner.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o create_run_cmds.o create_run_cmds.c create_run_cmds.c: In function ‘main’: create_run_cmds.c:54:164: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 6845 and 8101 [-Wformat-truncation=] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~ ~~~ create_run_cmds.c:54:76: note: directive argument in the range [0, 65535] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output between 124 and 17766 bytes into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o create_run_kalign_diff_cmds.o create_run_kalign_diff_cmds.c create_run_kalign_diff_cmds.c: In function ‘main’: create_run_kalign_diff_cmds.c:158:42: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size 512 [-Wformat-truncation=] 158 | snprintf(filename, 512, "%s", ret); | ^~ ~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin_snprintf’ output between 1 and 8192 bytes into a destination of size 512 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:181:113: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:181:52: note: directive argument in the range [1, 2147483647] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:185:113: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:185:52: note: directive argument in the range [2, 2147483647] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:189:120: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 7618 and 8129 [-Wformat-truncation=] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:189:52: note: directive argument in the range [3, 2147483647] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output 81 or more bytes (assuming 8792) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:193:122: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 7616 and 8127 [-Wformat-truncation=] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:193:52: note: directive argument in the range [4, 2147483647] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output 83 or more bytes (assuming 8794) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm -fopenmp /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm -fopenmp make[4]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/src' make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/src' Making all in dev make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/dev' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/dev' make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3' make[2]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3' make[2]: Entering directory '/build/kalign-V8kuw9/kalign-3.3' Making clean in src make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/src' rm -f kalign kchaos rm -f edist alphabet misc_test bpm_test rwaln rstdin_test test -z "ihmm_seq_itest_read_test.fa test_model_file.txt test.lfa test_dna.lfa libhdf5gluetest_exp.h5 libhdf5gluetest.h5 model_at_*h5 test1.h5 test2.h5" || rm -f ihmm_seq_itest_read_test.fa test_model_file.txt test.lfa test_dna.lfa libhdf5gluetest_exp.h5 libhdf5gluetest.h5 model_at_*h5 test1.h5 test2.h5 rm -rf .libs _libs rm -f timescorealn benchrunner genruncmds genkaligndiffcmds rm -f *.o test -z "edist.log alphabet.log misc_test.log bpm_test.log rstdin_test.log" || rm -f edist.log alphabet.log misc_test.log bpm_test.log rstdin_test.log test -z "edist.trs alphabet.trs misc_test.trs bpm_test.trs rstdin_test.trs" || rm -f edist.trs alphabet.trs misc_test.trs bpm_test.trs rstdin_test.trs test -z "test-suite.log" || rm -f test-suite.log rm -f *.lo make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/src' Making clean in dev make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/dev' test -z "rwtest.clu rwtest.fasta rwtest.msf test.afa" || rm -f rwtest.clu rwtest.fasta rwtest.msf test.afa rm -rf .libs _libs rm -f *.lo make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/dev' make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3' rm -rf .libs _libs rm -f *.lo make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3' make[2]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3' ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking "CFLAGS=-g -O2 -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1" checking for gcc... 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(cached) yes checking for GNU libc compatible realloc... yes checking for working strnlen... yes checking for error_at_line... yes checking for gettimeofday... yes checking for pow... yes checking for realpath... yes checking for sqrt... yes checking for strstr... yes checking for memset... yes checking for clock_gettime... yes checking for gethrtime... no checking for gettimeofday... (cached) yes checking for localtime_r... yes checking for strcspn... yes checking for valgrind... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating dev/Makefile config.status: creating src/config.h config.status: src/config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands configure: --------------------------------------------------------- configure: Configuration complete - kalign-3.3 configure: configure: General Information: configure: Version: 3.3 configure: Configured on: configure: Configured by: builduser configure: Host system: x86_64-pc-linux-gnu configure: Uname information: configure: Installation point: /usr configure: CFLAGS: -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 configure: CPFLAGS: -Wdate-time -D_FORTIFY_SOURCE=2 configure: LDFLAGS: -Wl,-z,relro -Wl,-z,now configure: SIMD flags: configure: --------------------------------------------------------- make -j4 make[2]: Entering directory '/build/kalign-V8kuw9/kalign-3.3' Making all in src make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/src' make all-am make[4]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/src' gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o run_kalign.o run_kalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o idata.o idata.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o tldevel.o tldevel.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o tlmisc.o tlmisc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o esl_stopwatch.o esl_stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o tlrng.o tlrng.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o alphabet.o alphabet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o alignment_parameters.o alignment_parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o pick_anchor.o pick_anchor.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o bisectingKmeans.o bisectingKmeans.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o sequence_distance.o sequence_distance.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o euclidean_dist.o euclidean_dist.c In file included from euclidean_dist.c:26: /usr/include/simde/x86/avx.h: In function ‘simde__m256_from_private’: /usr/include/simde/x86/avx.h:255:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 255 | simde__m256_from_private(simde__m256_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o weave_alignment.o weave_alignment.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o rwalign.o rwalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o misc.o misc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o bpm.o bpm.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o aln_task.o aln_task.c In file included from /usr/include/simde/x86/avx2.h:33, from bpm.c:29: /usr/include/simde/x86/avx.h: In function ‘simde__m256i_from_private’: gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o aln_mem.o aln_mem.c /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o aln_setup.o aln_setup.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o aln_run.o aln_run.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o aln_controller.o aln_controller.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o aln_seqseq.o aln_seqseq.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o aln_seqprofile.o aln_seqprofile.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o aln_profileprofile.o aln_profileprofile.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o queue.o queue.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o kchaos.o kchaos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o time_and_score_aln.o time_and_score_aln.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o benchrunner.o benchrunner.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o create_run_cmds.o create_run_cmds.c create_run_cmds.c: In function ‘main’: create_run_cmds.c:54:164: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 6845 and 8101 [-Wformat-truncation=] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~ ~~~ create_run_cmds.c:54:76: note: directive argument in the range [0, 65535] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output between 124 and 17766 bytes into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o create_run_kalign_diff_cmds.o create_run_kalign_diff_cmds.c /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm create_run_kalign_diff_cmds.c: In function ‘main’: create_run_kalign_diff_cmds.c:158:42: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size 512 [-Wformat-truncation=] 158 | snprintf(filename, 512, "%s", ret); | ^~ ~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin_snprintf’ output between 1 and 8192 bytes into a destination of size 512 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:181:113: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:181:52: note: directive argument in the range [1, 2147483647] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:185:113: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:185:52: note: directive argument in the range [2, 2147483647] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:189:120: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 7618 and 8129 [-Wformat-truncation=] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:189:52: note: directive argument in the range [3, 2147483647] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output 81 or more bytes (assuming 8792) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:193:122: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 7616 and 8127 [-Wformat-truncation=] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:193:52: note: directive argument in the range [4, 2147483647] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output 83 or more bytes (assuming 8794) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm -fopenmp /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm -fopenmp make[4]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/src' make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/src' Making all in dev make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/dev' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/dev' make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3' make[2]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3' make[2]: Entering directory '/build/kalign-V8kuw9/kalign-3.3' Making clean in src make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/src' rm -f kalign kchaos rm -f edist alphabet misc_test bpm_test rwaln rstdin_test test -z "ihmm_seq_itest_read_test.fa test_model_file.txt test.lfa test_dna.lfa libhdf5gluetest_exp.h5 libhdf5gluetest.h5 model_at_*h5 test1.h5 test2.h5" || rm -f ihmm_seq_itest_read_test.fa test_model_file.txt test.lfa test_dna.lfa libhdf5gluetest_exp.h5 libhdf5gluetest.h5 model_at_*h5 test1.h5 test2.h5 rm -rf .libs _libs rm -f timescorealn benchrunner genruncmds genkaligndiffcmds rm -f *.o test -z "edist.log alphabet.log misc_test.log bpm_test.log rstdin_test.log" || rm -f edist.log alphabet.log misc_test.log bpm_test.log rstdin_test.log test -z "edist.trs alphabet.trs misc_test.trs bpm_test.trs rstdin_test.trs" || rm -f edist.trs alphabet.trs misc_test.trs bpm_test.trs rstdin_test.trs test -z "test-suite.log" || rm -f test-suite.log rm -f *.lo make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/src' Making clean in dev make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/dev' test -z "rwtest.clu rwtest.fasta rwtest.msf test.afa" || rm -f rwtest.clu rwtest.fasta rwtest.msf test.afa rm -rf .libs _libs rm -f *.lo make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/dev' make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3' rm -rf .libs _libs rm -f *.lo make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3' make[2]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3' ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking "CFLAGS=-g -O2 -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3" checking for 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 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(cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether C compiler accepts -D_FORTIFY_SOURCE=2... yes checking whether C compiler accepts -ffunction-sections... yes checking whether C compiler accepts -fdata-sections... yes checking whether C compiler accepts --gc-sections... no checking for OpenMP flag of C compiler... -fopenmp checking for _Generic... yes checking for sqrt in -lm... yes checking for main in -lpthread... yes checking for library containing clock_gettime... none required checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... 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(cached) yes checking for GNU libc compatible realloc... yes checking for working strnlen... yes checking for error_at_line... yes checking for gettimeofday... yes checking for pow... yes checking for realpath... yes checking for sqrt... yes checking for strstr... yes checking for memset... yes checking for clock_gettime... yes checking for gethrtime... no checking for gettimeofday... (cached) yes checking for localtime_r... yes checking for strcspn... yes checking for valgrind... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating dev/Makefile config.status: creating src/config.h config.status: src/config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands configure: --------------------------------------------------------- configure: Configuration complete - kalign-3.3 configure: configure: General Information: configure: Version: 3.3 configure: Configured on: configure: Configured by: builduser configure: Host system: x86_64-pc-linux-gnu configure: Uname information: configure: Installation point: /usr configure: CFLAGS: -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 configure: CPFLAGS: -Wdate-time -D_FORTIFY_SOURCE=2 configure: LDFLAGS: -Wl,-z,relro -Wl,-z,now configure: SIMD flags: configure: --------------------------------------------------------- make -j4 make[2]: Entering directory '/build/kalign-V8kuw9/kalign-3.3' Making all in src make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/src' make all-am make[4]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/src' gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o run_kalign.o run_kalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o idata.o idata.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o tldevel.o tldevel.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o tlmisc.o tlmisc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o esl_stopwatch.o esl_stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o tlrng.o tlrng.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o alphabet.o alphabet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o alignment_parameters.o alignment_parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o pick_anchor.o pick_anchor.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o bisectingKmeans.o bisectingKmeans.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o sequence_distance.o sequence_distance.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o euclidean_dist.o euclidean_dist.c In file included from euclidean_dist.c:26: /usr/include/simde/x86/avx.h: In function ‘simde__m256_from_private’: /usr/include/simde/x86/avx.h:255:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 255 | simde__m256_from_private(simde__m256_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o weave_alignment.o weave_alignment.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o rwalign.o rwalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o misc.o misc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o bpm.o bpm.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o aln_task.o aln_task.c In file included from /usr/include/simde/x86/avx2.h:33, from bpm.c:29: /usr/include/simde/x86/avx.h: In function ‘simde__m256i_from_private’: /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o aln_mem.o aln_mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o aln_setup.o aln_setup.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o aln_run.o aln_run.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o aln_controller.o aln_controller.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o aln_seqseq.o aln_seqseq.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o aln_seqprofile.o aln_seqprofile.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o aln_profileprofile.o aln_profileprofile.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o queue.o queue.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o kchaos.o kchaos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o time_and_score_aln.o time_and_score_aln.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o benchrunner.o benchrunner.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o create_run_cmds.o create_run_cmds.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o create_run_kalign_diff_cmds.o create_run_kalign_diff_cmds.c create_run_cmds.c: In function ‘main’: create_run_cmds.c:54:164: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 6845 and 8101 [-Wformat-truncation=] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~ ~~~ create_run_cmds.c:54:76: note: directive argument in the range [0, 65535] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output between 124 and 17766 bytes into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c: In function ‘main’: create_run_kalign_diff_cmds.c:158:42: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size 512 [-Wformat-truncation=] 158 | snprintf(filename, 512, "%s", ret); | ^~ ~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin_snprintf’ output between 1 and 8192 bytes into a destination of size 512 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:181:113: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:181:52: note: directive argument in the range [1, 2147483647] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:185:113: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:185:52: note: directive argument in the range [2, 2147483647] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:189:120: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 7618 and 8129 [-Wformat-truncation=] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:189:52: note: directive argument in the range [3, 2147483647] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output 81 or more bytes (assuming 8792) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:193:122: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 7616 and 8127 [-Wformat-truncation=] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:193:52: note: directive argument in the range [4, 2147483647] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output 83 or more bytes (assuming 8794) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm -fopenmp /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm -fopenmp make[4]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/src' make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/src' Making all in dev make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/dev' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/dev' make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3' make[2]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3' make[2]: Entering directory '/build/kalign-V8kuw9/kalign-3.3' Making clean in src make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/src' rm -f kalign kchaos rm -f edist alphabet misc_test bpm_test rwaln rstdin_test test -z "ihmm_seq_itest_read_test.fa test_model_file.txt test.lfa test_dna.lfa libhdf5gluetest_exp.h5 libhdf5gluetest.h5 model_at_*h5 test1.h5 test2.h5" || rm -f ihmm_seq_itest_read_test.fa test_model_file.txt test.lfa test_dna.lfa libhdf5gluetest_exp.h5 libhdf5gluetest.h5 model_at_*h5 test1.h5 test2.h5 rm -rf .libs _libs rm -f timescorealn benchrunner genruncmds genkaligndiffcmds rm -f *.o test -z "edist.log alphabet.log misc_test.log bpm_test.log rstdin_test.log" || rm -f edist.log alphabet.log misc_test.log bpm_test.log rstdin_test.log test -z "edist.trs alphabet.trs misc_test.trs bpm_test.trs rstdin_test.trs" || rm -f edist.trs alphabet.trs misc_test.trs bpm_test.trs rstdin_test.trs test -z "test-suite.log" || rm -f test-suite.log rm -f *.lo make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/src' Making clean in dev make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/dev' test -z "rwtest.clu rwtest.fasta rwtest.msf test.afa" || rm -f rwtest.clu rwtest.fasta rwtest.msf test.afa rm -rf .libs _libs rm -f *.lo make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/dev' make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3' rm -rf .libs _libs rm -f *.lo make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3' make[2]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3' ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking "CFLAGS=-g -O2 -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3" checking for 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... 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(cached) ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... 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(cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether C compiler accepts -D_FORTIFY_SOURCE=2... yes checking whether C compiler accepts -ffunction-sections... yes checking whether C compiler accepts -fdata-sections... yes checking whether C compiler accepts --gc-sections... no checking for OpenMP flag of C compiler... -fopenmp checking for _Generic... yes checking for sqrt in -lm... yes checking for main in -lpthread... yes checking for library containing clock_gettime... none required checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... 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(cached) yes checking for GNU libc compatible realloc... yes checking for working strnlen... yes checking for error_at_line... yes checking for gettimeofday... yes checking for pow... yes checking for realpath... yes checking for sqrt... yes checking for strstr... yes checking for memset... yes checking for clock_gettime... yes checking for gethrtime... no checking for gettimeofday... (cached) yes checking for localtime_r... yes checking for strcspn... yes checking for valgrind... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating dev/Makefile config.status: creating src/config.h config.status: src/config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands configure: --------------------------------------------------------- configure: Configuration complete - kalign-3.3 configure: configure: General Information: configure: Version: 3.3 configure: Configured on: configure: Configured by: builduser configure: Host system: x86_64-pc-linux-gnu configure: Uname information: configure: Installation point: /usr configure: CFLAGS: -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 configure: CPFLAGS: -Wdate-time -D_FORTIFY_SOURCE=2 configure: LDFLAGS: -Wl,-z,relro -Wl,-z,now configure: SIMD flags: configure: --------------------------------------------------------- make -j4 make[2]: Entering directory '/build/kalign-V8kuw9/kalign-3.3' Making all in src make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/src' make all-am make[4]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/src' gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o run_kalign.o run_kalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o idata.o idata.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o tldevel.o tldevel.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o tlmisc.o tlmisc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o esl_stopwatch.o esl_stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o tlrng.o tlrng.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o alphabet.o alphabet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o alignment_parameters.o alignment_parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o pick_anchor.o pick_anchor.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o bisectingKmeans.o bisectingKmeans.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o sequence_distance.o sequence_distance.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o euclidean_dist.o euclidean_dist.c In file included from euclidean_dist.c:26: /usr/include/simde/x86/avx.h: In function ‘simde__m256_from_private’: /usr/include/simde/x86/avx.h:255:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 255 | simde__m256_from_private(simde__m256_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o weave_alignment.o weave_alignment.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o rwalign.o rwalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o misc.o misc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o bpm.o bpm.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o aln_task.o aln_task.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o aln_mem.o aln_mem.c In file included from /usr/include/simde/x86/avx2.h:33, from bpm.c:29: /usr/include/simde/x86/avx.h: In function ‘simde__m256i_from_private’: /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o aln_setup.o aln_setup.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o aln_run.o aln_run.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o aln_controller.o aln_controller.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o aln_seqseq.o aln_seqseq.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o aln_seqprofile.o aln_seqprofile.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o aln_profileprofile.o aln_profileprofile.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o queue.o queue.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o kchaos.o kchaos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o time_and_score_aln.o time_and_score_aln.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o benchrunner.o benchrunner.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o create_run_cmds.o create_run_cmds.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o create_run_kalign_diff_cmds.o create_run_kalign_diff_cmds.c create_run_cmds.c: In function ‘main’: create_run_cmds.c:54:164: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 6845 and 8101 [-Wformat-truncation=] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~ ~~~ create_run_cmds.c:54:76: note: directive argument in the range [0, 65535] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output between 124 and 17766 bytes into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm create_run_kalign_diff_cmds.c: In function ‘main’: create_run_kalign_diff_cmds.c:158:42: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size 512 [-Wformat-truncation=] 158 | snprintf(filename, 512, "%s", ret); | ^~ ~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin_snprintf’ output between 1 and 8192 bytes into a destination of size 512 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:181:113: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:181:52: note: directive argument in the range [1, 2147483647] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:185:113: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:185:52: note: directive argument in the range [2, 2147483647] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:189:120: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 7618 and 8129 [-Wformat-truncation=] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:189:52: note: directive argument in the range [3, 2147483647] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output 81 or more bytes (assuming 8792) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:193:122: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 7616 and 8127 [-Wformat-truncation=] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:193:52: note: directive argument in the range [4, 2147483647] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output 83 or more bytes (assuming 8794) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm -fopenmp /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm -fopenmp make[4]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/src' make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/src' Making all in dev make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/dev' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/dev' make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3' make[2]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3' make clean ; dh_auto_configure && dh_auto_build && \ cp src/kalign src/kalign-plain && \ cp src/timescorealn src/timescorealn-plain make[2]: Entering directory '/build/kalign-V8kuw9/kalign-3.3' Making clean in src make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/src' rm -f kalign kchaos rm -f edist alphabet misc_test bpm_test rwaln rstdin_test test -z "ihmm_seq_itest_read_test.fa test_model_file.txt test.lfa test_dna.lfa libhdf5gluetest_exp.h5 libhdf5gluetest.h5 model_at_*h5 test1.h5 test2.h5" || rm -f ihmm_seq_itest_read_test.fa test_model_file.txt test.lfa test_dna.lfa libhdf5gluetest_exp.h5 libhdf5gluetest.h5 model_at_*h5 test1.h5 test2.h5 rm -rf .libs _libs rm -f timescorealn benchrunner genruncmds genkaligndiffcmds rm -f *.o test -z "edist.log alphabet.log misc_test.log bpm_test.log rstdin_test.log" || rm -f edist.log alphabet.log misc_test.log bpm_test.log rstdin_test.log test -z "edist.trs alphabet.trs misc_test.trs bpm_test.trs rstdin_test.trs" || rm -f edist.trs alphabet.trs misc_test.trs bpm_test.trs rstdin_test.trs test -z "test-suite.log" || rm -f test-suite.log rm -f *.lo make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/src' Making clean in dev make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/dev' test -z "rwtest.clu rwtest.fasta rwtest.msf test.afa" || rm -f rwtest.clu rwtest.fasta rwtest.msf test.afa rm -rf .libs _libs rm 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(cached) yes checking for GNU libc compatible realloc... yes checking for working strnlen... yes checking for error_at_line... yes checking for gettimeofday... yes checking for pow... yes checking for realpath... yes checking for sqrt... yes checking for strstr... yes checking for memset... yes checking for clock_gettime... yes checking for gethrtime... no checking for gettimeofday... (cached) yes checking for localtime_r... yes checking for strcspn... yes checking for valgrind... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating dev/Makefile config.status: creating src/config.h config.status: src/config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands configure: --------------------------------------------------------- configure: Configuration complete - kalign-3.3 configure: configure: General Information: configure: Version: 3.3 configure: Configured on: configure: Configured by: builduser configure: Host system: x86_64-pc-linux-gnu configure: Uname information: configure: Installation point: /usr configure: CFLAGS: -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd configure: CPFLAGS: -Wdate-time -D_FORTIFY_SOURCE=2 configure: LDFLAGS: -Wl,-z,relro -Wl,-z,now configure: SIMD flags: configure: --------------------------------------------------------- make -j4 make[2]: Entering directory '/build/kalign-V8kuw9/kalign-3.3' Making all in src make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/src' make all-am make[4]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/src' gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o run_kalign.o run_kalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o idata.o idata.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o tldevel.o tldevel.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o tlmisc.o tlmisc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o esl_stopwatch.o esl_stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o tlrng.o tlrng.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o alphabet.o alphabet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o alignment_parameters.o alignment_parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o pick_anchor.o pick_anchor.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o bisectingKmeans.o bisectingKmeans.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o sequence_distance.o sequence_distance.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o euclidean_dist.o euclidean_dist.c In file included from euclidean_dist.c:26: /usr/include/simde/x86/avx.h: In function ‘simde__m256_from_private’: /usr/include/simde/x86/avx.h:255:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 255 | simde__m256_from_private(simde__m256_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o weave_alignment.o weave_alignment.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o rwalign.o rwalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o misc.o misc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o bpm.o bpm.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o aln_task.o aln_task.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o aln_mem.o aln_mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o aln_setup.o aln_setup.c In file included from /usr/include/simde/x86/avx2.h:33, from bpm.c:29: /usr/include/simde/x86/avx.h: In function ‘simde__m256i_from_private’: /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o aln_run.o aln_run.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o aln_controller.o aln_controller.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o aln_seqseq.o aln_seqseq.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o aln_seqprofile.o aln_seqprofile.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o aln_profileprofile.o aln_profileprofile.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o queue.o queue.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o kchaos.o kchaos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o time_and_score_aln.o time_and_score_aln.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o benchrunner.o benchrunner.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o create_run_cmds.o create_run_cmds.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o create_run_kalign_diff_cmds.o create_run_kalign_diff_cmds.c create_run_cmds.c: In function ‘main’: create_run_cmds.c:54:164: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 6845 and 8101 [-Wformat-truncation=] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~ ~~~ create_run_cmds.c:54:76: note: directive argument in the range [0, 65535] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output between 124 and 17766 bytes into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm create_run_kalign_diff_cmds.c: In function ‘main’: create_run_kalign_diff_cmds.c:158:42: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size 512 [-Wformat-truncation=] 158 | snprintf(filename, 512, "%s", ret); | ^~ ~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin_snprintf’ output between 1 and 8192 bytes into a destination of size 512 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:181:113: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:181:52: note: directive argument in the range [1, 2147483647] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:185:113: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:185:52: note: directive argument in the range [2, 2147483647] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:189:120: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 7618 and 8129 [-Wformat-truncation=] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:189:52: note: directive argument in the range [3, 2147483647] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output 81 or more bytes (assuming 8792) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:193:122: warning: ‘%s’ directive output may be truncated writing up to 8191 bytes into a region of size between 7616 and 8127 [-Wformat-truncation=] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:193:52: note: directive argument in the range [4, 2147483647] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output 83 or more bytes (assuming 8794) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm -fopenmp /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm -fopenmp /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm -fopenmp /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm -fopenmp make[4]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/src' make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/src' Making all in dev make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/dev' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/dev' make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3' make[2]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3' make[1]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3' dh_auto_test -a make -j4 check VERBOSE=1 make[1]: Entering directory '/build/kalign-V8kuw9/kalign-3.3' Making check in src make[2]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/src' make edist alphabet misc_test bpm_test rwaln rstdin_test make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/src' gcc -DHAVE_CONFIG_H -I. -DITEST_EDIST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o edist-tldevel.o `test -f 'tldevel.c' || echo './'`tldevel.c gcc -DHAVE_CONFIG_H -I. -DITEST_EDIST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o edist-esl_stopwatch.o `test -f 'esl_stopwatch.c' || echo './'`esl_stopwatch.c gcc -DHAVE_CONFIG_H -I. -DITEST_EDIST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o edist-tlrng.o `test -f 'tlrng.c' || echo './'`tlrng.c gcc -DHAVE_CONFIG_H -I. -DITEST_EDIST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o edist-euclidean_dist.o `test -f 'euclidean_dist.c' || echo './'`euclidean_dist.c gcc -DHAVE_CONFIG_H -I. -DITEST_ALPHABET -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o alphabet-tldevel.o `test -f 'tldevel.c' || echo './'`tldevel.c In file included from euclidean_dist.c:26: /usr/include/simde/x86/avx.h: In function ‘simde__m256_from_private’: /usr/include/simde/x86/avx.h:255:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 255 | simde__m256_from_private(simde__m256_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -DITEST_ALPHABET -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o alphabet-alphabet.o `test -f 'alphabet.c' || echo './'`alphabet.c gcc -DHAVE_CONFIG_H -I. -DITEST_MISC -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o misc_test-tldevel.o `test -f 'tldevel.c' || echo './'`tldevel.c gcc -DHAVE_CONFIG_H -I. -DITEST_MISC -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o misc_test-tlrng.o `test -f 'tlrng.c' || echo './'`tlrng.c gcc -DHAVE_CONFIG_H -I. -DITEST_MISC -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o misc_test-misc.o `test -f 'misc.c' || echo './'`misc.c gcc -DHAVE_CONFIG_H -I. -DITEST_MISC -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o misc_test-alphabet.o `test -f 'alphabet.c' || echo './'`alphabet.c gcc -DHAVE_CONFIG_H -I. -DBPM_UTEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o bpm_test-tldevel.o `test -f 'tldevel.c' || echo './'`tldevel.c gcc -DHAVE_CONFIG_H -I. -DBPM_UTEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o bpm_test-esl_stopwatch.o `test -f 'esl_stopwatch.c' || echo './'`esl_stopwatch.c gcc -DHAVE_CONFIG_H -I. -DBPM_UTEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o bpm_test-tlrng.o `test -f 'tlrng.c' || echo './'`tlrng.c gcc -DHAVE_CONFIG_H -I. -DBPM_UTEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o bpm_test-bpm.o `test -f 'bpm.c' || echo './'`bpm.c bpm.c: In function ‘print_256’: bpm.c:361:6: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 361 | void print_256(__m256i X) | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -DBPM_UTEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o bpm_test-alphabet.o `test -f 'alphabet.c' || echo './'`alphabet.c gcc -DHAVE_CONFIG_H -I. -DRWALIGN_TEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o rwaln-tldevel.o `test -f 'tldevel.c' || echo './'`tldevel.c gcc -DHAVE_CONFIG_H -I. -DRWALIGN_TEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o rwaln-tlmisc.o `test -f 'tlmisc.c' || echo './'`tlmisc.c gcc -DHAVE_CONFIG_H -I. -DRWALIGN_TEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o rwaln-esl_stopwatch.o `test -f 'esl_stopwatch.c' || echo './'`esl_stopwatch.c gcc -DHAVE_CONFIG_H -I. -DRWALIGN_TEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o rwaln-rwalign.o `test -f 'rwalign.c' || echo './'`rwalign.c gcc -DHAVE_CONFIG_H -I. -DRWALIGN_TEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o rwaln-alphabet.o `test -f 'alphabet.c' || echo './'`alphabet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o read_from_stdin_test.o read_from_stdin_test.c /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o edist edist-tldevel.o edist-esl_stopwatch.o edist-tlrng.o edist-euclidean_dist.o -lpthread -lm /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o alphabet alphabet-tldevel.o alphabet-alphabet.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o edist edist-tldevel.o edist-esl_stopwatch.o edist-tlrng.o edist-euclidean_dist.o -lpthread -lm -fopenmp /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o misc_test misc_test-tldevel.o misc_test-tlrng.o misc_test-misc.o misc_test-alphabet.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o alphabet alphabet-tldevel.o alphabet-alphabet.o -lpthread -lm -fopenmp /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o bpm_test bpm_test-tldevel.o bpm_test-esl_stopwatch.o bpm_test-tlrng.o bpm_test-bpm.o bpm_test-alphabet.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o misc_test misc_test-tldevel.o misc_test-tlrng.o misc_test-misc.o misc_test-alphabet.o -lpthread -lm -fopenmp /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o rstdin_test read_from_stdin_test.o tldevel.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bpm_test bpm_test-tldevel.o bpm_test-esl_stopwatch.o bpm_test-tlrng.o bpm_test-bpm.o bpm_test-alphabet.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o rstdin_test read_from_stdin_test.o tldevel.o -lpthread -lm -fopenmp /bin/bash ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o rwaln rwaln-tldevel.o rwaln-tlmisc.o rwaln-esl_stopwatch.o rwaln-rwalign.o rwaln-alphabet.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-V8kuw9/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o rwaln rwaln-tldevel.o rwaln-tlmisc.o rwaln-esl_stopwatch.o rwaln-rwalign.o rwaln-alphabet.o -lpthread -lm -fopenmp make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/src' make check-TESTS make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/src' make[4]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/src' PASS: misc_test PASS: alphabet PASS: edist PASS: rstdin_test PASS: bpm_test ============================================================================ Testsuite summary for kalign 3.3 ============================================================================ # TOTAL: 5 # PASS: 5 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/src' make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/src' make[2]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/src' Making check in dev make[2]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/dev' make check-TESTS make[3]: Entering directory '/build/kalign-V8kuw9/kalign-3.3/dev' Running kalign basic io test: a2m.good.1 read/writea2m.good.1 SUCCESS a2m.good.2 read/writea2m.good.2 SUCCESS afa.good.1 read/writeafa.good.1 SUCCESS afa.good.2 read/writeafa.good.2 SUCCESS afa.good.3 read/writeafa.good.3 SUCCESS clustal.good.1 read/writeclustal.good.1 SUCCESS clustal.good.2 read/writeclustal.good.2 SUCCESS PASS: run_io_test.sh Running kalign basic alignment tests: BB11001.msf read/writeBB11001.msf SUCCESS BB11001_EOF.msf read/writeBB11001_EOF.msf SUCCESS BB11001.tfa read/writeBB11001.tfa SUCCESS BB12006.msf read/writeBB12006.msf SUCCESS BB12006.tfa read/writeBB12006.tfa SUCCESS BB30014.msf read/writeBB30014.msf SUCCESS BB30014.tfa read/writeBB30014.tfa SUCCESS PASS: run_aln_test.sh ================== All 2 tests passed ================== make[3]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/dev' make[2]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3/dev' make[2]: Entering directory '/build/kalign-V8kuw9/kalign-3.3' make[2]: Nothing to be done for 'check-am'. make[2]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3' make[1]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3' create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/kalign-V8kuw9/kalign-3.3' dh_install debian/bin/simd-dispatch /usr/lib/kalign/ dh_install src/kalign-* usr/lib/kalign/ dh_install src/timescorealn-* usr/lib/kalign/ mkdir -p /build/kalign-V8kuw9/kalign-3.3/debian/kalign/usr/bin cd /build/kalign-V8kuw9/kalign-3.3/debian/kalign/usr/bin \ && ln -s ../lib/kalign/simd-dispatch kalign && ln -s ../lib/kalign/simd-dispatch timescorealn && true make[1]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3' dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a -a dh_strip -a -a dh_makeshlibs -a -a dh_shlibdeps -a -a dh_installdeb -a debian/rules override_dh_gencontrol make[1]: Entering directory '/build/kalign-V8kuw9/kalign-3.3' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.7.2-4), " make[1]: Leaving directory '/build/kalign-V8kuw9/kalign-3.3' dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'kalign-dbgsym' in '../kalign-dbgsym_3.3-1+b3_amd64.deb'. dpkg-deb: building package 'kalign' in '../kalign_3.3-1+b3_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../kalign_3.3-1+b3_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/kalign-V8kuw9 /tmp/kalign-3.3-1+b3839ozb5d I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.bTqD9H0hZk... I: success in 643.4112 seconds md5: kalign-dbgsym_3.3-1+b3_amd64.deb: OK md5: kalign_3.3-1+b3_amd64.deb: OK sha1: kalign-dbgsym_3.3-1+b3_amd64.deb: OK sha1: kalign_3.3-1+b3_amd64.deb: OK sha256: kalign-dbgsym_3.3-1+b3_amd64.deb: OK sha256: kalign_3.3-1+b3_amd64.deb: OK Checksums: OK