Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/k/kalign/kalign_3.3.2-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/kalign-3.3.2-15angqgao/kalign_3.3.2-1_amd64.buildinfo Get source package info: kalign=1:3.3.2-1 Source URL: http://snapshot.notset.fr/mr/package/kalign/1:3.3.2-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.5-1.3 autopoint=0.21-6 autotools-dev=20220109.1 base-files=12.2 base-passwd=3.5.52 bash=5.1-6 binutils=2.38-3 binutils-common=2.38-3 binutils-x86-64-linux-gnu=2.38-3 bsdextrautils=2.38-4 bsdutils=1:2.38-4 build-essential=12.9 bzip2=1.0.8-5 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.3.0-1 dash=0.5.11+git20210903+057cd650a4ed-8 debconf=1.5.79 debhelper=13.7.1 debianutils=5.7-0.2 dh-autoreconf=20 dh-strip-nondeterminism=1.13.0-1 diffutils=1:3.7-5 dpkg=1.21.7 dpkg-dev=1.21.7 dwz=0.14-1 file=1:5.41-4 findutils=4.9.0-3 g++=4:11.2.0-2 g++-11=11.3.0-1 gcc=4:11.2.0-2 gcc-11=11.3.0-1 gcc-11-base=11.3.0-1 gcc-12-base=12-20220428-1 gettext=0.21-6 gettext-base=0.21-6 grep=3.7-1 groff-base=1.22.4-8 gzip=1.12-1 hostname=3.23 init-system-helpers=1.62 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libarchive-zip-perl=1.68-1 libasan6=11.3.0-1 libatomic1=12-20220428-1 libattr1=1:2.5.1-1 libaudit-common=1:3.0.7-1 libaudit1=1:3.0.7-1+b1 libbinutils=2.38-3 libblkid1=2.38-4 libbz2-1.0=1.0.8-5 libc-bin=2.33-7 libc-dev-bin=2.33-7 libc6=2.33-7 libc6-dev=2.33-7 libcap-ng0=0.7.9-2.2+b2 libcap2=1:2.44-1 libcc1-0=12-20220428-1 libcom-err2=1.46.5-2 libcrypt-dev=1:4.4.27-1.1 libcrypt1=1:4.4.27-1.1 libctf-nobfd0=2.38-3 libctf0=2.38-3 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.262 libdebhelper-perl=13.7.1 libdpkg-perl=1.21.7 libelf1=0.186-1 libfile-stripnondeterminism-perl=1.13.0-1 libgcc-11-dev=11.3.0-1 libgcc-s1=12-20220428-1 libgcrypt20=1.10.1-2 libgdbm-compat4=1.23-1 libgdbm6=1.23-1 libgmp10=2:6.2.1+dfsg-3 libgomp1=12-20220428-1 libgpg-error0=1.45-2 libgssapi-krb5-2=1.19.2-2+b1 libicu71=71.1-2 libisl23=0.24-2 libitm1=12-20220428-1 libk5crypto3=1.19.2-2+b1 libkeyutils1=1.6.1-3 libkrb5-3=1.19.2-2+b1 libkrb5support0=1.19.2-2+b1 liblsan0=12-20220428-1 liblz4-1=1.9.3-2 liblzma5=5.2.5-2.1 libmagic-mgc=1:5.41-4 libmagic1=1:5.41-4 libmount1=2.38-4 libmpc3=1.2.1-2 libmpfr6=4.1.0-3 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libpam-modules=1.4.0-13 libpam-modules-bin=1.4.0-13 libpam-runtime=1.4.0-13 libpam0g=1.4.0-13 libpcre2-8-0=10.40-1 libpcre3=2:8.39-14 libperl5.34=5.34.0-4 libpipeline1=1.5.6-1 libquadmath0=12-20220428-1 libseccomp2=2.5.4-1 libselinux1=3.3-1+b2 libsigsegv2=2.14-1 libsimde-dev=0.7.2-6 libsmartcols1=2.38-4 libssl1.1=1.1.1n-1 libstdc++-11-dev=11.3.0-1 libstdc++6=12-20220428-1 libsub-override-perl=0.09-2 libsystemd0=250.4-1 libtinfo6=6.3+20220423-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.7-3 libtsan0=11.3.0-1 libubsan1=12-20220428-1 libuchardet0=0.0.7-1 libudev1=250.4-1 libunistring2=1.0-1 libuuid1=2.38-4 libxml2=2.9.13+dfsg-1+b1 libzstd1=1.5.2+dfsg-1 linux-libc-dev=5.17.3-1 login=1:4.11.1+dfsg1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.10.2-1 mawk=1.3.4.20200120-3+b1 ncurses-base=6.3+20220423-1 ncurses-bin=6.3+20220423-1 patch=2.7.6-7 perl=5.34.0-4 perl-base=5.34.0-4 perl-modules-5.34=5.34.0-4 po-debconf=1.0.21+nmu1 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.03-1 tar=1.34+dfsg-1 util-linux=2.38-4 util-linux-extra=2.38-4 xz-utils=5.2.5-2.1 zlib1g=1:1.2.11.dfsg-4 --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/20220505T025003Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220505T025003Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220501T215056Z/ 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=1:3.3.2-1 && mkdir -p /build/kalign-GHGNo8 && dpkg-source --no-check -x /*.dsc /build/kalign-GHGNo8/kalign-3.3.2 && chown -R builduser:builduser /build/kalign-GHGNo8" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/kalign-GHGNo8/kalign-3.3.2 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1651495181" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/kalign-GHGNo8 /tmp/kalign-3.3.2-15angqgao bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220501T215056Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.Iiu1NjHeYk 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.Iiu1NjHeYk Reading package lists... Building dependency tree... util-linux is already the newest version (2.38-4). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 135 kB of archives. After this operation, 406 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220501T215056Z unstable/main amd64 libfakeroot amd64 1.28-1 [48.2 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220501T215056Z unstable/main amd64 fakeroot amd64 1.28-1 [87.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 135 kB in 0s (922 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 ... 4627 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.28-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.28-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.28-1_amd64.deb ... Unpacking fakeroot (1.28-1) ... Setting up libfakeroot:amd64 (1.28-1) ... Setting up fakeroot (1.28-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-7) ... 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/20220505T025003Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220505T025003Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220501T215056Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.Iiu1NjHeYk Get:1 http://snapshot.notset.fr/archive/debian/20220505T025003Z bookworm InRelease [130 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20220501T215056Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20220505T025003Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220505T025003Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20220505T025003Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220505T025003Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20220505T025003Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220505T025003Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20220505T025003Z bookworm/main Sources [11.9 MB] Get:4 http://snapshot.notset.fr/archive/debian/20220505T025003Z bookworm/main amd64 Packages [11.4 MB] Fetched 23.5 MB in 19s (1228 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.Iiu1NjHeYk I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d kalign=1:3.3.2-1 && mkdir -p /build/kalign-GHGNo8 && dpkg-source --no-check -x /*.dsc /build/kalign-GHGNo8/kalign-3.3.2 && chown -R builduser:builduser /build/kalign-GHGNo8"' exec /tmp/mmdebstrap.Iiu1NjHeYk 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 957 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20220505T025003Z bookworm/main kalign 1:3.3.2-1 (dsc) [1980 B] Get:2 http://snapshot.notset.fr/archive/debian/20220505T025003Z bookworm/main kalign 1:3.3.2-1 (tar) [941 kB] Get:3 http://snapshot.notset.fr/archive/debian/20220505T025003Z bookworm/main kalign 1:3.3.2-1 (diff) [13.8 kB] Fetched 957 kB in 1s (1193 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'kalign_3.3.2-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting kalign in /build/kalign-GHGNo8/kalign-3.3.2 dpkg-source: info: unpacking kalign_3.3.2.orig.tar.gz dpkg-source: info: unpacking kalign_3.3.2-1.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-GHGNo8/kalign-3.3.2 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1651495181" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.Iiu1NjHeYk dpkg-buildpackage: info: source package kalign dpkg-buildpackage: info: source version 1:3.3.2-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille 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:26: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:26: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:26: the top level configure.ac:143: warning: The macro `AC_CONFIG_HEADER' is obsolete. configure.ac:143: You should run autoupdate. ./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from... configure.ac:143: the top level 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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for wchar.h... yes checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking whether _XOPEN_SOURCE should be defined... no checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free 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 the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed 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 grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E 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 file... file 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 for math.h... yes checking for float.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/time.h... yes checking for mach/mach.h... no 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 GNU libc compatible malloc... 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-3.3.2 configure: configure: General Information: configure: Version: 3.3.2 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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2' mkdir -p /build/kalign-GHGNo8/kalign-3.3.2/debian/kalign/usr mkdir -p /build/kalign-GHGNo8/kalign-3.3.2/debian/kalign/usr/lib/kalign make clean ; dh_auto_configure -- CFLAGS="-g -O2 -ffile-prefix-map=/build/kalign-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2' Making clean in src make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/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-GHGNo8/kalign-3.3.2/src' Making clean in dev make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/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-GHGNo8/kalign-3.3.2/dev' make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2' rm -rf .libs _libs rm -f *.lo make[3]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2' make[2]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2' ./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-GHGNo8/kalign-3.3.2=. -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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for wchar.h... yes checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking whether _XOPEN_SOURCE should be defined... no checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free 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 the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed 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 grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E 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 file... file 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 for math.h... yes checking for float.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/time.h... yes checking for mach/mach.h... no 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 GNU libc compatible malloc... 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-3.3.2 configure: configure: General Information: configure: Version: 3.3.2 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-GHGNo8/kalign-3.3.2=. -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 -j10 make[2]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2' Making all in src make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/src' make all-am make[4]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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_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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin_snprintf’ output between 1 and 8192 bytes into a destination of size 512 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output 74 or more bytes (assuming 8785) into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output 74 or more bytes (assuming 8785) into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output 81 or more bytes (assuming 8792) into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output 83 or more bytes (assuming 8794) into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ 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:866, from tldevel.h:5, from create_run_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output between 124 and 17766 bytes into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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 /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-GHGNo8/kalign-3.3.2=. -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 /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-GHGNo8/kalign-3.3.2=. -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 /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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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 libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-GHGNo8/kalign-3.3.2=. -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 libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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 libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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 make[4]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2/src' make[3]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2/src' Making all in dev make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/dev' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2/dev' make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2' make[2]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2' make[2]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2' Making clean in src make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/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-GHGNo8/kalign-3.3.2/src' Making clean in dev make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/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-GHGNo8/kalign-3.3.2/dev' make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2' rm -rf .libs _libs rm -f *.lo make[3]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2' make[2]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2' ./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-GHGNo8/kalign-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx" 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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for 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(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-3.3.2 configure: configure: General Information: configure: Version: 3.3.2 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-GHGNo8/kalign-3.3.2=. -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 -j10 make[2]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2' Making all in src make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/src' make all-am make[4]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -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-GHGNo8/kalign-3.3.2=. -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_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:866, from tldevel.h:5, from create_run_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output between 124 and 17766 bytes into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin_snprintf’ output between 1 and 8192 bytes into a destination of size 512 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output 74 or more bytes (assuming 8785) into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output 74 or more bytes (assuming 8785) into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output 81 or more bytes (assuming 8792) into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output 83 or more bytes (assuming 8794) into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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 /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-GHGNo8/kalign-3.3.2=. -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 /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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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 libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-GHGNo8/kalign-3.3.2=. -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 libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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 libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-GHGNo8/kalign-3.3.2=. -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 /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-GHGNo8/kalign-3.3.2=. -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 libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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 make[4]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2/src' make[3]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2/src' Making all in dev make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/dev' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2/dev' make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2' make[2]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2' make[2]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2' Making clean in src make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/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-GHGNo8/kalign-3.3.2/src' Making clean in dev make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/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-GHGNo8/kalign-3.3.2/dev' make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2' rm -rf .libs _libs rm -f *.lo make[3]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2' make[2]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2' ./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-GHGNo8/kalign-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1" 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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking 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(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-3.3.2 configure: configure: General Information: configure: Version: 3.3.2 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-GHGNo8/kalign-3.3.2=. -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 -j10 make[2]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2' Making all in src make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/src' make all-am make[4]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o bpm.o bpm.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-GHGNo8/kalign-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -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-GHGNo8/kalign-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o aln_seqseq.o aln_seqseq.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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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:866, from tldevel.h:5, from create_run_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output between 124 and 17766 bytes into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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-GHGNo8/kalign-3.3.2=. -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 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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin_snprintf’ output between 1 and 8192 bytes into a destination of size 512 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output 74 or more bytes (assuming 8785) into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output 74 or more bytes (assuming 8785) into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output 81 or more bytes (assuming 8792) into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output 83 or more bytes (assuming 8794) into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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 /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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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 /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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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 libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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 libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-GHGNo8/kalign-3.3.2=. -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 libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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 make[4]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2/src' make[3]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2/src' Making all in dev make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/dev' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2/dev' make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2' make[2]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2' make[2]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2' Making clean in src make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/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-GHGNo8/kalign-3.3.2/src' Making clean in dev make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/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-GHGNo8/kalign-3.3.2/dev' make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2' rm -rf .libs _libs rm -f *.lo make[3]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2' make[2]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2' ./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-GHGNo8/kalign-3.3.2=. -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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for wchar.h... yes checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking whether _XOPEN_SOURCE should be defined... no checking 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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 for math.h... yes checking for float.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/time.h... yes checking for mach/mach.h... no 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 GNU libc compatible malloc... 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-3.3.2 configure: configure: General Information: configure: Version: 3.3.2 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-GHGNo8/kalign-3.3.2=. -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 -j10 make[2]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2' Making all in src make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/src' make all-am make[4]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o bpm.o bpm.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-GHGNo8/kalign-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o aln_controller.o aln_controller.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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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:866, from tldevel.h:5, from create_run_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output between 124 and 17766 bytes into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin_snprintf’ output between 1 and 8192 bytes into a destination of size 512 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output 74 or more bytes (assuming 8785) into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output 74 or more bytes (assuming 8785) into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output 81 or more bytes (assuming 8792) into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output 83 or more bytes (assuming 8794) into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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 /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-GHGNo8/kalign-3.3.2=. -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 /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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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 libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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 libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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 make[4]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2/src' make[3]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2/src' Making all in dev make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/dev' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2/dev' make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2' make[2]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2' make[2]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2' Making clean in src make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/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-GHGNo8/kalign-3.3.2/src' Making clean in dev make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/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-GHGNo8/kalign-3.3.2/dev' make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2' rm -rf .libs _libs rm -f *.lo make[3]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2' make[2]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2' ./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-GHGNo8/kalign-3.3.2=. -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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for wchar.h... yes checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking whether _XOPEN_SOURCE should be defined... no checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /bin/mkdir -p checking for gawk... 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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 file... file 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 for math.h... yes checking for float.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/time.h... yes checking for mach/mach.h... no 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 GNU libc compatible malloc... 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-3.3.2 configure: configure: General Information: configure: Version: 3.3.2 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-GHGNo8/kalign-3.3.2=. -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 -j10 make[2]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2' Making all in src make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/src' make all-am make[4]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o bpm.o bpm.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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o aln_profileprofile.o aln_profileprofile.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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -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:866, from tldevel.h:5, from create_run_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output between 124 and 17766 bytes into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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-GHGNo8/kalign-3.3.2=. -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_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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin_snprintf’ output between 1 and 8192 bytes into a destination of size 512 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output 74 or more bytes (assuming 8785) into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output 74 or more bytes (assuming 8785) into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output 81 or more bytes (assuming 8792) into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output 83 or more bytes (assuming 8794) into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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-GHGNo8/kalign-3.3.2=. -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 /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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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 /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-GHGNo8/kalign-3.3.2=. -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 /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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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 libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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 libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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 libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-GHGNo8/kalign-3.3.2=. -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 make[4]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2/src' make[3]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2/src' Making all in dev make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/dev' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2/dev' make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2' make[2]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2' 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-GHGNo8/kalign-3.3.2' Making clean in src make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/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-GHGNo8/kalign-3.3.2/src' Making clean in dev make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/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-GHGNo8/kalign-3.3.2/dev' make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2' rm -rf .libs _libs rm -f *.lo make[3]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2' make[2]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2' ./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 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(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 grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E 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 file... file 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 for math.h... yes checking for float.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/time.h... yes checking for mach/mach.h... no 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 GNU libc compatible malloc... 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-3.3.2 configure: configure: General Information: configure: Version: 3.3.2 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-GHGNo8/kalign-3.3.2=. -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 -j10 make[2]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2' Making all in src make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/src' make all-am make[4]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o bpm.o bpm.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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o aln_seqprofile.o aln_seqprofile.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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -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:866, from tldevel.h:5, from create_run_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output between 124 and 17766 bytes into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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-GHGNo8/kalign-3.3.2=. -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_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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin_snprintf’ output between 1 and 8192 bytes into a destination of size 512 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output 74 or more bytes (assuming 8785) into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output 74 or more bytes (assuming 8785) into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output 81 or more bytes (assuming 8792) into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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:866, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output 83 or more bytes (assuming 8794) into a destination of size 8192 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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 /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-GHGNo8/kalign-3.3.2=. -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 /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-GHGNo8/kalign-3.3.2=. -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 /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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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 libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-GHGNo8/kalign-3.3.2=. -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 libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-GHGNo8/kalign-3.3.2=. -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 libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -ffile-prefix-map=/build/kalign-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2=. -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-GHGNo8/kalign-3.3.2/src' make[3]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2/src' Making all in dev make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2/dev' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2/dev' make[3]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2' make[2]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2' make[1]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2' dh: command-omitted: The call to "dh_auto_test -a" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2' 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-GHGNo8/kalign-3.3.2/debian/kalign/usr/bin cd /build/kalign-GHGNo8/kalign-3.3.2/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-GHGNo8/kalign-3.3.2' 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 dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a debian/rules override_dh_gencontrol make[1]: Entering directory '/build/kalign-GHGNo8/kalign-3.3.2' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.7.2-6), " make[1]: Leaving directory '/build/kalign-GHGNo8/kalign-3.3.2' dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'kalign-dbgsym' in '../kalign-dbgsym_3.3.2-1_amd64.deb'. dpkg-deb: building package 'kalign' in '../kalign_3.3.2-1_amd64.deb'. dpkg-genbuildinfo --build=any -O../kalign_3.3.2-1_amd64.buildinfo dpkg-genchanges --build=any -O../kalign_3.3.2-1_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-GHGNo8 /tmp/kalign-3.3.2-15angqgao I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.Iiu1NjHeYk... I: success in 403.8350 seconds md5: kalign-dbgsym_3.3.2-1_amd64.deb: OK md5: kalign_3.3.2-1_amd64.deb: OK sha1: kalign-dbgsym_3.3.2-1_amd64.deb: OK sha1: kalign_3.3.2-1_amd64.deb: OK sha256: kalign-dbgsym_3.3.2-1_amd64.deb: OK sha256: kalign_3.3.2-1_amd64.deb: OK Checksums: OK