Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/l/last-align/last-align_1179-1+b1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/last-align-1179-1+b13cwiirun/last-align_1179-1+b1_amd64.buildinfo Get source package info: last-align=1179-1 Source URL: http://snapshot.notset.fr/mr/package/last-align/1179-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-14 automake=1:1.16.3-2 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=11 base-passwd=3.5.49 bash=5.1-2+b1 binutils=2.35.2-2 binutils-common=2.35.2-2 binutils-x86-64-linux-gnu=2.35.2-2 bsdextrautils=2.36.1-7 bsdutils=1:2.36.1-7 build-essential=12.9 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.2.1-6 dash=0.5.11+git20210120+802ebd4-1 debconf=1.5.75 debhelper=13.3.4 debianutils=4.11.2 dh-autoreconf=20 dh-strip-nondeterminism=1.11.0-1 diffutils=1:3.7-5 dpkg=1.20.7.1 dpkg-dev=1.20.7.1 dwz=0.14-1 file=1:5.39-3 findutils=4.8.0-1 g++=4:10.2.1-1 g++-10=10.2.1-6 gcc=4:10.2.1-1 gcc-10=10.2.1-6 gcc-10-base=10.2.1-6 gettext=0.21-4 gettext-base=0.21-4 grep=3.6-1 groff-base=1.22.4-6 gzip=1.10-4 help2man=1.48.2 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-10 libarchive-zip-perl=1.68-1 libasan6=10.2.1-6 libatomic1=10.2.1-6 libattr1=1:2.4.48-6 libaudit-common=1:3.0-2 libaudit1=1:3.0-2 libbinutils=2.35.2-2 libblkid1=2.36.1-7 libbrotli1=1.0.9-2+b2 libbsd0=0.11.3-1 libbz2-1.0=1.0.8-4 libc-bin=2.31-9 libc-dev-bin=2.31-9 libc6=2.31-9 libc6-dev=2.31-9 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-6 libcom-err2=1.46.2-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.2-2 libctf0=2.35.2-2 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.256 libdebhelper-perl=13.3.4 libdeflate0=1.7-1 libdpkg-perl=1.20.7.1 libelf1=0.183-3 libexpat1=2.2.10-2 libffi7=3.3-6 libfile-stripnondeterminism-perl=1.11.0-1 libfreetype6=2.10.4+dfsg-1 libgcc-10-dev=10.2.1-6 libgcc-s1=10.2.1-6 libgcrypt20=1.8.7-3 libgdbm-compat4=1.19-2 libgdbm6=1.19-2 libgmp10=2:6.2.1+dfsg-1 libgomp1=10.2.1-6 libgpg-error0=1.38-2 libgssapi-krb5-2=1.18.3-4 libicu67=67.1-6 libimagequant0=2.12.2-1.1 libisl23=0.23-1 libitm1=10.2.1-6 libjbig0=2.1-3.1+b2 libjpeg62-turbo=1:2.0.6-2 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 liblcms2-2=2.12~rc1-2 liblocale-gettext-perl=1.07-4+b1 liblsan0=10.2.1-6 liblz4-1=1.9.3-1 liblzma5=5.2.5-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmd0=1.0.3-3 libmount1=2.36.1-7 libmpc3=1.2.0-1 libmpdec3=2.5.1-1 libmpfr6=4.1.0-3 libncursesw6=6.2+20201114-2 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libpam-modules=1.4.0-6 libpam-modules-bin=1.4.0-6 libpam-runtime=1.4.0-6 libpam0g=1.4.0-6 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.1-3 libpipeline1=1.5.3-1 libpng16-16=1.6.37-3 libpython3-stdlib=3.9.2-2 libpython3.9-minimal=3.9.2-1 libpython3.9-stdlib=3.9.2-1 libquadmath0=10.2.1-6 libreadline8=8.1-1 libseccomp2=2.5.1-1 libselinux1=3.1-3 libsigsegv2=2.13-1 libsimde-dev=0.7.2-4 libsmartcols1=2.36.1-7 libsqlite3-0=3.34.1-3 libssl1.1=1.1.1j-1 libstdc++-10-dev=10.2.1-6 libstdc++6=10.2.1-6 libsub-override-perl=0.09-2 libsystemd0=247.3-2 libtiff5=4.2.0-1 libtinfo6=6.2+20201114-2 libtirpc-common=1.3.1-1 libtirpc-dev=1.3.1-1 libtirpc3=1.3.1-1 libtool=2.4.6-15 libtsan0=10.2.1-6 libubsan1=10.2.1-6 libuchardet0=0.0.7-1 libudev1=247.3-2 libunistring2=0.9.10-4 libuuid1=2.36.1-7 libwebp6=0.6.1-2+b1 libwebpdemux2=0.6.1-2+b1 libwebpmux3=0.6.1-2+b1 libxau6=1:1.0.9-1 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxml2=2.9.10+dfsg-6.3+b1 libzstd1=1.4.8+dfsg-2.1 linux-libc-dev=5.10.19-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 mailcap=3.69 make=4.3-4 man-db=2.9.4-2 mawk=1.3.4.20200120-2 media-types=4.0.0 mime-support=3.66 ncurses-base=6.2+20201114-2 ncurses-bin=6.2+20201114-2 patch=2.7.6-7 perl=5.32.1-3 perl-base=5.32.1-3 perl-modules-5.32=5.32.1-3 po-debconf=1.0.21+nmu1 python3=3.9.2-2 python3-minimal=3.9.2-2 python3-pil=8.1.2-1 python3.9=3.9.2-1 python3.9-minimal=3.9.2-1 readline-common=8.1-1 sed=4.7-1 sensible-utils=0.0.14 sysvinit-utils=2.96-6 tar=1.34+dfsg-1 tzdata=2021a-1 util-linux=2.36.1-7 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210311T143034Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d last-align=1179-1 && mkdir -p /build/last-align-dc9ynT && dpkg-source --no-check -x /*.dsc /build/last-align-dc9ynT/last-align-1179 && cd /build/last-align-dc9ynT/last-align-1179 && { printf '%s' 'last-align (1179-1+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * rebuild for outdated built-using -- all / amd64 / i386 Build Daemon (x86-conova-01) Thu, 11 Mar 2021 23:21:54 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/last-align-dc9ynT" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/last-align-dc9ynT/last-align-1179 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1615504914" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/last-align-dc9ynT /tmp/last-align-1179-1+b13cwiirun bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20210311T143034Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.LUGrjkgMM7 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.LUGrjkgMM7 Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-7). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20210311T143034Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210311T143034Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (1076 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4663 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-9) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210311T143034Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.LUGrjkgMM7 Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20210311T143034Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 24s (933 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.LUGrjkgMM7 I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d last-align=1179-1 && mkdir -p /build/last-align-dc9ynT && dpkg-source --no-check -x /*.dsc /build/last-align-dc9ynT/last-align-1179 && cd /build/last-align-dc9ynT/last-align-1179 && { printf '%s' 'last-align (1179-1+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * rebuild for outdated built-using -- all / amd64 / i386 Build Daemon (x86-conova-01) Thu, 11 Mar 2021 23:21:54 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/last-align-dc9ynT"' exec /tmp/mmdebstrap.LUGrjkgMM7 Reading package lists... NOTICE: 'last-align' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/last-align.git Please use: git clone https://salsa.debian.org/med-team/last-align.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 456 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main last-align 1179-1 (dsc) [2120 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main last-align 1179-1 (tar) [437 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main last-align 1179-1 (diff) [17.0 kB] Fetched 456 kB in 0s (1299 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'last-align_1179-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting last-align in /build/last-align-dc9ynT/last-align-1179 dpkg-source: info: unpacking last-align_1179.orig.tar.xz dpkg-source: info: unpacking last-align_1179-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 2to3.patch dpkg-source: info: applying helpMakefiles.patch dpkg-source: info: applying simde dpkg-source: info: applying fix-959866.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/last-align-dc9ynT/last-align-1179 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1615504914" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.LUGrjkgMM7 dpkg-buildpackage: info: source package last-align dpkg-buildpackage: info: source version 1179-1+b1 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by all / amd64 / i386 Build Daemon (x86-conova-01) dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/last-align-dc9ynT/last-align-1179' for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \ dh_auto_clean -- SFX=-${SIMD} ; done make -j4 clean SFX=-avx2 make[2]: Entering directory '/build/last-align-dc9ynT/last-align-1179' make[3]: Entering directory '/build/last-align-dc9ynT/last-align-1179/src' rm -f lastdb-avx2 lastal-avx2 last-split-avx2 last-merge-batches-avx2 last-pair-probs-avx2 lastdb8-avx2 lastal8-avx2 last-split8-avx2 *.o* */*.o* make[3]: Leaving directory '/build/last-align-dc9ynT/last-align-1179/src' make[2]: Leaving directory '/build/last-align-dc9ynT/last-align-1179' make -j4 clean SFX=-avx make[2]: Entering directory '/build/last-align-dc9ynT/last-align-1179' make[3]: Entering directory '/build/last-align-dc9ynT/last-align-1179/src' rm -f lastdb-avx lastal-avx last-split-avx last-merge-batches-avx last-pair-probs-avx lastdb8-avx lastal8-avx last-split8-avx *.o* */*.o* make[3]: Leaving directory '/build/last-align-dc9ynT/last-align-1179/src' make[2]: Leaving directory '/build/last-align-dc9ynT/last-align-1179' make -j4 clean SFX=-sse4.1 make[2]: Entering directory '/build/last-align-dc9ynT/last-align-1179' make[3]: Entering directory '/build/last-align-dc9ynT/last-align-1179/src' rm -f lastdb-sse4.1 lastal-sse4.1 last-split-sse4.1 last-merge-batches-sse4.1 last-pair-probs-sse4.1 lastdb8-sse4.1 lastal8-sse4.1 last-split8-sse4.1 *.o* */*.o* make[3]: Leaving directory '/build/last-align-dc9ynT/last-align-1179/src' make[2]: Leaving directory '/build/last-align-dc9ynT/last-align-1179' make -j4 clean SFX=-ssse3 make[2]: Entering directory '/build/last-align-dc9ynT/last-align-1179' make[3]: Entering directory '/build/last-align-dc9ynT/last-align-1179/src' rm -f lastdb-ssse3 lastal-ssse3 last-split-ssse3 last-merge-batches-ssse3 last-pair-probs-ssse3 lastdb8-ssse3 lastal8-ssse3 last-split8-ssse3 *.o* */*.o* make[3]: Leaving directory '/build/last-align-dc9ynT/last-align-1179/src' make[2]: Leaving directory '/build/last-align-dc9ynT/last-align-1179' make -j4 clean SFX=-sse3 make[2]: Entering directory '/build/last-align-dc9ynT/last-align-1179' make[3]: Entering directory '/build/last-align-dc9ynT/last-align-1179/src' rm -f lastdb-sse3 lastal-sse3 last-split-sse3 last-merge-batches-sse3 last-pair-probs-sse3 lastdb8-sse3 lastal8-sse3 last-split8-sse3 *.o* */*.o* make[3]: Leaving directory '/build/last-align-dc9ynT/last-align-1179/src' make[2]: Leaving directory '/build/last-align-dc9ynT/last-align-1179' make -j4 clean SFX=-sse2 make[2]: Entering directory '/build/last-align-dc9ynT/last-align-1179' make[3]: Entering directory '/build/last-align-dc9ynT/last-align-1179/src' rm -f lastdb-sse2 lastal-sse2 last-split-sse2 last-merge-batches-sse2 last-pair-probs-sse2 lastdb8-sse2 lastal8-sse2 last-split8-sse2 *.o* */*.o* make[3]: Leaving directory '/build/last-align-dc9ynT/last-align-1179/src' make[2]: Leaving directory '/build/last-align-dc9ynT/last-align-1179' for i in last-merge-batches last-pair-probs last-split last-split8 lastal lastal8 lastdb lastdb8; \ do \ for j in avx avx2 sse2 sse3 sse4.1 ssse3 sse3 sse2 sse ; \ do \ rm -f src/$i-$j ; \ done ; \ done make[1]: Leaving directory '/build/last-align-dc9ynT/last-align-1179' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/build/last-align-dc9ynT/last-align-1179' mkdir -p /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr mkdir -p /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/lib/last-align for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \ export CXXFLAGS="-g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -m${SIMD}" && export CFLAGS="-g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -m${SIMD}" && \ dh_auto_build -- all SFX=-${SIMD} ; \ find . -name '*.o' -delete ; \ find . -name '*.o8' -delete ; \ done make -j4 "INSTALL=install --strip-program=true" all SFX=-avx2 make[2]: Entering directory '/build/last-align-dc9ynT/last-align-1179' make[3]: Entering directory '/build/last-align-dc9ynT/last-align-1179/src' g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alphabet.o Alphabet.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o CyclicSubsetSeed.o CyclicSubsetSeed.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LambdaCalculator.o LambdaCalculator.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o ScoreMatrix.o ScoreMatrix.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetMinimizerFinder.o SubsetMinimizerFinder.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o TantanMasker.o TantanMasker.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o dna_words_finder.o dna_words_finder.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o fileMap.o fileMap.cc dna_words_finder.cc: In member function ‘void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)’: dna_words_finder.cc:50:41: warning: array subscript has type ‘char’ [-Wchar-subscripts] 50 | baseToCode[lettersToNumbers["ACGT"[i]]] = c; | ~~~~~~~~^ dna_words_finder.cc:51:63: warning: array subscript has type ‘char’ [-Wchar-subscripts] 51 | if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c; | ~~~~~~~~^ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o cbrc_linalg.o cbrc_linalg.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_substitution_matrix_stats.o mcf_substitution_matrix_stats.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o tantan.o tantan.cc if test -e ../.hg ; \ then echo \"`hg id -n`\" | cmp -s version.hh - || echo \"`hg id -n`\" > version.hh ; \ elif test -e ../.hg_archival.txt ; \ then echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" | cmp -s version.hh - || echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" > version.hh ; \ else test -e version.hh || echo \"UNKNOWN\" > version.hh ; \ fi g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequence.o MultiSequence.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o lastdb.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastalArguments.o LastalArguments.cc LastalArguments.cc: In member function ‘void cbrc::LastalArguments::writeCommented(std::ostream&) const’: LastalArguments.cc:615:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 615 | if( isTranslated() ) | ^~ LastalArguments.cc:616:22: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 616 | stream << " F="; writeIntList(stream, frameshiftCosts); | ^~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerDna.o GappedXdropAlignerDna.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner2qual.o GappedXdropAligner2qual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_gap_costs.o mcf_gap_costs.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GeneticCode.o GeneticCode.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GreedyXdropAligner.o GreedyXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastEvaluer.o LastEvaluer.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o OneQualityScoreMatrix.o OneQualityScoreMatrix.cc g++ 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-O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/last-split-main.o split/last-split-main.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/cbrc_split_aligner.o split/cbrc_split_aligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/last-split.o split/last-split.cc cc -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -mavx2 -c -o last-merge-batches.o last-merge-batches.c g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o last-pair-probs.o last-pair-probs.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o last-pair-probs-main.o last-pair-probs-main.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequence.o8 MultiSequence.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequenceQual.o8 MultiSequenceQual.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArray.o8 SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o8 SubsetSuffixArraySort.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o8 lastdb.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alignment.o8 Alignment.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentPot.o8 AlignmentPot.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentWrite.o8 AlignmentWrite.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Centroid.o8 Centroid.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o DiagonalTable.o8 DiagonalTable.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPair.o8 SegmentPair.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPairPot.o8 SegmentPairPot.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySearch.o8 SubsetSuffixArraySearch.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastal.o8 lastal.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/cbrc_split_aligner.o8 split/cbrc_split_aligner.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/last-split.o8 split/last-split.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastdbArguments.o LastdbArguments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastal-avx2 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o AlignmentPot.o AlignmentWrite.o Centroid.o DiagonalTable.o MultiSequence.o MultiSequenceQual.o SegmentPair.o SegmentPairPot.o SubsetSuffixArray.o SubsetSuffixArraySearch.o lastal.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o last-split-avx2 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o split/cbrc_split_aligner.o split/last-split.o cc -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -mavx2 -Wl,-z,relro -Wl,-z,now -pthread -o last-merge-batches-avx2 last-merge-batches.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o last-pair-probs-avx2 last-pair-probs.o last-pair-probs-main.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastdb8-avx2 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o8 MultiSequenceQual.o8 SubsetSuffixArray.o8 SubsetSuffixArraySort.o8 lastdb.o8 -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastdb-avx2 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o MultiSequenceQual.o SubsetSuffixArray.o SubsetSuffixArraySort.o lastdb.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o last-split8-avx2 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o8 split/cbrc_split_aligner.o8 split/last-split.o8 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastal8-avx2 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o8 AlignmentPot.o8 AlignmentWrite.o8 Centroid.o8 DiagonalTable.o8 MultiSequence.o8 MultiSequenceQual.o8 SegmentPair.o8 SegmentPairPot.o8 SubsetSuffixArray.o8 SubsetSuffixArraySearch.o8 lastal.o8 -lz make[3]: Leaving directory '/build/last-align-dc9ynT/last-align-1179/src' make[2]: Leaving directory '/build/last-align-dc9ynT/last-align-1179' make -j4 "INSTALL=install --strip-program=true" all SFX=-avx make[2]: Entering directory '/build/last-align-dc9ynT/last-align-1179' make[3]: Entering directory '/build/last-align-dc9ynT/last-align-1179/src' g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alphabet.o Alphabet.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o CyclicSubsetSeed.o CyclicSubsetSeed.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LambdaCalculator.o LambdaCalculator.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o ScoreMatrix.o ScoreMatrix.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetMinimizerFinder.o SubsetMinimizerFinder.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o TantanMasker.o TantanMasker.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o dna_words_finder.o dna_words_finder.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o fileMap.o fileMap.cc dna_words_finder.cc: In member function ‘void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)’: dna_words_finder.cc:50:41: warning: array subscript has type ‘char’ [-Wchar-subscripts] 50 | baseToCode[lettersToNumbers["ACGT"[i]]] = c; | ~~~~~~~~^ dna_words_finder.cc:51:63: warning: array subscript has type ‘char’ [-Wchar-subscripts] 51 | if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c; | ~~~~~~~~^ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o cbrc_linalg.o cbrc_linalg.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_substitution_matrix_stats.o mcf_substitution_matrix_stats.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o tantan.o tantan.cc if test -e ../.hg ; \ then echo \"`hg id -n`\" | cmp -s version.hh - || echo \"`hg id -n`\" > version.hh ; \ elif test -e ../.hg_archival.txt ; \ then echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" | cmp -s version.hh - || echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" > version.hh ; \ else test -e version.hh || echo \"UNKNOWN\" > version.hh ; \ fi g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequence.o MultiSequence.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o lastdb.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastalArguments.o LastalArguments.cc LastalArguments.cc: In member function ‘void cbrc::LastalArguments::writeCommented(std::ostream&) const’: LastalArguments.cc:615:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 615 | if( isTranslated() ) | ^~ LastalArguments.cc:616:22: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 616 | stream << " F="; writeIntList(stream, frameshiftCosts); | ^~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerDna.o GappedXdropAlignerDna.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner2qual.o GappedXdropAligner2qual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 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GreedyXdropAligner.o GreedyXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastEvaluer.o LastEvaluer.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o OneQualityScoreMatrix.o OneQualityScoreMatrix.cc g++ 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-mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/last-split-main.o split/last-split-main.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/cbrc_split_aligner.o split/cbrc_split_aligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/last-split.o split/last-split.cc cc -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -mavx -c -o last-merge-batches.o last-merge-batches.c g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o last-pair-probs.o last-pair-probs.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o last-pair-probs-main.o last-pair-probs-main.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequence.o8 MultiSequence.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequenceQual.o8 MultiSequenceQual.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArray.o8 SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o8 SubsetSuffixArraySort.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o8 lastdb.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alignment.o8 Alignment.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentPot.o8 AlignmentPot.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentWrite.o8 AlignmentWrite.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Centroid.o8 Centroid.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o DiagonalTable.o8 DiagonalTable.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPair.o8 SegmentPair.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPairPot.o8 SegmentPairPot.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySearch.o8 SubsetSuffixArraySearch.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastal.o8 lastal.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/cbrc_split_aligner.o8 split/cbrc_split_aligner.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/last-split.o8 split/last-split.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastdbArguments.o LastdbArguments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastal-avx Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o AlignmentPot.o AlignmentWrite.o Centroid.o DiagonalTable.o MultiSequence.o MultiSequenceQual.o SegmentPair.o SegmentPairPot.o SubsetSuffixArray.o SubsetSuffixArraySearch.o lastal.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o last-split-avx Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o split/cbrc_split_aligner.o split/last-split.o cc -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -mavx -Wl,-z,relro -Wl,-z,now -pthread -o last-merge-batches-avx last-merge-batches.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o last-pair-probs-avx last-pair-probs.o last-pair-probs-main.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastdb8-avx Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o8 MultiSequenceQual.o8 SubsetSuffixArray.o8 SubsetSuffixArraySort.o8 lastdb.o8 -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastdb-avx Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o MultiSequenceQual.o SubsetSuffixArray.o SubsetSuffixArraySort.o lastdb.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o last-split8-avx Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o8 split/cbrc_split_aligner.o8 split/last-split.o8 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastal8-avx Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o8 AlignmentPot.o8 AlignmentWrite.o8 Centroid.o8 DiagonalTable.o8 MultiSequence.o8 MultiSequenceQual.o8 SegmentPair.o8 SegmentPairPot.o8 SubsetSuffixArray.o8 SubsetSuffixArraySearch.o8 lastal.o8 -lz make[3]: Leaving directory '/build/last-align-dc9ynT/last-align-1179/src' make[2]: Leaving directory '/build/last-align-dc9ynT/last-align-1179' make -j4 "INSTALL=install --strip-program=true" all SFX=-sse4.1 make[2]: Entering directory '/build/last-align-dc9ynT/last-align-1179' make[3]: Entering directory '/build/last-align-dc9ynT/last-align-1179/src' g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alphabet.o Alphabet.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o CyclicSubsetSeed.o CyclicSubsetSeed.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LambdaCalculator.o LambdaCalculator.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o ScoreMatrix.o ScoreMatrix.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetMinimizerFinder.o SubsetMinimizerFinder.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o TantanMasker.o TantanMasker.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o dna_words_finder.o dna_words_finder.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o fileMap.o fileMap.cc dna_words_finder.cc: In member function ‘void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)’: dna_words_finder.cc:50:41: warning: array subscript has type ‘char’ [-Wchar-subscripts] 50 | baseToCode[lettersToNumbers["ACGT"[i]]] = c; | ~~~~~~~~^ dna_words_finder.cc:51:63: warning: array subscript has type ‘char’ [-Wchar-subscripts] 51 | if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c; | ~~~~~~~~^ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o cbrc_linalg.o cbrc_linalg.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_substitution_matrix_stats.o mcf_substitution_matrix_stats.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o tantan.o tantan.cc if test -e ../.hg ; \ then echo \"`hg id -n`\" | cmp -s version.hh - || echo \"`hg id -n`\" > version.hh ; \ elif test -e ../.hg_archival.txt ; \ then echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" | cmp -s version.hh - || echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" > version.hh ; \ else test -e version.hh || echo \"UNKNOWN\" > version.hh ; \ fi g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequence.o MultiSequence.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o lastdb.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastalArguments.o LastalArguments.cc LastalArguments.cc: In member function ‘void cbrc::LastalArguments::writeCommented(std::ostream&) const’: LastalArguments.cc:615:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 615 | if( isTranslated() ) | ^~ LastalArguments.cc:616:22: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 616 | stream << " F="; writeIntList(stream, frameshiftCosts); | ^~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerDna.o GappedXdropAlignerDna.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAligner.cc:49: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_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) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAlignerDna.cc:4: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_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) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner2qual.o GappedXdropAligner2qual.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAlignerPssm.cc:3: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_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) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAligner2qual.cc:3: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_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) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_gap_costs.o mcf_gap_costs.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAlignerFrame.cc:4: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_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) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GeneticCode.o GeneticCode.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GreedyXdropAligner.o GreedyXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastEvaluer.o LastEvaluer.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 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-pthread -DHAS_CXX_THREADS -I. -c -o split/cbrc_unsplit_alignment.o split/cbrc_unsplit_alignment.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/last-split-main.o split/last-split-main.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/cbrc_split_aligner.o split/cbrc_split_aligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/last-split.o split/last-split.cc cc -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -msse4.1 -c -o last-merge-batches.o last-merge-batches.c g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o last-pair-probs.o last-pair-probs.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o last-pair-probs-main.o last-pair-probs-main.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequence.o8 MultiSequence.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequenceQual.o8 MultiSequenceQual.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArray.o8 SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o8 SubsetSuffixArraySort.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o8 lastdb.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alignment.o8 Alignment.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentPot.o8 AlignmentPot.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentWrite.o8 AlignmentWrite.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Centroid.o8 Centroid.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o DiagonalTable.o8 DiagonalTable.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPair.o8 SegmentPair.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPairPot.o8 SegmentPairPot.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySearch.o8 SubsetSuffixArraySearch.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastal.o8 lastal.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/cbrc_split_aligner.o8 split/cbrc_split_aligner.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/last-split.o8 split/last-split.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastdbArguments.o LastdbArguments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastal-sse4.1 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o AlignmentPot.o AlignmentWrite.o Centroid.o DiagonalTable.o MultiSequence.o MultiSequenceQual.o SegmentPair.o SegmentPairPot.o SubsetSuffixArray.o SubsetSuffixArraySearch.o lastal.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o last-split-sse4.1 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o split/cbrc_split_aligner.o split/last-split.o cc -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -msse4.1 -Wl,-z,relro -Wl,-z,now -pthread -o last-merge-batches-sse4.1 last-merge-batches.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o last-pair-probs-sse4.1 last-pair-probs.o last-pair-probs-main.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastdb8-sse4.1 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o8 MultiSequenceQual.o8 SubsetSuffixArray.o8 SubsetSuffixArraySort.o8 lastdb.o8 -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastdb-sse4.1 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o MultiSequenceQual.o SubsetSuffixArray.o SubsetSuffixArraySort.o lastdb.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o last-split8-sse4.1 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o8 split/cbrc_split_aligner.o8 split/last-split.o8 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastal8-sse4.1 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o8 AlignmentPot.o8 AlignmentWrite.o8 Centroid.o8 DiagonalTable.o8 MultiSequence.o8 MultiSequenceQual.o8 SegmentPair.o8 SegmentPairPot.o8 SubsetSuffixArray.o8 SubsetSuffixArraySearch.o8 lastal.o8 -lz make[3]: Leaving directory '/build/last-align-dc9ynT/last-align-1179/src' make[2]: Leaving directory '/build/last-align-dc9ynT/last-align-1179' make -j4 "INSTALL=install --strip-program=true" all SFX=-ssse3 make[2]: Entering directory '/build/last-align-dc9ynT/last-align-1179' make[3]: Entering directory '/build/last-align-dc9ynT/last-align-1179/src' g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alphabet.o Alphabet.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o CyclicSubsetSeed.o CyclicSubsetSeed.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LambdaCalculator.o LambdaCalculator.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o ScoreMatrix.o ScoreMatrix.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetMinimizerFinder.o SubsetMinimizerFinder.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o TantanMasker.o TantanMasker.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o dna_words_finder.o dna_words_finder.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o fileMap.o fileMap.cc dna_words_finder.cc: In member function ‘void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)’: dna_words_finder.cc:50:41: warning: array subscript has type ‘char’ [-Wchar-subscripts] 50 | baseToCode[lettersToNumbers["ACGT"[i]]] = c; | ~~~~~~~~^ dna_words_finder.cc:51:63: warning: array subscript has type ‘char’ [-Wchar-subscripts] 51 | if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c; | ~~~~~~~~^ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o cbrc_linalg.o cbrc_linalg.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_substitution_matrix_stats.o mcf_substitution_matrix_stats.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o tantan.o tantan.cc if test -e ../.hg ; \ then echo \"`hg id -n`\" | cmp -s version.hh - || echo \"`hg id -n`\" > version.hh ; \ elif test -e ../.hg_archival.txt ; \ then echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" | cmp -s version.hh - || echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" > version.hh ; \ else test -e version.hh || echo \"UNKNOWN\" > version.hh ; \ fi g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequence.o MultiSequence.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o lastdb.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastalArguments.o LastalArguments.cc LastalArguments.cc: In member function ‘void cbrc::LastalArguments::writeCommented(std::ostream&) const’: LastalArguments.cc:615:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 615 | if( isTranslated() ) | ^~ LastalArguments.cc:616:22: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 616 | stream << " F="; writeIntList(stream, frameshiftCosts); | ^~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerDna.o GappedXdropAlignerDna.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAligner.cc:49: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_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) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAlignerDna.cc:4: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_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) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner2qual.o GappedXdropAligner2qual.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAlignerPssm.cc:3: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_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) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAligner2qual.cc:3: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_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) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_gap_costs.o mcf_gap_costs.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAlignerFrame.cc:4: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_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) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GeneticCode.o GeneticCode.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS 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-DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySearch.o SubsetSuffixArraySearch.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastal.o lastal.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/cbrc_unsplit_alignment.o split/cbrc_unsplit_alignment.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/last-split-main.o split/last-split-main.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/cbrc_split_aligner.o split/cbrc_split_aligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/last-split.o split/last-split.cc cc -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -mssse3 -c -o last-merge-batches.o last-merge-batches.c g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o last-pair-probs.o last-pair-probs.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o last-pair-probs-main.o last-pair-probs-main.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequence.o8 MultiSequence.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequenceQual.o8 MultiSequenceQual.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArray.o8 SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o8 SubsetSuffixArraySort.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o8 lastdb.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alignment.o8 Alignment.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentPot.o8 AlignmentPot.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentWrite.o8 AlignmentWrite.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Centroid.o8 Centroid.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o DiagonalTable.o8 DiagonalTable.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPair.o8 SegmentPair.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPairPot.o8 SegmentPairPot.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySearch.o8 SubsetSuffixArraySearch.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastal.o8 lastal.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/cbrc_split_aligner.o8 split/cbrc_split_aligner.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/last-split.o8 split/last-split.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastdbArguments.o LastdbArguments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastal-ssse3 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o AlignmentPot.o AlignmentWrite.o Centroid.o DiagonalTable.o MultiSequence.o MultiSequenceQual.o SegmentPair.o SegmentPairPot.o SubsetSuffixArray.o SubsetSuffixArraySearch.o lastal.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o last-split-ssse3 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o split/cbrc_split_aligner.o split/last-split.o cc -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -mssse3 -Wl,-z,relro -Wl,-z,now -pthread -o last-merge-batches-ssse3 last-merge-batches.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o last-pair-probs-ssse3 last-pair-probs.o last-pair-probs-main.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastdb8-ssse3 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o8 MultiSequenceQual.o8 SubsetSuffixArray.o8 SubsetSuffixArraySort.o8 lastdb.o8 -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastdb-ssse3 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o MultiSequenceQual.o SubsetSuffixArray.o SubsetSuffixArraySort.o lastdb.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o last-split8-ssse3 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o8 split/cbrc_split_aligner.o8 split/last-split.o8 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastal8-ssse3 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o8 AlignmentPot.o8 AlignmentWrite.o8 Centroid.o8 DiagonalTable.o8 MultiSequence.o8 MultiSequenceQual.o8 SegmentPair.o8 SegmentPairPot.o8 SubsetSuffixArray.o8 SubsetSuffixArraySearch.o8 lastal.o8 -lz make[3]: Leaving directory '/build/last-align-dc9ynT/last-align-1179/src' make[2]: Leaving directory '/build/last-align-dc9ynT/last-align-1179' make -j4 "INSTALL=install --strip-program=true" all SFX=-sse3 make[2]: Entering directory '/build/last-align-dc9ynT/last-align-1179' make[3]: Entering directory '/build/last-align-dc9ynT/last-align-1179/src' g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alphabet.o Alphabet.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o CyclicSubsetSeed.o CyclicSubsetSeed.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LambdaCalculator.o LambdaCalculator.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o ScoreMatrix.o ScoreMatrix.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetMinimizerFinder.o SubsetMinimizerFinder.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o TantanMasker.o TantanMasker.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o dna_words_finder.o dna_words_finder.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o fileMap.o fileMap.cc dna_words_finder.cc: In member function ‘void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)’: dna_words_finder.cc:50:41: warning: array subscript has type ‘char’ [-Wchar-subscripts] 50 | baseToCode[lettersToNumbers["ACGT"[i]]] = c; | ~~~~~~~~^ dna_words_finder.cc:51:63: warning: array subscript has type ‘char’ [-Wchar-subscripts] 51 | if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c; | ~~~~~~~~^ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o cbrc_linalg.o cbrc_linalg.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_substitution_matrix_stats.o mcf_substitution_matrix_stats.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o tantan.o tantan.cc if test -e ../.hg ; \ then echo \"`hg id -n`\" | cmp -s version.hh - || echo \"`hg id -n`\" > version.hh ; \ elif test -e ../.hg_archival.txt ; \ then echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" | cmp -s version.hh - || echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" > version.hh ; \ else test -e version.hh || echo \"UNKNOWN\" > version.hh ; \ fi g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequence.o MultiSequence.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o lastdb.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastalArguments.o LastalArguments.cc LastalArguments.cc: In member function ‘void cbrc::LastalArguments::writeCommented(std::ostream&) const’: LastalArguments.cc:615:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 615 | if( isTranslated() ) | ^~ LastalArguments.cc:616:22: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 616 | stream << " F="; writeIntList(stream, frameshiftCosts); | ^~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerDna.o GappedXdropAlignerDna.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAligner.cc:49: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_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) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAlignerDna.cc:4: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_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) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAlignerPssm.cc:3: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_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) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner2qual.o GappedXdropAligner2qual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAligner2qual.cc:3: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_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) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_gap_costs.o mcf_gap_costs.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAlignerFrame.cc:4: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_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) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GeneticCode.o GeneticCode.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GreedyXdropAligner.o GreedyXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastEvaluer.o LastEvaluer.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o OneQualityScoreMatrix.o OneQualityScoreMatrix.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o QualityPssmMaker.o QualityPssmMaker.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o TwoQualityScoreMatrix.o TwoQualityScoreMatrix.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o gaplessXdrop.o gaplessXdrop.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o gaplessPssmXdrop.o gaplessPssmXdrop.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o gaplessTwoQualityXdrop.o gaplessTwoQualityXdrop.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_alp.o alp/sls_alp.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_basic.o alp/sls_basic.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_localmaxstatutil.o alp/njn_localmaxstatutil.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_dynprogprob.o alp/njn_dynprogprob.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_dynprogprobproto.o alp/njn_dynprogprobproto.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_dynprogproblim.o alp/njn_dynprogproblim.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_ioutil.o alp/njn_ioutil.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual 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-ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_fsa1_parameters.o alp/sls_fsa1_parameters.cpp g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alignment.o Alignment.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentPot.o AlignmentPot.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentWrite.o AlignmentWrite.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Centroid.o Centroid.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o DiagonalTable.o DiagonalTable.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPair.o SegmentPair.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPairPot.o SegmentPairPot.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySearch.o SubsetSuffixArraySearch.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastal.o lastal.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/cbrc_unsplit_alignment.o split/cbrc_unsplit_alignment.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/last-split-main.o split/last-split-main.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/cbrc_split_aligner.o split/cbrc_split_aligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/last-split.o split/last-split.cc cc -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -msse3 -c -o last-merge-batches.o last-merge-batches.c g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o last-pair-probs.o last-pair-probs.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o last-pair-probs-main.o last-pair-probs-main.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequence.o8 MultiSequence.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequenceQual.o8 MultiSequenceQual.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArray.o8 SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o8 SubsetSuffixArraySort.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o8 lastdb.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alignment.o8 Alignment.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentPot.o8 AlignmentPot.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentWrite.o8 AlignmentWrite.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Centroid.o8 Centroid.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o DiagonalTable.o8 DiagonalTable.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPair.o8 SegmentPair.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPairPot.o8 SegmentPairPot.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySearch.o8 SubsetSuffixArraySearch.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastal.o8 lastal.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/cbrc_split_aligner.o8 split/cbrc_split_aligner.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/last-split.o8 split/last-split.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastdbArguments.o LastdbArguments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastal-sse3 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o AlignmentPot.o AlignmentWrite.o Centroid.o DiagonalTable.o MultiSequence.o MultiSequenceQual.o SegmentPair.o SegmentPairPot.o SubsetSuffixArray.o SubsetSuffixArraySearch.o lastal.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o last-split-sse3 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o split/cbrc_split_aligner.o split/last-split.o cc -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -msse3 -Wl,-z,relro -Wl,-z,now -pthread -o last-merge-batches-sse3 last-merge-batches.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o last-pair-probs-sse3 last-pair-probs.o last-pair-probs-main.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastdb8-sse3 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o8 MultiSequenceQual.o8 SubsetSuffixArray.o8 SubsetSuffixArraySort.o8 lastdb.o8 -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastdb-sse3 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o MultiSequenceQual.o SubsetSuffixArray.o SubsetSuffixArraySort.o lastdb.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o last-split8-sse3 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o8 split/cbrc_split_aligner.o8 split/last-split.o8 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastal8-sse3 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o8 AlignmentPot.o8 AlignmentWrite.o8 Centroid.o8 DiagonalTable.o8 MultiSequence.o8 MultiSequenceQual.o8 SegmentPair.o8 SegmentPairPot.o8 SubsetSuffixArray.o8 SubsetSuffixArraySearch.o8 lastal.o8 -lz make[3]: Leaving directory '/build/last-align-dc9ynT/last-align-1179/src' make[2]: Leaving directory '/build/last-align-dc9ynT/last-align-1179' make -j4 "INSTALL=install --strip-program=true" all SFX=-sse2 make[2]: Entering directory '/build/last-align-dc9ynT/last-align-1179' make[3]: Entering directory '/build/last-align-dc9ynT/last-align-1179/src' g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alphabet.o Alphabet.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o CyclicSubsetSeed.o CyclicSubsetSeed.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LambdaCalculator.o LambdaCalculator.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o ScoreMatrix.o ScoreMatrix.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetMinimizerFinder.o SubsetMinimizerFinder.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o TantanMasker.o TantanMasker.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o dna_words_finder.o dna_words_finder.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o fileMap.o fileMap.cc dna_words_finder.cc: In member function ‘void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)’: dna_words_finder.cc:50:41: warning: array subscript has type ‘char’ [-Wchar-subscripts] 50 | baseToCode[lettersToNumbers["ACGT"[i]]] = c; | ~~~~~~~~^ dna_words_finder.cc:51:63: warning: array subscript has type ‘char’ [-Wchar-subscripts] 51 | if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c; | ~~~~~~~~^ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o cbrc_linalg.o cbrc_linalg.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_substitution_matrix_stats.o mcf_substitution_matrix_stats.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o tantan.o tantan.cc if test -e ../.hg ; \ then echo \"`hg id -n`\" | cmp -s version.hh - || echo \"`hg id -n`\" > version.hh ; \ elif test -e ../.hg_archival.txt ; \ then echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" | cmp -s version.hh - || echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" > version.hh ; \ else test -e version.hh || echo \"UNKNOWN\" > version.hh ; \ fi g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequence.o MultiSequence.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o lastdb.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastalArguments.o LastalArguments.cc LastalArguments.cc: In member function ‘void cbrc::LastalArguments::writeCommented(std::ostream&) const’: LastalArguments.cc:615:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 615 | if( isTranslated() ) | ^~ LastalArguments.cc:616:22: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 616 | stream << " F="; writeIntList(stream, frameshiftCosts); | ^~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerDna.o GappedXdropAlignerDna.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAligner.cc:49: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_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) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAlignerDna.cc:4: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_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) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner2qual.o GappedXdropAligner2qual.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAlignerPssm.cc:3: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_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) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAligner2qual.cc:3: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_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) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_gap_costs.o mcf_gap_costs.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GeneticCode.o GeneticCode.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAlignerFrame.cc:4: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_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) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GreedyXdropAligner.o GreedyXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastEvaluer.o LastEvaluer.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o OneQualityScoreMatrix.o OneQualityScoreMatrix.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o QualityPssmMaker.o QualityPssmMaker.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o TwoQualityScoreMatrix.o TwoQualityScoreMatrix.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o gaplessXdrop.o gaplessXdrop.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o gaplessPssmXdrop.o gaplessPssmXdrop.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o gaplessTwoQualityXdrop.o gaplessTwoQualityXdrop.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_alp.o alp/sls_alp.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_basic.o alp/sls_basic.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_localmaxstatutil.o alp/njn_localmaxstatutil.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_dynprogprob.o alp/njn_dynprogprob.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_dynprogprobproto.o alp/njn_dynprogprobproto.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_dynprogproblim.o alp/njn_dynprogproblim.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_ioutil.o alp/njn_ioutil.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_random.o alp/njn_random.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_falp_alignment_evaluer.o alp/sls_falp_alignment_evaluer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_fsa1_pvalues.o alp/sls_fsa1_pvalues.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_fsa1_utils.o alp/sls_fsa1_utils.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_fsa1_parameters.o alp/sls_fsa1_parameters.cpp g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alignment.o Alignment.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentPot.o AlignmentPot.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentWrite.o AlignmentWrite.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Centroid.o Centroid.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o DiagonalTable.o DiagonalTable.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPair.o SegmentPair.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPairPot.o SegmentPairPot.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySearch.o SubsetSuffixArraySearch.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastal.o lastal.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/cbrc_unsplit_alignment.o split/cbrc_unsplit_alignment.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/last-split-main.o split/last-split-main.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/cbrc_split_aligner.o split/cbrc_split_aligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/last-split.o split/last-split.cc cc -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -c -o last-merge-batches.o last-merge-batches.c g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o last-pair-probs.o last-pair-probs.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o last-pair-probs-main.o last-pair-probs-main.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequence.o8 MultiSequence.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequenceQual.o8 MultiSequenceQual.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArray.o8 SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o8 SubsetSuffixArraySort.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o8 lastdb.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alignment.o8 Alignment.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentPot.o8 AlignmentPot.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentWrite.o8 AlignmentWrite.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Centroid.o8 Centroid.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o DiagonalTable.o8 DiagonalTable.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPair.o8 SegmentPair.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPairPot.o8 SegmentPairPot.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySearch.o8 SubsetSuffixArraySearch.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastal.o8 lastal.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/cbrc_split_aligner.o8 split/cbrc_split_aligner.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/last-split.o8 split/last-split.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastdbArguments.o LastdbArguments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastal-sse2 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o AlignmentPot.o AlignmentWrite.o Centroid.o DiagonalTable.o MultiSequence.o MultiSequenceQual.o SegmentPair.o SegmentPairPot.o SubsetSuffixArray.o SubsetSuffixArraySearch.o lastal.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o last-split-sse2 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o split/cbrc_split_aligner.o split/last-split.o cc -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wl,-z,relro -Wl,-z,now -pthread -o last-merge-batches-sse2 last-merge-batches.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o last-pair-probs-sse2 last-pair-probs.o last-pair-probs-main.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastdb8-sse2 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o8 MultiSequenceQual.o8 SubsetSuffixArray.o8 SubsetSuffixArraySort.o8 lastdb.o8 -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastdb-sse2 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o MultiSequenceQual.o SubsetSuffixArray.o SubsetSuffixArraySort.o lastdb.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o last-split8-sse2 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o8 split/cbrc_split_aligner.o8 split/last-split.o8 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-dc9ynT/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastal8-sse2 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o8 AlignmentPot.o8 AlignmentWrite.o8 Centroid.o8 DiagonalTable.o8 MultiSequence.o8 MultiSequenceQual.o8 SegmentPair.o8 SegmentPairPot.o8 SubsetSuffixArray.o8 SubsetSuffixArraySearch.o8 lastal.o8 -lz make[3]: Leaving directory '/build/last-align-dc9ynT/last-align-1179/src' make[2]: Leaving directory '/build/last-align-dc9ynT/last-align-1179' make[1]: Leaving directory '/build/last-align-dc9ynT/last-align-1179' dh_auto_test -a create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/last-align-dc9ynT/last-align-1179' dh_install debian/bin/simd-dispatch /usr/lib/last-align/ dh_install src/lastdb-* src/lastal-* src/last-split-* src/last-merge-batches-* src/last-pair-probs-* src/lastdb8-* src/lastal8-* src/last-split8-* usr/lib/last-align dh_install scripts/* usr/bin mkdir -p /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/bin cd /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/bin \ && for prog in lastdb lastal last-split last-merge-batches last-pair-probs lastdb8 lastal8 last-split8 ; do \ ln -s ../lib/last-align/simd-dispatch ${prog} ; done make[1]: Leaving directory '/build/last-align-dc9ynT/last-align-1179' dh_installdocs -a debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/last-align-dc9ynT/last-align-1179' dh_installchangelogs ChangeLog.txt make[1]: Leaving directory '/build/last-align-dc9ynT/last-align-1179' dh_installexamples -a debian/rules override_dh_installman make[1]: Entering directory '/build/last-align-dc9ynT/last-align-1179' dh_installman help2man --no-info --version-string="1179" \ --name='make a dotplot, a.k.a. Oxford Grid, of alignments in LAST tabular format' \ /build/last-align-dc9ynT/last-align-1179/scripts/last-dotplot > /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/share/man/man1/last-dotplot.1 help2man --no-info --version-string="1179" \ --name="genome-scale comparison of biological sequences" \ --help-option="-h" \ /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/bin/lastal > /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/share/man/man1/lastal.1 help2man --no-info --version-string="1179" \ --name="genome-scale comparison of biological sequences" \ --help-option="-h" \ /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/bin/lastal8 > /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/share/man/man1/lastal8.1 # help2man output needs manual postprocessing - see debian/mans #help2man --no-info --version-string="1179" \ # --name="genome-scale comparison of biological sequences" \ # --help-option="-h" \ # /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/bin/lastdb > /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/share/man/man1/lastdb.1 help2man --no-info --version-string="1179" \ --name="Sort MAF-format alignments by sequence name" \ /build/last-align-dc9ynT/last-align-1179/scripts/maf-sort > /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/share/man/man1/maf-sort.1 help2man --no-info --version-string="1179" \ --name="changes the order of the sequences in MAF-format alignments" \ /build/last-align-dc9ynT/last-align-1179/scripts/maf-swap > /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/share/man/man1/maf-swap.1 # help2man output needs manual postprocessing - see debian/mans #help2man --no-info --version-string="1179" \ # --name="Add extra column with mapping probabilities" \ # /build/last-align-dc9ynT/last-align-1179/scripts/last-map-probs > /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/share/man/man1/last-map-probs.1 # This script has not enough to put in a manual page. #help2man --no-info --version-string="1179" \ # --name="Read files of lastal output, merge corresponding batches, and write them." \ # /build/last-align-dc9ynT/last-align-1179/scripts/last-merge-batches > /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/share/man/man1/last-merge-batches.1 # # These scripts were droped #help2man --no-info --version-string="1179" \ # --name="Clean up MAF-format alignments" \ # /build/last-align-dc9ynT/last-align-1179/scripts/last-reduce-alignments > /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/share/man/man1/last-reduce-alignments.1 #help2man --no-info --version-string="1179" \ # --name='Remove MAF-format alignments which are "dominated" by others' \ # /build/last-align-dc9ynT/last-align-1179/scripts/last-remove-dominated > /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/share/man/man1/last-remove-dominated.1 help2man --no-info --version-string="1179" \ --name='Estimates "split" or "spliced" alignments.' \ /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/bin/last-split > /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/share/man/man1/last-split.1 help2man --no-info --version-string="1179" \ --name='Estimates "split" or "spliced" alignments.' \ /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/bin/last-split8 > /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/share/man/man1/last-split8.1 help2man --no-info --version-string="1179" \ --name="Join two or more sets of MAF-format multiple alignments" \ /build/last-align-dc9ynT/last-align-1179/scripts/maf-join > /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/share/man/man1/maf-join.1 help2man --no-info --version-string="1179" \ --name="Convert MAF-format alignments to tabular format" \ /build/last-align-dc9ynT/last-align-1179/scripts/maf-convert > /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/share/man/man1/maf-convert.1 help2man --no-info --version-string="1179" \ --name="Read 2 fastq files, and write them interleaved" \ /build/last-align-dc9ynT/last-align-1179/scripts/fastq-interleave > /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/share/man/man1/fastq-interleave.1 help2man --no-info --version-string="1179" \ --name="Read files of lastal output, merge corresponding batches, and write them" \ /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/bin/last-merge-batches > /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/share/man/man1/last-merge-batches.1 # help2man output needs manual postprocessing - see debian/mans #help2man --no-info --version-string="1179" \ # --name="Read alignments of paired DNA reads to a genome, and do estimations" \ # /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/bin/last-pair-probs > /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/share/man/man1/last-pair-probs.1 help2man --no-info --version-string="1179" \ --name="Get alignments that have a segment with score >= threshold, with gentle masking of lowercase letters" \ /build/last-align-dc9ynT/last-align-1179/scripts/last-postmask > /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/share/man/man1/last-postmask.1 help2man --no-info --version-string="1179" \ --name="Try to find suitable score parameters for aligning the given sequences" \ /build/last-align-dc9ynT/last-align-1179/scripts/last-train > /build/last-align-dc9ynT/last-align-1179/debian/last-align/usr/share/man/man1/last-train.1 make[1]: Leaving directory '/build/last-align-dc9ynT/last-align-1179' dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a -a dh_strip -a -a dh_makeshlibs -a -a dh_shlibdeps -a -a dh_installdeb -a debian/rules override_dh_gencontrol make[1]: Entering directory '/build/last-align-dc9ynT/last-align-1179' dh_gencontrol -- -VBuilt-Using="simde (= 0.7.2-4), " make[1]: Leaving directory '/build/last-align-dc9ynT/last-align-1179' dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'last-align-dbgsym' in '../last-align-dbgsym_1179-1+b1_amd64.deb'. dpkg-deb: building package 'last-align' in '../last-align_1179-1+b1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../last-align_1179-1+b1_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/last-align-dc9ynT /tmp/last-align-1179-1+b13cwiirun I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.LUGrjkgMM7... I: success in 3296.6579 seconds md5: last-align-dbgsym_1179-1+b1_amd64.deb: OK md5: Value of 'md5' differs for last-align_1179-1+b1_amd64.deb md5: Size differs for last-align_1179-1+b1_amd64.deb sha1: last-align-dbgsym_1179-1+b1_amd64.deb: OK sha1: Value of 'sha1' differs for last-align_1179-1+b1_amd64.deb sha1: Size differs for last-align_1179-1+b1_amd64.deb sha256: last-align-dbgsym_1179-1+b1_amd64.deb: OK sha256: Value of 'sha256' differs for last-align_1179-1+b1_amd64.deb sha256: Size differs for last-align_1179-1+b1_amd64.deb Checksums: FAIL diffoscope run passed