https://launchpad.net/ubuntu/+source/last-align/1447-1/+build/25558855 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy02-amd64-117 5.4.0-137-generic #154-Ubuntu SMP Thu Jan 5 17:03:22 UTC 2023 x86_64 Buildd toolchain package versions: launchpad-buildd_229~619~ubuntu20.04.1 python3-lpbuildd_229~619~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.8 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 6 Feb 05:31:30 ntpdate[1806]: adjust time server 10.131.248.1 offset -0.002592 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-25558855 --image-type chroot /home/buildd/filecache-default/1fc1752c0976ad9eb0e621fd063fde252dab04e3 Creating target for build PACKAGEBUILD-25558855 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-25558855 Starting target for build PACKAGEBUILD-25558855 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-25558855 'deb http://ftpmaster.internal/ubuntu lunar main universe' 'deb http://ftpmaster.internal/ubuntu lunar-security main universe' 'deb http://ftpmaster.internal/ubuntu lunar-updates main universe' 'deb http://ftpmaster.internal/ubuntu lunar-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-25558855 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-25558855 Updating target for build PACKAGEBUILD-25558855 Get:1 http://ftpmaster.internal/ubuntu lunar InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu lunar-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu lunar-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main amd64 Packages [1385 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main Translation-en [509 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/universe amd64 Packages [14.6 MB] Get:8 http://ftpmaster.internal/ubuntu lunar/universe Translation-en [5907 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 Packages [142 kB] Get:10 http://ftpmaster.internal/ubuntu lunar-proposed/main Translation-en [56.2 kB] Get:11 http://ftpmaster.internal/ubuntu lunar-proposed/universe amd64 Packages [728 kB] Get:12 http://ftpmaster.internal/ubuntu lunar-proposed/universe Translation-en [261 kB] Fetched 24.2 MB in 2s (10.4 MB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: adduser advancecomp apt bash binutils binutils-common binutils-x86-64-linux-gnu coreutils cpp-12 debconf diffutils dpkg dpkg-dev fakeroot g++-12 gcc-12 gcc-12-base gpg gpg-agent gpgconf gpgv grep libacl1 libapt-pkg6.0 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libc-bin libc-dev-bin libc6 libc6-dev libcap2 libcc1-0 libcrypt-dev libcrypt1 libctf-nobfd0 libctf0 libdb5.3 libdpkg-perl libfakeroot libgcc-12-dev libgcc-s1 libgcrypt20 libgnutls30 libgomp1 libgprofng0 libitm1 liblsan0 liblzma5 libmpfr6 libncurses6 libncursesw6 libp11-kit0 libpcre2-8-0 libperl5.36 libquadmath0 libreadline8 libselinux1 libsemanage-common libsemanage2 libsqlite3-0 libssl3 libstdc++-12-dev libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libtsan2 libubsan1 libudev1 libzstd1 linux-libc-dev lsb-base ncurses-base ncurses-bin openssl perl perl-base perl-modules-5.36 pkgbinarymangler readline-common sed sensible-utils systemd systemd-sysv sysvinit-utils tzdata xz-utils zlib1g 92 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 102 MB of archives. After this operation, 2400 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu lunar/main amd64 bash amd64 5.2.15-2ubuntu1 [795 kB] Get:2 http://ftpmaster.internal/ubuntu lunar/main amd64 coreutils amd64 9.1-1ubuntu2 [1407 kB] Get:3 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 diffutils amd64 1:3.8-4 [176 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libc-bin amd64 2.37-0ubuntu1 [670 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main amd64 libcrypt-dev amd64 1:4.4.33-2 [113 kB] Get:6 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libc6-dev amd64 2.37-0ubuntu1 [2091 kB] Get:7 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libc-dev-bin amd64 2.37-0ubuntu1 [20.0 kB] Get:8 http://ftpmaster.internal/ubuntu lunar/main amd64 libcrypt1 amd64 1:4.4.33-2 [80.7 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 linux-libc-dev amd64 6.1.0-14.14 [1495 kB] Get:10 http://ftpmaster.internal/ubuntu lunar/main amd64 libcc1-0 amd64 12.2.0-14ubuntu1 [46.5 kB] Get:11 http://ftpmaster.internal/ubuntu lunar/main amd64 libgprofng0 amd64 2.40-2ubuntu1 [897 kB] Get:12 http://ftpmaster.internal/ubuntu lunar/main amd64 libctf0 amd64 2.40-2ubuntu1 [97.4 kB] Get:13 http://ftpmaster.internal/ubuntu lunar/main amd64 libctf-nobfd0 amd64 2.40-2ubuntu1 [100 kB] Get:14 http://ftpmaster.internal/ubuntu lunar/main amd64 binutils-x86-64-linux-gnu amd64 2.40-2ubuntu1 [2484 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/main amd64 libbinutils amd64 2.40-2ubuntu1 [633 kB] Get:16 http://ftpmaster.internal/ubuntu lunar/main amd64 binutils-common amd64 2.40-2ubuntu1 [236 kB] Get:17 http://ftpmaster.internal/ubuntu lunar/main amd64 binutils amd64 2.40-2ubuntu1 [3196 B] Get:18 http://ftpmaster.internal/ubuntu lunar/main amd64 gcc-12-base amd64 12.2.0-14ubuntu1 [19.2 kB] Get:19 http://ftpmaster.internal/ubuntu lunar/main amd64 libgcc-s1 amd64 12.2.0-14ubuntu1 [53.9 kB] Get:20 http://ftpmaster.internal/ubuntu lunar/main amd64 libgomp1 amd64 12.2.0-14ubuntu1 [125 kB] Get:21 http://ftpmaster.internal/ubuntu lunar/main amd64 libitm1 amd64 12.2.0-14ubuntu1 [29.5 kB] Get:22 http://ftpmaster.internal/ubuntu lunar/main amd64 libatomic1 amd64 12.2.0-14ubuntu1 [10.4 kB] Get:23 http://ftpmaster.internal/ubuntu lunar/main amd64 libasan8 amd64 12.2.0-14ubuntu1 [2429 kB] Get:24 http://ftpmaster.internal/ubuntu lunar/main amd64 liblsan0 amd64 12.2.0-14ubuntu1 [1061 kB] Get:25 http://ftpmaster.internal/ubuntu lunar/main amd64 libtsan2 amd64 12.2.0-14ubuntu1 [2456 kB] Get:26 http://ftpmaster.internal/ubuntu lunar/main amd64 libubsan1 amd64 12.2.0-14ubuntu1 [969 kB] Get:27 http://ftpmaster.internal/ubuntu lunar/main amd64 libquadmath0 amd64 12.2.0-14ubuntu1 [152 kB] Get:28 http://ftpmaster.internal/ubuntu lunar/main amd64 g++-12 amd64 12.2.0-14ubuntu1 [12.0 MB] Get:29 http://ftpmaster.internal/ubuntu lunar/main amd64 libstdc++-12-dev amd64 12.2.0-14ubuntu1 [2157 kB] Get:30 http://ftpmaster.internal/ubuntu lunar/main amd64 libgcc-12-dev amd64 12.2.0-14ubuntu1 [2577 kB] Get:31 http://ftpmaster.internal/ubuntu lunar/main amd64 gcc-12 amd64 12.2.0-14ubuntu1 [21.4 MB] Get:32 http://ftpmaster.internal/ubuntu lunar/main amd64 cpp-12 amd64 12.2.0-14ubuntu1 [10.6 MB] Get:33 http://ftpmaster.internal/ubuntu lunar/main amd64 libstdc++6 amd64 12.2.0-14ubuntu1 [678 kB] Get:34 http://ftpmaster.internal/ubuntu lunar/main amd64 zlib1g amd64 1:1.2.13.dfsg-1ubuntu4 [61.2 kB] Get:35 http://ftpmaster.internal/ubuntu lunar/main amd64 libmpfr6 amd64 4.2.0-1 [352 kB] Get:36 http://ftpmaster.internal/ubuntu lunar/main amd64 libzstd1 amd64 1.5.2+dfsg2-3 [282 kB] Get:37 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libc6 amd64 2.37-0ubuntu1 [3164 kB] Get:38 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 liblzma5 amd64 5.4.1-0.1 [125 kB] Get:39 http://ftpmaster.internal/ubuntu lunar/main amd64 libgcrypt20 amd64 1.10.1-3ubuntu1 [529 kB] Get:40 http://ftpmaster.internal/ubuntu lunar/main amd64 libacl1 amd64 2.3.1-3 [16.4 kB] Get:41 http://ftpmaster.internal/ubuntu lunar/main amd64 libaudit-common all 1:3.0.7-1.1 [5108 B] Get:42 http://ftpmaster.internal/ubuntu lunar/main amd64 libaudit1 amd64 1:3.0.7-1.1 [45.3 kB] Get:43 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libcap2 amd64 1:2.66-3ubuntu1 [28.0 kB] Get:44 http://ftpmaster.internal/ubuntu lunar/main amd64 libpcre2-8-0 amd64 10.42-1 [228 kB] Get:45 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libselinux1 amd64 3.4-1build3 [77.9 kB] Get:46 http://ftpmaster.internal/ubuntu lunar/main amd64 libperl5.36 amd64 5.36.0-7 [4834 kB] Get:47 http://ftpmaster.internal/ubuntu lunar/main amd64 perl amd64 5.36.0-7 [235 kB] Get:48 http://ftpmaster.internal/ubuntu lunar/main amd64 perl-base amd64 5.36.0-7 [1779 kB] Get:49 http://ftpmaster.internal/ubuntu lunar/main amd64 perl-modules-5.36 all 5.36.0-7 [2984 kB] Get:50 http://ftpmaster.internal/ubuntu lunar/main amd64 libdb5.3 amd64 5.3.28+dfsg2-1 [742 kB] Get:51 http://ftpmaster.internal/ubuntu lunar/main amd64 debconf all 1.5.82 [125 kB] Get:52 http://ftpmaster.internal/ubuntu lunar/main amd64 libssl3 amd64 3.0.7-1ubuntu1 [1896 kB] Get:53 http://ftpmaster.internal/ubuntu lunar/main amd64 systemd-sysv amd64 252.4-1ubuntu1 [11.4 kB] Get:54 http://ftpmaster.internal/ubuntu lunar/main amd64 systemd amd64 252.4-1ubuntu1 [3001 kB] Get:55 http://ftpmaster.internal/ubuntu lunar/main amd64 libsystemd-shared amd64 252.4-1ubuntu1 [1771 kB] Get:56 http://ftpmaster.internal/ubuntu lunar/main amd64 libp11-kit0 amd64 0.24.1-2ubuntu1 [248 kB] Get:57 http://ftpmaster.internal/ubuntu lunar/main amd64 libsystemd0 amd64 252.4-1ubuntu1 [328 kB] Get:58 http://ftpmaster.internal/ubuntu lunar/main amd64 libudev1 amd64 252.4-1ubuntu1 [89.6 kB] Get:59 http://ftpmaster.internal/ubuntu lunar/main amd64 libapt-pkg6.0 amd64 2.5.5 [903 kB] Get:60 http://ftpmaster.internal/ubuntu lunar/main amd64 dpkg amd64 1.21.19ubuntu3 [1336 kB] Get:61 http://ftpmaster.internal/ubuntu lunar/main amd64 grep amd64 3.8-5 [160 kB] Get:62 http://ftpmaster.internal/ubuntu lunar/main amd64 ncurses-bin amd64 6.4-2 [185 kB] Get:63 http://ftpmaster.internal/ubuntu lunar/main amd64 sed amd64 4.9-1 [193 kB] Get:64 http://ftpmaster.internal/ubuntu lunar/main amd64 ncurses-base all 6.4-2 [21.3 kB] Get:65 http://ftpmaster.internal/ubuntu lunar/main amd64 sysvinit-utils amd64 3.05-7ubuntu2 [27.4 kB] Get:66 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 lsb-base all 11.6 [4606 B] Get:67 http://ftpmaster.internal/ubuntu lunar/main amd64 adduser all 3.129ubuntu1 [59.0 kB] Get:68 http://ftpmaster.internal/ubuntu lunar/main amd64 gpgv amd64 2.2.40-1ubuntu2 [137 kB] Get:69 http://ftpmaster.internal/ubuntu lunar/main amd64 libgnutls30 amd64 3.7.8-4ubuntu1 [986 kB] Get:70 http://ftpmaster.internal/ubuntu lunar/main amd64 apt amd64 2.5.5 [1378 kB] Get:71 http://ftpmaster.internal/ubuntu lunar/main amd64 libattr1 amd64 1:2.5.1-4 [12.4 kB] Get:72 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libsemanage-common all 3.4-1build3 [9808 B] Get:73 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libsemanage2 amd64 3.4-1build3 [92.7 kB] Get:74 http://ftpmaster.internal/ubuntu lunar/main amd64 libncurses6 amd64 6.4-2 [112 kB] Get:75 http://ftpmaster.internal/ubuntu lunar/main amd64 libncursesw6 amd64 6.4-2 [147 kB] Get:76 http://ftpmaster.internal/ubuntu lunar/main amd64 libtinfo6 amd64 6.4-2 [101 kB] Get:77 http://ftpmaster.internal/ubuntu lunar/main amd64 sensible-utils all 0.0.17+nmu1 [19.3 kB] Get:78 http://ftpmaster.internal/ubuntu lunar/main amd64 readline-common all 8.2-1.3 [55.7 kB] Get:79 http://ftpmaster.internal/ubuntu lunar/main amd64 libreadline8 amd64 8.2-1.3 [151 kB] Get:80 http://ftpmaster.internal/ubuntu lunar/main amd64 libsqlite3-0 amd64 3.40.1-1 [654 kB] Get:81 http://ftpmaster.internal/ubuntu lunar/main amd64 openssl amd64 3.0.7-1ubuntu1 [1179 kB] Get:82 http://ftpmaster.internal/ubuntu lunar/main amd64 tzdata all 2022g-2ubuntu1 [397 kB] Get:83 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 xz-utils amd64 5.4.1-0.1 [268 kB] Get:84 http://ftpmaster.internal/ubuntu lunar/main amd64 advancecomp amd64 2.5-1 [180 kB] Get:85 http://ftpmaster.internal/ubuntu lunar/main amd64 dpkg-dev all 1.21.19ubuntu3 [1067 kB] Get:86 http://ftpmaster.internal/ubuntu lunar/main amd64 libdpkg-perl all 1.21.19ubuntu3 [247 kB] Get:87 http://ftpmaster.internal/ubuntu lunar/main amd64 libfakeroot amd64 1.30.1-1.1ubuntu1 [30.9 kB] Get:88 http://ftpmaster.internal/ubuntu lunar/main amd64 fakeroot amd64 1.30.1-1.1ubuntu1 [60.2 kB] Get:89 http://ftpmaster.internal/ubuntu lunar/main amd64 gpg amd64 2.2.40-1ubuntu2 [523 kB] Get:90 http://ftpmaster.internal/ubuntu lunar/main amd64 gpgconf amd64 2.2.40-1ubuntu2 [93.7 kB] Get:91 http://ftpmaster.internal/ubuntu lunar/main amd64 gpg-agent amd64 2.2.40-1ubuntu2 [217 kB] Get:92 http://ftpmaster.internal/ubuntu lunar/main amd64 pkgbinarymangler all 151 [16.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 102 MB in 5s (22.3 MB/s) (Reading database ... 13093 files and directories currently installed.) 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Setting up systemd-sysv (252.4-1ubuntu1) ... Setting up gpg-agent (2.2.40-1ubuntu2) ... Setting up libstdc++-12-dev:amd64 (12.2.0-14ubuntu1) ... Setting up binutils (2.40-2ubuntu1) ... Setting up dpkg-dev (1.21.19ubuntu3) ... Setting up gcc-12 (12.2.0-14ubuntu1) ... Setting up g++-12 (12.2.0-14ubuntu1) ... Processing triggers for debianutils (5.7-0.4) ... Processing triggers for libc-bin (2.37-0ubuntu1) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-25558855 amd64 lunar-proposed -c chroot:build-PACKAGEBUILD-25558855 --arch=amd64 --dist=lunar-proposed --nolog -A last-align_1447-1.dsc Initiating build PACKAGEBUILD-25558855 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-137-generic #154-Ubuntu SMP Thu Jan 5 17:03:22 UTC 2023 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lcy02-amd64-117.buildd +==============================================================================+ | last-align 1447-1 (amd64) Mon, 06 Feb 2023 05:31:57 +0000 | +==============================================================================+ Package: last-align Version: 1447-1 Source Version: 1447-1 Distribution: lunar-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-25558855/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/last-align-0Itpmu/resolver-QiWs3g' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- last-align_1447-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/last-align-0Itpmu/last-align-1447' with '<>' I: NOTICE: Log filtering will replace 'build/last-align-0Itpmu' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), help2man, python3-pil, zlib1g-dev, libsimde-dev, debhelper, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), help2man, python3-pil, zlib1g-dev, libsimde-dev, debhelper, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [400 B] Get:5 copy:/<>/apt_archive ./ Packages [485 B] Fetched 1842 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbrotli1 libbsd0 libdebhelper-perl libdeflate0 libdw1 libelf1 libexpat1 libfile-stripnondeterminism-perl libfreetype6 libfribidi0 libglib2.0-0 libgraphite2-3 libharfbuzz0b libicu72 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblcms2-2 liblerc4 liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec3 libopenjp2-7 libpipeline1 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libraqm0 libsimde-dev libsub-override-perl libtiff6 libtool libuchardet0 libwebp7 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 libxml2 m4 mailcap man-db media-types mime-support po-debconf python3 python3-minimal python3-pil python3.11 python3.11-minimal zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff low-memory-monitor liblcms2-utils libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python-pil-doc python3.11-venv python3.11-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl python3-olefile The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbrotli1 libbsd0 libdebhelper-perl libdeflate0 libdw1 libelf1 libexpat1 libfile-stripnondeterminism-perl libfreetype6 libfribidi0 libglib2.0-0 libgraphite2-3 libharfbuzz0b libicu72 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblcms2-2 liblerc4 liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec3 libopenjp2-7 libpipeline1 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libraqm0 libsimde-dev libsub-override-perl libtiff6 libtool libuchardet0 libwebp7 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 libxml2 m4 mailcap man-db media-types mime-support po-debconf python3 python3-minimal python3-pil python3.11 python3.11-minimal sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 72 newly installed, 0 to remove and 0 not upgraded. Need to get 30.5 MB of archives. After this operation, 112 MB of additional disk space will be used. 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lunar/main amd64 libpython3.11-stdlib amd64 3.11.1-2 [1816 kB] Get:12 http://ftpmaster.internal/ubuntu lunar/main amd64 python3.11 amd64 3.11.1-2 [561 kB] Get:13 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libpython3-stdlib amd64 3.11.1-3 [7208 B] Get:14 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 python3 amd64 3.11.1-3 [22.9 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/main amd64 libbsd0 amd64 0.11.7-2 [44.1 kB] Get:16 http://ftpmaster.internal/ubuntu lunar/main amd64 libelf1 amd64 0.188-2.1 [53.4 kB] Get:17 http://ftpmaster.internal/ubuntu lunar/main amd64 libfribidi0 amd64 1.0.8-2.1ubuntu1 [25.9 kB] Get:18 http://ftpmaster.internal/ubuntu lunar/main amd64 libglib2.0-0 amd64 2.74.5-1 [1458 kB] Get:19 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libicu72 amd64 72.1-3ubuntu1 [10.8 MB] Get:20 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libxml2 amd64 2.9.14+dfsg-1.1build1 [762 kB] Get:21 http://ftpmaster.internal/ubuntu lunar/main amd64 bsdextrautils amd64 2.38.1-4ubuntu1 [71.0 kB] Get:22 http://ftpmaster.internal/ubuntu lunar/main amd64 libmagic-mgc amd64 1:5.44-3 [293 kB] Get:23 http://ftpmaster.internal/ubuntu lunar/main amd64 libmagic1 amd64 1:5.44-3 [85.6 kB] Get:24 http://ftpmaster.internal/ubuntu lunar/main amd64 file amd64 1:5.44-3 [21.8 kB] Get:25 http://ftpmaster.internal/ubuntu lunar/main amd64 gettext-base amd64 0.21-11 [36.5 kB] Get:26 http://ftpmaster.internal/ubuntu lunar/main amd64 libuchardet0 amd64 0.0.7-1build2 [76.9 kB] Get:27 http://ftpmaster.internal/ubuntu lunar/main amd64 groff-base amd64 1.22.4-9 [937 kB] Get:28 http://ftpmaster.internal/ubuntu lunar/main amd64 libpipeline1 amd64 1.5.7-1 [23.3 kB] Get:29 http://ftpmaster.internal/ubuntu lunar/main amd64 libxau6 amd64 1:1.0.9-1build5 [7634 B] Get:30 http://ftpmaster.internal/ubuntu lunar/main amd64 libxdmcp6 amd64 1:1.1.3-0ubuntu5 [10.9 kB] Get:31 http://ftpmaster.internal/ubuntu lunar/main amd64 libxcb1 amd64 1.15-1 [48.0 kB] 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all 0.09-4 [8706 B] Get:43 http://ftpmaster.internal/ubuntu lunar/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:44 http://ftpmaster.internal/ubuntu lunar/main amd64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:45 http://ftpmaster.internal/ubuntu lunar/main amd64 libdw1 amd64 0.188-2.1 [251 kB] Get:46 http://ftpmaster.internal/ubuntu lunar/main amd64 debugedit amd64 1:5.0-5 [46.1 kB] Get:47 http://ftpmaster.internal/ubuntu lunar/main amd64 dwz amd64 0.15-1 [112 kB] Get:48 http://ftpmaster.internal/ubuntu lunar/main amd64 gettext amd64 0.21-11 [867 kB] Get:49 http://ftpmaster.internal/ubuntu lunar/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:50 http://ftpmaster.internal/ubuntu lunar/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] Get:51 http://ftpmaster.internal/ubuntu lunar/main amd64 debhelper all 13.11.4ubuntu3 [925 kB] Get:52 http://ftpmaster.internal/ubuntu lunar/universe amd64 help2man amd64 1.49.3 [201 kB] Get:53 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Get:63 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libraqm0 amd64 0.7.0-4.1 [11.3 kB] Get:64 http://ftpmaster.internal/ubuntu lunar-proposed/universe amd64 libsimde-dev all 0.7.4~rc1-1 [379 kB] Get:65 http://ftpmaster.internal/ubuntu lunar/main amd64 libjbig0 amd64 2.1-6ubuntu1 [29.1 kB] Get:66 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libwebp7 amd64 1.2.4-0.1build1 [212 kB] Get:67 http://ftpmaster.internal/ubuntu lunar/main amd64 libtiff6 amd64 4.5.0-4ubuntu1 [195 kB] Get:68 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libwebpdemux2 amd64 1.2.4-0.1build1 [9886 B] Get:69 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libwebpmux3 amd64 1.2.4-0.1build1 [20.8 kB] Get:70 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libopenjp2-7 amd64 2.5.0-1build1 [174 kB] Get:71 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 python3-pil amd64 9.4.0-1.1build1 [431 kB] Get:72 http://ftpmaster.internal/ubuntu lunar/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1ubuntu4 [895 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 30.5 MB in 3s (10.5 MB/s) Selecting previously unselected package liblocale-gettext-perl. 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Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:amd64 (2.74.5-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.11.4ubuntu3) ... Setting up libbrotli1:amd64 (1.0.9-2build7) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up libdeflate0:amd64 (1.14-1) ... Setting up gettext-base (0.21-11) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libjbig0:amd64 (2.1-6ubuntu1) ... Setting up autotools-dev (20220109.1) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-4) ... Setting up libfribidi0:amd64 (1.0.8-2.1ubuntu1) ... Setting up libimagequant0:amd64 (2.17.0-1) ... Setting up autopoint (0.21-11) ... Setting up libjpeg-turbo8:amd64 (2.1.2-0ubuntu1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:amd64 (1.2.4-0.1build1) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1ubuntu4) ... Setting up libuchardet0:amd64 (0.0.7-1build2) ... Setting up libmpdec3:amd64 (2.5.1-2build2) ... Setting up libopenjp2-7:amd64 (2.5.0-1build1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3build1) ... Setting up libwebpmux3:amd64 (1.2.4-0.1build1) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up mailcap (3.70+nmu1ubuntu1) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.1build1) ... Setting up liblocale-gettext-perl (1.07-5) ... Setting up libjpeg8:amd64 (8c-2ubuntu10) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libdw1:amd64 (0.188-2.1) ... Setting up libxdmcp6:amd64 (1:1.1.3-0ubuntu5) ... Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-11) ... Setting up mime-support (3.66) ... Setting up libtool (2.4.7-5) ... Setting up libwebpdemux2:amd64 (1.2.4-0.1build1) ... Setting up libpython3.11-stdlib:amd64 (3.11.1-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up libraqm0:amd64 (0.7.0-4.1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-9) ... Setting up libtiff6:amd64 (4.5.0-4ubuntu1) ... Setting up debugedit (1:5.0-5) ... Setting up libpython3-stdlib:amd64 (3.11.1-3) ... Setting up python3.11 (3.11.1-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.11.1-3) ... Setting up man-db (2.11.2-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up python3-pil:amd64 (9.4.0-1.1build1) ... Setting up debhelper (13.11.4ubuntu3) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for systemd (252.4-1ubuntu1) ... Processing triggers for libc-bin (2.37-0ubuntu1) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-137-generic #154-Ubuntu SMP Thu Jan 5 17:03:22 UTC 2023 amd64 (x86_64) Toolchain package versions: binutils_2.40-2ubuntu1 dpkg-dev_1.21.19ubuntu3 g++-12_12.2.0-14ubuntu1 gcc-12_12.2.0-14ubuntu1 libc6-dev_2.37-0ubuntu1 libstdc++-12-dev_12.2.0-14ubuntu1 libstdc++6_12.2.0-14ubuntu1 linux-libc-dev_6.1.0-14.14 Package versions: adduser_3.129ubuntu1 advancecomp_2.5-1 apt_2.5.5 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-11 autotools-dev_20220109.1 base-files_12.3ubuntu1 base-passwd_3.6.1 bash_5.2.15-2ubuntu1 binutils_2.40-2ubuntu1 binutils-common_2.40-2ubuntu1 binutils-x86-64-linux-gnu_2.40-2ubuntu1 bsdextrautils_2.38.1-4ubuntu1 bsdutils_1:2.38.1-4ubuntu1 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20211016ubuntu1 coreutils_9.1-1ubuntu2 cpp_4:12.2.0-1ubuntu1 cpp-12_12.2.0-14ubuntu1 dash_0.5.11+git20210903+057cd650a4ed-9ubuntu1 debconf_1.5.82 debhelper_13.11.4ubuntu3 debianutils_5.7-0.4 debugedit_1:5.0-5 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-4 dpkg_1.21.19ubuntu3 dpkg-dev_1.21.19ubuntu3 dwz_0.15-1 e2fsprogs_1.46.6~rc1-1ubuntu1 fakeroot_1.30.1-1.1ubuntu1 file_1:5.44-3 findutils_4.9.0-3ubuntu1 g++_4:12.2.0-1ubuntu1 g++-12_12.2.0-14ubuntu1 gcc_4:12.2.0-1ubuntu1 gcc-12_12.2.0-14ubuntu1 gcc-12-base_12.2.0-14ubuntu1 gettext_0.21-11 gettext-base_0.21-11 gpg_2.2.40-1ubuntu2 gpg-agent_2.2.40-1ubuntu2 gpgconf_2.2.40-1ubuntu2 gpgv_2.2.40-1ubuntu2 grep_3.8-5 groff-base_1.22.4-9 gzip_1.12-1ubuntu1 help2man_1.49.3 hostname_3.23ubuntu2 init_1.65.2 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zlib1g-dev_1:1.2.13.dfsg-1ubuntu4 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: last-align Binary: last-align Architecture: any Version: 1447-1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Nilesh Patra Homepage: https://gitlab.com/mcfrith/last Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/last-align Vcs-Git: https://salsa.debian.org/med-team/last-align.git Testsuite: autopkgtest Testsuite-Triggers: python3-pil Build-Depends: debhelper-compat (= 13), help2man, python3-pil, zlib1g-dev, libsimde-dev, debhelper Package-List: last-align deb science optional arch=any Checksums-Sha1: 20d16d5e26809cb71a2c325e2f457729ccd8b4f9 1342124 last-align_1447.orig.tar.xz 3140d0ea0f273617de5b9316d36cce83bd4f0e13 17528 last-align_1447-1.debian.tar.xz Checksums-Sha256: b2b8c968aec480043be16ca7ff2b6635a42267d55bc034903fb3114542247aa1 1342124 last-align_1447.orig.tar.xz 8fb96684b58021b432ed5ed281a8cc0ecebbc02c66f7f9f0595118b63b380c6f 17528 last-align_1447-1.debian.tar.xz Files: 176dc12169e8f070a374726a6a563abc 1342124 last-align_1447.orig.tar.xz 8db21418c0d27e763cc37225f3ae542a 17528 last-align_1447-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmPgEbIRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtF9tQ/+N+ywmj/RIN5kunzVbiFRtcvL90uNaHYB XdGFCeC9KsthL2wqJKSegvH2WxZyZgEWJoA/8gZvo7wdHcxLoY4+rASMJgKbZ8+U fmojAKCd+35tF/qhNfAm3GTj4gYKZCmjfvVBs23ZEhsECydVmPR82WTjIDK7Bcc7 CmITF6qW5+F/lblKfdSRpUi2ubaxFxGMs9wa3Kw0yd2h36S/slKhKZnfvoyGzvZo qsWUEAkjGq2BUiUp5/RViT5K1FV1IbLQciR+LmfstEy7fOihYpkITRjzHlF025F1 IXUMsLsbMBhhmu5SnXssGn4Gu7SnDJ0nPyXy1zY9WEPbqlSSiyLkJaEQY11YZkis iho6NEJb5JdKJWoTgxSFRVFF7bcG7xoKulMb9N/m0J8HVQd9OOrx+rolwKRAdgC9 hvuwiJxdqwpCtqTxokL9LIiTp1h1xcTckbAKYG4wGH4UvC560gEKgTC8ZQFbYVjn c8lx+nOJgQi9/0ZYe2ojKzE1W86BH6c5uGsLMneY6+ZCaMj5X84t1FXljI/EZZHs TfRNdCcLeCGZsfuK0A6lm8f8EdjUibaoqrhXL01612uisKluIJ16NK66SjZYV1/9 1hEng2IeUu6gT0AXcnwjV2dgJhHTEQ/wgj8u04wHWinhrLwetP4SybItyWEmXpjd 5NFyNldgNdU= =KOt2 -----END PGP SIGNATURE----- gpgv: Signature made Sun Feb 5 20:29:38 2023 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./last-align_1447-1.dsc: no acceptable signature found dpkg-source: info: extracting last-align in /<> dpkg-source: info: unpacking last-align_1447.orig.tar.xz dpkg-source: info: unpacking last-align_1447-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying helpMakefiles.patch dpkg-source: info: applying simde dpkg-source: info: applying fix-shebang.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-25558855 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-25558855 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-25558855 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -b -rfakeroot dpkg-buildpackage: info: source package last-align dpkg-buildpackage: info: source version 1447-1 dpkg-buildpackage: info: source distribution unstable 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 '/<>' 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 '/<>' make[3]: Entering directory '/<>/src' rm -f ../bin/lastdb-avx2 ../bin/lastal-avx2 ../bin/last-split-avx2 ../bin/lastdb5-avx2 ../bin/lastal5-avx2 ../bin/last-split5-avx2 ../bin/last-merge-batches-avx2 ../bin/last-pair-probs-avx2 ../bin/lastdb8-avx2 ../bin/lastal8-avx2 ../bin/last-split8-avx2 *.o* */*.o* make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' make -j4 clean SFX=-avx make[2]: Entering directory '/<>' make[3]: Entering directory '/<>/src' rm -f ../bin/lastdb-avx ../bin/lastal-avx ../bin/last-split-avx ../bin/lastdb5-avx ../bin/lastal5-avx ../bin/last-split5-avx ../bin/last-merge-batches-avx ../bin/last-pair-probs-avx ../bin/lastdb8-avx ../bin/lastal8-avx ../bin/last-split8-avx *.o* */*.o* make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' make -j4 clean SFX=-sse4.1 make[2]: Entering directory '/<>' make[3]: Entering directory '/<>/src' rm -f ../bin/lastdb-sse4.1 ../bin/lastal-sse4.1 ../bin/last-split-sse4.1 ../bin/lastdb5-sse4.1 ../bin/lastal5-sse4.1 ../bin/last-split5-sse4.1 ../bin/last-merge-batches-sse4.1 ../bin/last-pair-probs-sse4.1 ../bin/lastdb8-sse4.1 ../bin/lastal8-sse4.1 ../bin/last-split8-sse4.1 *.o* */*.o* make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' make -j4 clean SFX=-ssse3 make[2]: Entering directory '/<>' make[3]: Entering directory '/<>/src' rm -f ../bin/lastdb-ssse3 ../bin/lastal-ssse3 ../bin/last-split-ssse3 ../bin/lastdb5-ssse3 ../bin/lastal5-ssse3 ../bin/last-split5-ssse3 ../bin/last-merge-batches-ssse3 ../bin/last-pair-probs-ssse3 ../bin/lastdb8-ssse3 ../bin/lastal8-ssse3 ../bin/last-split8-ssse3 *.o* */*.o* make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' make -j4 clean SFX=-sse3 make[2]: Entering directory '/<>' make[3]: Entering directory '/<>/src' rm -f ../bin/lastdb-sse3 ../bin/lastal-sse3 ../bin/last-split-sse3 ../bin/lastdb5-sse3 ../bin/lastal5-sse3 ../bin/last-split5-sse3 ../bin/last-merge-batches-sse3 ../bin/last-pair-probs-sse3 ../bin/lastdb8-sse3 ../bin/lastal8-sse3 ../bin/last-split8-sse3 *.o* */*.o* make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' make -j4 clean SFX=-sse2 make[2]: Entering directory '/<>' make[3]: Entering directory '/<>/src' rm -f ../bin/lastdb-sse2 ../bin/lastal-sse2 ../bin/last-split-sse2 ../bin/lastdb5-sse2 ../bin/lastal5-sse2 ../bin/last-split5-sse2 ../bin/last-merge-batches-sse2 ../bin/last-pair-probs-sse2 ../bin/lastdb8-sse2 ../bin/lastal8-sse2 ../bin/last-split8-sse2 *.o* */*.o* make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' for i in last-merge-batches last-pair-probs last-split last-split5 lastal lastal5 lastdb lastdb5; \ do \ for j in avx avx2 sse2 sse3 sse4.1 ssse3 sse3 sse2 sse ; \ do \ rm -f bin/$i-$j ; \ done ; \ done make[1]: Leaving directory '/<>' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/<>' mkdir -p /<>/debian/last-align/usr mkdir -p /<>/debian/last-align/usr/lib/last-align for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \ dh_auto_build -- all SFX=-${SIMD} CFLAGS="-g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -m${SIMD}" CXXFLAGS="-g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -m${SIMD}" ; \ find . -name '*.o' -delete ; \ find . -name '*.o5' -delete ; \ done make -j4 "INSTALL=install --strip-program=true" all SFX=-avx2 "CFLAGS=-g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -mavx2" "CXXFLAGS=-g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2" make[2]: Entering directory '/<>' make[3]: Entering directory '/<>/src' g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o Alphabet.o Alphabet.cc ../build/seed-inc.sh ../data/*.seed > CyclicSubsetSeedData.hh g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o LambdaCalculator.o LambdaCalculator.cc ../build/mat-inc.sh ../data/*.mat > ScoreMatrixData.hh g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o SubsetMinimizerFinder.o SubsetMinimizerFinder.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o TantanMasker.o TantanMasker.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o dna_words_finder.o dna_words_finder.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o fileMap.o fileMap.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o cbrc_linalg.o cbrc_linalg.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o mcf_substitution_matrix_stats.o mcf_substitution_matrix_stats.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_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o tantan.o tantan.cc echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1447) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" | cmp -s version.hh - || echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1447) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" > version.hh g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o MultiSequence.o MultiSequence.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o lastdb.o lastdb.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o LastalArguments.o LastalArguments.cc lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int)’: lastdb.cc:343:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual] 343 | std::cout.write((char *)m.qualityReader() + m.seqBeg(i), m.seqLen(i)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o GappedXdropAlignerDna.o GappedXdropAlignerDna.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o GappedXdropAligner2qual.o GappedXdropAligner2qual.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o mcf_aligment_path_adder.o mcf_aligment_path_adder.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o mcf_gap_costs.o mcf_gap_costs.cc ../build/gc-inc.sh ../data/gc.prt > GeneticCodeData.hh g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o GreedyXdropAligner.o GreedyXdropAligner.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o LastEvaluer.o LastEvaluer.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o OneQualityScoreMatrix.o OneQualityScoreMatrix.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o QualityPssmMaker.o QualityPssmMaker.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o TwoQualityScoreMatrix.o TwoQualityScoreMatrix.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o split/cbrc_unsplit_alignment.o split/cbrc_unsplit_alignment.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o split/last_split_options.o split/last_split_options.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_alp.o alp/sls_alp.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_basic.o alp/sls_basic.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/njn_localmaxstatutil.o alp/njn_localmaxstatutil.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/njn_dynprogprob.o alp/njn_dynprogprob.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/njn_dynprogprobproto.o alp/njn_dynprogprobproto.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/njn_dynprogproblim.o alp/njn_dynprogproblim.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/njn_ioutil.o alp/njn_ioutil.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/njn_random.o alp/njn_random.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_falp_alignment_evaluer.o alp/sls_falp_alignment_evaluer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_fsa1_pvalues.o alp/sls_fsa1_pvalues.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_fsa1_utils.o alp/sls_fsa1_utils.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_fsa1_parameters.o alp/sls_fsa1_parameters.cpp g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o Alignment.o Alignment.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o AlignmentPot.o AlignmentPot.cc Alignment.cc: In member function ‘cbrc::Alignment::extend(std::vector >&, std::vector >&, cbrc::Aligners&, bool, bool, mcf::BigSeq, unsigned char const*, unsigned long, unsigned long, bool, int, int const (*) [66], int, int, double const* const*, double, int, mcf::GapCosts const&, unsigned long, int const (*) [66], cbrc::TwoQualityScoreMatrix const&, unsigned char const*, unsigned char const*, cbrc::Alphabet const&, cbrc::AlignmentExtras&, double, int)’: Alignment.cc:423:33: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized] 423 | centroid.addExpectedCounts(start2, isForward, probMat, gap, alph.size, | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 424 | subsCounts, tranCounts); | ~~~~~~~~~~~~~~~~~~~~~~~ Alignment.cc:282:11: note: ‘tranCounts’ was declared here 282 | double *tranCounts; | ^~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o AlignmentWrite.o AlignmentWrite.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o Centroid.o Centroid.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o DiagonalTable.o DiagonalTable.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o SegmentPair.o SegmentPair.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o SegmentPairPot.o SegmentPairPot.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o SubsetSuffixArraySearch.o SubsetSuffixArraySearch.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o lastal.o lastal.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o split/cbrc_split_aligner.o split/cbrc_split_aligner.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o split/mcf_last_splitter.o split/mcf_last_splitter.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o split/last-split-main.o split/last-split-main.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o split/last-split.o split/last-split.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o MultiSequence.o5 MultiSequence.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o MultiSequenceQual.o5 MultiSequenceQual.cc lastal.cc: In function ‘alignGapless1(LastAligner&, cbrc::SegmentPairPot&, cbrc::MultiSequence const&, SeqData const&, Dispatcher const&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, cbrc::SubsetSuffixArray const&, unsigned char const*, unsigned int)’: lastal.cc:640:78: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:22: note: ‘fwdLen’ was declared here 637 | size_t revLen, fwdLen; | ^~~~~~ lastal.cc:640:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:14: note: ‘revLen’ was declared here 637 | size_t revLen, fwdLen; | ^~~~~~ g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o SubsetSuffixArray.o5 SubsetSuffixArray.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o SubsetSuffixArraySort.o5 SubsetSuffixArraySort.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o lastdb.o5 lastdb.cc lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int)’: lastdb.cc:343:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual] 343 | std::cout.write((char *)m.qualityReader() + m.seqBeg(i), m.seqLen(i)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o Alignment.o5 Alignment.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o AlignmentPot.o5 AlignmentPot.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o AlignmentWrite.o5 AlignmentWrite.cc Alignment.cc: In member function ‘cbrc::Alignment::extend(std::vector >&, std::vector >&, cbrc::Aligners&, bool, bool, mcf::BigSeq, unsigned char const*, unsigned long, unsigned long, bool, int, int const (*) [66], int, int, double const* const*, double, int, mcf::GapCosts const&, unsigned long, int const (*) [66], cbrc::TwoQualityScoreMatrix const&, unsigned char const*, unsigned char const*, cbrc::Alphabet const&, cbrc::AlignmentExtras&, double, int)’: Alignment.cc:423:33: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized] 423 | centroid.addExpectedCounts(start2, isForward, probMat, gap, alph.size, | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 424 | subsCounts, tranCounts); | ~~~~~~~~~~~~~~~~~~~~~~~ Alignment.cc:282:11: note: ‘tranCounts’ was declared here 282 | double *tranCounts; | ^~~~~~~~~~ g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o Centroid.o5 Centroid.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o DiagonalTable.o5 DiagonalTable.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o SegmentPair.o5 SegmentPair.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o SegmentPairPot.o5 SegmentPairPot.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o SubsetSuffixArraySearch.o5 SubsetSuffixArraySearch.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o lastal.o5 lastal.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o split/cbrc_split_aligner.o5 split/cbrc_split_aligner.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o split/mcf_last_splitter.o5 split/mcf_last_splitter.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o split/last-split.o5 split/last-split.cc cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -mavx2 -c -o last-merge-batches.o last-merge-batches.c g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o last-pair-probs.o last-pair-probs.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o last-pair-probs-main.o last-pair-probs-main.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o CyclicSubsetSeed.o CyclicSubsetSeed.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o ScoreMatrix.o ScoreMatrix.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o LastdbArguments.o LastdbArguments.cc In file included from Centroid.hh:9, from Alignment.hh:8, from AlignmentPot.hh:8, from lastal.cc:14: In member function ‘cbrc::SegmentPair::end2() const’, inlined from ‘alignGapless1(LastAligner&, cbrc::SegmentPairPot&, cbrc::MultiSequence const&, SeqData const&, Dispatcher const&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, cbrc::SubsetSuffixArray const&, unsigned char const*, unsigned int)’ at lastal.cc:641:21: SegmentPair.hh:36:40: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 36 | indexT end2() const{ return start2 + size; } // end in sequence 2 | ^~~~ lastal.cc: In function ‘alignGapless1(LastAligner&, cbrc::SegmentPairPot&, cbrc::MultiSequence const&, SeqData const&, Dispatcher const&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, cbrc::SubsetSuffixArray const&, unsigned char const*, unsigned int)’: lastal.cc:637:22: note: ‘fwdLen’ was declared here 637 | size_t revLen, fwdLen; | ^~~~~~ lastal.cc:640:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:14: note: ‘revLen’ was declared here 637 | size_t revLen, fwdLen; | ^~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o GeneticCode.o GeneticCode.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/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_options.o split/last-split-main.o MultiSequence.o split/cbrc_split_aligner.o split/mcf_last_splitter.o split/last-split.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split5-avx2 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/last-split-main.o MultiSequence.o5 split/cbrc_split_aligner.o5 split/mcf_last_splitter.o5 split/last-split.o5 cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -mavx2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-merge-batches-avx2 last-merge-batches.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-pair-probs-avx2 last-pair-probs.o last-pair-probs-main.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/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 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/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_aligment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.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 split/cbrc_split_aligner.o split/mcf_last_splitter.o -lz alp/sls_alp_data.hpp:101:36: warning: type ‘struct array_positive’ violates the C++ One Definition Rule [-Wodr] 101 | template class array_positive{ | ^ alp/sls_fsa1_utils.hpp:555:36: note: a different type is defined in another translation unit 555 | template class array_positive{ | ^ alp/sls_alp_data.hpp:163:27: note: the first difference of corresponding definitions is field ‘d_alp_data’ 163 | alp_data *d_alp_data;//initial data | ^ alp/sls_fsa1_utils.hpp:641:23: note: a field with different name is defined in another translation unit 641 | void *d_fsa;//initial data | ^ alp/sls_alp_data.hpp:101:36: warning: type ‘struct array_positive’ violates the C++ One Definition Rule [-Wodr] 101 | template class array_positive{ | ^ alp/sls_fsa1_utils.hpp:555:36: note: a different type is defined in another translation unit 555 | template class array_positive{ | ^ alp/sls_alp_data.hpp:163:27: note: the first difference of corresponding definitions is field ‘d_alp_data’ 163 | alp_data *d_alp_data;//initial data | ^ alp/sls_fsa1_utils.hpp:641:23: note: a field with different name is defined in another translation unit 641 | void *d_fsa;//initial data | ^ alp/sls_alp_sim.hpp:54:16: warning: type ‘struct struct_for_lambda_calculation’ violates the C++ One Definition Rule [-Wodr] 54 | struct struct_for_lambda_calculation | ^ alp/sls_fsa1_parameters.hpp:47:16: note: a different type is defined in another translation unit 47 | struct struct_for_lambda_calculation | ^ alp/sls_alp_sim.hpp:64:22: note: the first difference of corresponding definitions is field ‘d_calculate_alp_number’ 64 | bool d_calculate_alp_number; | ^ alp/sls_fsa1_parameters.hpp:57:24: note: a field with different name is defined in another translation unit 57 | double d_before_last_sum; | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastdb5-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.o5 MultiSequenceQual.o5 SubsetSuffixArray.o5 SubsetSuffixArraySort.o5 lastdb.o5 -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastal5-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_aligment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.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.o5 AlignmentPot.o5 AlignmentWrite.o5 Centroid.o5 DiagonalTable.o5 MultiSequence.o5 MultiSequenceQual.o5 SegmentPair.o5 SegmentPairPot.o5 SubsetSuffixArray.o5 SubsetSuffixArraySearch.o5 lastal.o5 split/cbrc_split_aligner.o5 split/mcf_last_splitter.o5 -lz alp/sls_alp_data.hpp:101:36: warning: type ‘struct array_positive’ violates the C++ One Definition Rule [-Wodr] 101 | template class array_positive{ | ^ alp/sls_fsa1_utils.hpp:555:36: note: a different type is defined in another translation unit 555 | template class array_positive{ | ^ alp/sls_alp_data.hpp:163:27: note: the first difference of corresponding definitions is field ‘d_alp_data’ 163 | alp_data *d_alp_data;//initial data | ^ alp/sls_fsa1_utils.hpp:641:23: note: a field with different name is defined in another translation unit 641 | void *d_fsa;//initial data | ^ alp/sls_alp_data.hpp:101:36: warning: type ‘struct array_positive’ violates the C++ One Definition Rule [-Wodr] 101 | template class array_positive{ | ^ alp/sls_fsa1_utils.hpp:555:36: note: a different type is defined in another translation unit 555 | template class array_positive{ | ^ alp/sls_alp_data.hpp:163:27: note: the first difference of corresponding definitions is field ‘d_alp_data’ 163 | alp_data *d_alp_data;//initial data | ^ alp/sls_fsa1_utils.hpp:641:23: note: a field with different name is defined in another translation unit 641 | void *d_fsa;//initial data | ^ alp/sls_alp_sim.hpp:54:16: warning: type ‘struct struct_for_lambda_calculation’ violates the C++ One Definition Rule [-Wodr] 54 | struct struct_for_lambda_calculation | ^ alp/sls_fsa1_parameters.hpp:47:16: note: a different type is defined in another translation unit 47 | struct struct_for_lambda_calculation | ^ alp/sls_alp_sim.hpp:64:22: note: the first difference of corresponding definitions is field ‘d_calculate_alp_number’ 64 | bool d_calculate_alp_number; | ^ alp/sls_fsa1_parameters.hpp:57:24: note: a field with different name is defined in another translation unit 57 | double d_before_last_sum; | ^ lastal.cc: In function ‘alignGapless1’: lastal.cc:640:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:14: note: ‘revLen’ was declared here 637 | size_t revLen, fwdLen; | ^ In member function ‘end2’, inlined from ‘alignGapless1’ at lastal.cc:641:21: SegmentPair.hh:36:40: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 36 | indexT end2() const{ return start2 + size; } // end in sequence 2 | ^ lastal.cc: In function ‘alignGapless1’: lastal.cc:637:22: note: ‘fwdLen’ was declared here 637 | size_t revLen, fwdLen; | ^ lastal.cc: In function ‘alignGapless1’: lastal.cc:640:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:14: note: ‘revLen’ was declared here 637 | size_t revLen, fwdLen; | ^ lastal.cc:640:78: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:22: note: ‘fwdLen’ was declared here 637 | size_t revLen, fwdLen; | ^ In member function ‘addExpectedCounts’, inlined from ‘extend.constprop.isra’ at Alignment.cc:423:33: Centroid.cc:607:23: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized] 607 | transitionCounts[3] += delCount - delNextCount; // delete open/close count | ^ Alignment.cc: In member function ‘extend.constprop.isra’: Alignment.cc:282:11: note: ‘tranCounts’ was declared here 282 | double *tranCounts; | ^ In member function ‘addExpectedCounts’, inlined from ‘extend.constprop.isra’ at Alignment.cc:423:33: Centroid.cc:607:23: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized] 607 | transitionCounts[3] += delCount - delNextCount; // delete open/close count | ^ Alignment.cc: In member function ‘extend.constprop.isra’: Alignment.cc:282:11: note: ‘tranCounts’ was declared here 282 | double *tranCounts; | ^ make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' make -j4 "INSTALL=install --strip-program=true" all SFX=-avx "CFLAGS=-g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -mavx" "CXXFLAGS=-g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx" make[2]: Entering directory '/<>' make[3]: Entering directory '/<>/src' g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o Alphabet.o Alphabet.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o CyclicSubsetSeed.o CyclicSubsetSeed.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o LambdaCalculator.o LambdaCalculator.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o ScoreMatrix.o ScoreMatrix.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o SubsetMinimizerFinder.o SubsetMinimizerFinder.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o TantanMasker.o TantanMasker.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o dna_words_finder.o dna_words_finder.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o cbrc_linalg.o cbrc_linalg.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o mcf_substitution_matrix_stats.o mcf_substitution_matrix_stats.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o tantan.o tantan.cc echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1447) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" | cmp -s version.hh - || echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1447) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" > version.hh g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o MultiSequence.o MultiSequence.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o lastdb.o lastdb.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o LastalArguments.o LastalArguments.cc lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int)’: lastdb.cc:343:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual] 343 | std::cout.write((char *)m.qualityReader() + m.seqBeg(i), m.seqLen(i)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o GappedXdropAlignerDna.o GappedXdropAlignerDna.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o GappedXdropAligner2qual.o GappedXdropAligner2qual.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o mcf_aligment_path_adder.o mcf_aligment_path_adder.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o mcf_gap_costs.o mcf_gap_costs.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o GeneticCode.o GeneticCode.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o GreedyXdropAligner.o GreedyXdropAligner.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o LastEvaluer.o LastEvaluer.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o OneQualityScoreMatrix.o OneQualityScoreMatrix.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o QualityPssmMaker.o QualityPssmMaker.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o TwoQualityScoreMatrix.o TwoQualityScoreMatrix.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o split/cbrc_unsplit_alignment.o split/cbrc_unsplit_alignment.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o split/last_split_options.o split/last_split_options.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_alp.o alp/sls_alp.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_basic.o alp/sls_basic.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/njn_localmaxstatutil.o alp/njn_localmaxstatutil.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/njn_dynprogprob.o alp/njn_dynprogprob.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/njn_dynprogprobproto.o alp/njn_dynprogprobproto.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/njn_dynprogproblim.o alp/njn_dynprogproblim.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/njn_ioutil.o alp/njn_ioutil.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/njn_random.o alp/njn_random.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_falp_alignment_evaluer.o alp/sls_falp_alignment_evaluer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_fsa1_pvalues.o alp/sls_fsa1_pvalues.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_fsa1_utils.o alp/sls_fsa1_utils.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_fsa1_parameters.o alp/sls_fsa1_parameters.cpp g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o Alignment.o Alignment.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o AlignmentPot.o AlignmentPot.cc Alignment.cc: In member function ‘cbrc::Alignment::extend(std::vector >&, std::vector >&, cbrc::Aligners&, bool, bool, mcf::BigSeq, unsigned char const*, unsigned long, unsigned long, bool, int, int const (*) [66], int, int, double const* const*, double, int, mcf::GapCosts const&, unsigned long, int const (*) [66], cbrc::TwoQualityScoreMatrix const&, unsigned char const*, unsigned char const*, cbrc::Alphabet const&, cbrc::AlignmentExtras&, double, int)’: Alignment.cc:423:33: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized] 423 | centroid.addExpectedCounts(start2, isForward, probMat, gap, alph.size, | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 424 | subsCounts, tranCounts); | ~~~~~~~~~~~~~~~~~~~~~~~ Alignment.cc:282:11: note: ‘tranCounts’ was declared here 282 | double *tranCounts; | ^~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o AlignmentWrite.o AlignmentWrite.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o Centroid.o Centroid.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o DiagonalTable.o DiagonalTable.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o SegmentPair.o SegmentPair.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o SegmentPairPot.o SegmentPairPot.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o SubsetSuffixArraySearch.o SubsetSuffixArraySearch.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o lastal.o lastal.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o split/cbrc_split_aligner.o split/cbrc_split_aligner.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o split/mcf_last_splitter.o split/mcf_last_splitter.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o split/last-split-main.o split/last-split-main.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o split/last-split.o split/last-split.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o MultiSequence.o5 MultiSequence.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o MultiSequenceQual.o5 MultiSequenceQual.cc lastal.cc: In function ‘alignGapless1(LastAligner&, cbrc::SegmentPairPot&, cbrc::MultiSequence const&, SeqData const&, Dispatcher const&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, cbrc::SubsetSuffixArray const&, unsigned char const*, unsigned int)’: lastal.cc:640:78: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:22: note: ‘fwdLen’ was declared here 637 | size_t revLen, fwdLen; | ^~~~~~ lastal.cc:640:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:14: note: ‘revLen’ was declared here 637 | size_t revLen, fwdLen; | ^~~~~~ g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o SubsetSuffixArray.o5 SubsetSuffixArray.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o SubsetSuffixArraySort.o5 SubsetSuffixArraySort.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o lastdb.o5 lastdb.cc lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int)’: lastdb.cc:343:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual] 343 | std::cout.write((char *)m.qualityReader() + m.seqBeg(i), m.seqLen(i)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o Alignment.o5 Alignment.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o AlignmentPot.o5 AlignmentPot.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o AlignmentWrite.o5 AlignmentWrite.cc Alignment.cc: In member function ‘cbrc::Alignment::extend(std::vector >&, std::vector >&, cbrc::Aligners&, bool, bool, mcf::BigSeq, unsigned char const*, unsigned long, unsigned long, bool, int, int const (*) [66], int, int, double const* const*, double, int, mcf::GapCosts const&, unsigned long, int const (*) [66], cbrc::TwoQualityScoreMatrix const&, unsigned char const*, unsigned char const*, cbrc::Alphabet const&, cbrc::AlignmentExtras&, double, int)’: Alignment.cc:423:33: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized] 423 | centroid.addExpectedCounts(start2, isForward, probMat, gap, alph.size, | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 424 | subsCounts, tranCounts); | ~~~~~~~~~~~~~~~~~~~~~~~ Alignment.cc:282:11: note: ‘tranCounts’ was declared here 282 | double *tranCounts; | ^~~~~~~~~~ g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o Centroid.o5 Centroid.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o DiagonalTable.o5 DiagonalTable.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o SegmentPair.o5 SegmentPair.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o SegmentPairPot.o5 SegmentPairPot.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o SubsetSuffixArraySearch.o5 SubsetSuffixArraySearch.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o lastal.o5 lastal.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o split/cbrc_split_aligner.o5 split/cbrc_split_aligner.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o split/mcf_last_splitter.o5 split/mcf_last_splitter.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o split/last-split.o5 split/last-split.cc cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -mavx -c -o last-merge-batches.o last-merge-batches.c g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o last-pair-probs.o last-pair-probs.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o last-pair-probs-main.o last-pair-probs-main.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o LastdbArguments.o LastdbArguments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/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_aligment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.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 split/cbrc_split_aligner.o split/mcf_last_splitter.o -lz alp/sls_alp_data.hpp:101:36: warning: type ‘struct array_positive’ violates the C++ One Definition Rule [-Wodr] 101 | template class array_positive{ | ^ alp/sls_fsa1_utils.hpp:555:36: note: a different type is defined in another translation unit 555 | template class array_positive{ | ^ alp/sls_alp_data.hpp:163:27: note: the first difference of corresponding definitions is field ‘d_alp_data’ 163 | alp_data *d_alp_data;//initial data | ^ alp/sls_fsa1_utils.hpp:641:23: note: a field with different name is defined in another translation unit 641 | void *d_fsa;//initial data | ^ alp/sls_alp_data.hpp:101:36: warning: type ‘struct array_positive’ violates the C++ One Definition Rule [-Wodr] 101 | template class array_positive{ | ^ alp/sls_fsa1_utils.hpp:555:36: note: a different type is defined in another translation unit 555 | template class array_positive{ | ^ alp/sls_alp_data.hpp:163:27: note: the first difference of corresponding definitions is field ‘d_alp_data’ 163 | alp_data *d_alp_data;//initial data | ^ alp/sls_fsa1_utils.hpp:641:23: note: a field with different name is defined in another translation unit 641 | void *d_fsa;//initial data | ^ alp/sls_alp_sim.hpp:54:16: warning: type ‘struct struct_for_lambda_calculation’ violates the C++ One Definition Rule [-Wodr] 54 | struct struct_for_lambda_calculation | ^ alp/sls_fsa1_parameters.hpp:47:16: note: a different type is defined in another translation unit 47 | struct struct_for_lambda_calculation | ^ alp/sls_alp_sim.hpp:64:22: note: the first difference of corresponding definitions is field ‘d_calculate_alp_number’ 64 | bool d_calculate_alp_number; | ^ alp/sls_fsa1_parameters.hpp:57:24: note: a field with different name is defined in another translation unit 57 | double d_before_last_sum; | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/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_options.o split/last-split-main.o MultiSequence.o split/cbrc_split_aligner.o split/mcf_last_splitter.o split/last-split.o In file included from Centroid.hh:9, from Alignment.hh:8, from AlignmentPot.hh:8, from lastal.cc:14: In member function ‘cbrc::SegmentPair::end2() const’, inlined from ‘alignGapless1(LastAligner&, cbrc::SegmentPairPot&, cbrc::MultiSequence const&, SeqData const&, Dispatcher const&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, cbrc::SubsetSuffixArray const&, unsigned char const*, unsigned int)’ at lastal.cc:641:21: SegmentPair.hh:36:40: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 36 | indexT end2() const{ return start2 + size; } // end in sequence 2 | ^~~~ lastal.cc: In function ‘alignGapless1(LastAligner&, cbrc::SegmentPairPot&, cbrc::MultiSequence const&, SeqData const&, Dispatcher const&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, cbrc::SubsetSuffixArray const&, unsigned char const*, unsigned int)’: lastal.cc:637:22: note: ‘fwdLen’ was declared here 637 | size_t revLen, fwdLen; | ^~~~~~ lastal.cc:640:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:14: note: ‘revLen’ was declared here 637 | size_t revLen, fwdLen; | ^~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split5-avx Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/last-split-main.o MultiSequence.o5 split/cbrc_split_aligner.o5 split/mcf_last_splitter.o5 split/last-split.o5 lastal.cc: In function ‘alignGapless1’: lastal.cc:640:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:14: note: ‘revLen’ was declared here 637 | size_t revLen, fwdLen; | ^ lastal.cc:640:78: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:22: note: ‘fwdLen’ was declared here 637 | size_t revLen, fwdLen; | ^ cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -mavx -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-merge-batches-avx last-merge-batches.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-pair-probs-avx last-pair-probs.o last-pair-probs-main.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/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 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastdb5-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.o5 MultiSequenceQual.o5 SubsetSuffixArray.o5 SubsetSuffixArraySort.o5 lastdb.o5 -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastal5-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_aligment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.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.o5 AlignmentPot.o5 AlignmentWrite.o5 Centroid.o5 DiagonalTable.o5 MultiSequence.o5 MultiSequenceQual.o5 SegmentPair.o5 SegmentPairPot.o5 SubsetSuffixArray.o5 SubsetSuffixArraySearch.o5 lastal.o5 split/cbrc_split_aligner.o5 split/mcf_last_splitter.o5 -lz alp/sls_alp_data.hpp:101:36: warning: type ‘struct array_positive’ violates the C++ One Definition Rule [-Wodr] 101 | template class array_positive{ | ^ alp/sls_fsa1_utils.hpp:555:36: note: a different type is defined in another translation unit 555 | template class array_positive{ | ^ alp/sls_alp_data.hpp:163:27: note: the first difference of corresponding definitions is field ‘d_alp_data’ 163 | alp_data *d_alp_data;//initial data | ^ alp/sls_fsa1_utils.hpp:641:23: note: a field with different name is defined in another translation unit 641 | void *d_fsa;//initial data | ^ alp/sls_alp_data.hpp:101:36: warning: type ‘struct array_positive’ violates the C++ One Definition Rule [-Wodr] 101 | template class array_positive{ | ^ alp/sls_fsa1_utils.hpp:555:36: note: a different type is defined in another translation unit 555 | template class array_positive{ | ^ alp/sls_alp_data.hpp:163:27: note: the first difference of corresponding definitions is field ‘d_alp_data’ 163 | alp_data *d_alp_data;//initial data | ^ alp/sls_fsa1_utils.hpp:641:23: note: a field with different name is defined in another translation unit 641 | void *d_fsa;//initial data | ^ alp/sls_alp_sim.hpp:54:16: warning: type ‘struct struct_for_lambda_calculation’ violates the C++ One Definition Rule [-Wodr] 54 | struct struct_for_lambda_calculation | ^ alp/sls_fsa1_parameters.hpp:47:16: note: a different type is defined in another translation unit 47 | struct struct_for_lambda_calculation | ^ alp/sls_alp_sim.hpp:64:22: note: the first difference of corresponding definitions is field ‘d_calculate_alp_number’ 64 | bool d_calculate_alp_number; | ^ alp/sls_fsa1_parameters.hpp:57:24: note: a field with different name is defined in another translation unit 57 | double d_before_last_sum; | ^ In member function ‘addExpectedCounts’, inlined from ‘extend.constprop.isra’ at Alignment.cc:423:33: Centroid.cc:607:23: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized] 607 | transitionCounts[3] += delCount - delNextCount; // delete open/close count | ^ Alignment.cc: In member function ‘extend.constprop.isra’: Alignment.cc:282:11: note: ‘tranCounts’ was declared here 282 | double *tranCounts; | ^ lastal.cc: In function ‘alignGapless1’: lastal.cc:640:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:14: note: ‘revLen’ was declared here 637 | size_t revLen, fwdLen; | ^ In member function ‘end2’, inlined from ‘alignGapless1’ at lastal.cc:641:21: SegmentPair.hh:36:40: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 36 | indexT end2() const{ return start2 + size; } // end in sequence 2 | ^ lastal.cc: In function ‘alignGapless1’: lastal.cc:637:22: note: ‘fwdLen’ was declared here 637 | size_t revLen, fwdLen; | ^ In member function ‘addExpectedCounts’, inlined from ‘extend.constprop.isra’ at Alignment.cc:423:33: Centroid.cc:607:23: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized] 607 | transitionCounts[3] += delCount - delNextCount; // delete open/close count | ^ Alignment.cc: In member function ‘extend.constprop.isra’: Alignment.cc:282:11: note: ‘tranCounts’ was declared here 282 | double *tranCounts; | ^ make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' make -j4 "INSTALL=install --strip-program=true" all SFX=-sse4.1 "CFLAGS=-g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -msse4.1" "CXXFLAGS=-g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1" make[2]: Entering directory '/<>' make[3]: Entering directory '/<>/src' g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o Alphabet.o Alphabet.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o CyclicSubsetSeed.o CyclicSubsetSeed.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o LambdaCalculator.o LambdaCalculator.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o ScoreMatrix.o ScoreMatrix.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o SubsetMinimizerFinder.o SubsetMinimizerFinder.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o TantanMasker.o TantanMasker.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o dna_words_finder.o dna_words_finder.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o cbrc_linalg.o cbrc_linalg.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o mcf_substitution_matrix_stats.o mcf_substitution_matrix_stats.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o tantan.o tantan.cc echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1447) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" | cmp -s version.hh - || echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1447) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" > version.hh g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o MultiSequence.o MultiSequence.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from tantan.cc:4: /usr/include/simde/x86/avx.h: In function ‘__vector(4) double simde__m256d_from_private(simde__m256d_private)’: /usr/include/simde/x86/avx.h:290:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 290 | simde__m256d_from_private(simde__m256d_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o lastdb.o lastdb.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o LastalArguments.o LastalArguments.cc lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int)’: lastdb.cc:343:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual] 343 | std::cout.write((char *)m.qualityReader() + m.seqBeg(i), m.seqLen(i)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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:52, 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:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | 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:52, 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:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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:52, 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:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | 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:52, 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:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o mcf_aligment_path_adder.o mcf_aligment_path_adder.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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:52, 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:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o mcf_gap_costs.o mcf_gap_costs.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o GeneticCode.o GeneticCode.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o GreedyXdropAligner.o GreedyXdropAligner.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o LastEvaluer.o LastEvaluer.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o OneQualityScoreMatrix.o OneQualityScoreMatrix.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o QualityPssmMaker.o QualityPssmMaker.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o TwoQualityScoreMatrix.o TwoQualityScoreMatrix.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o split/cbrc_unsplit_alignment.o split/cbrc_unsplit_alignment.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o split/last_split_options.o split/last_split_options.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_alp.o alp/sls_alp.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_basic.o alp/sls_basic.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/njn_localmaxstatutil.o alp/njn_localmaxstatutil.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/njn_dynprogprob.o alp/njn_dynprogprob.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/njn_dynprogprobproto.o alp/njn_dynprogprobproto.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/njn_dynprogproblim.o alp/njn_dynprogproblim.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/njn_ioutil.o alp/njn_ioutil.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/njn_random.o alp/njn_random.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_falp_alignment_evaluer.o alp/sls_falp_alignment_evaluer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_fsa1_pvalues.o alp/sls_fsa1_pvalues.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_fsa1_utils.o alp/sls_fsa1_utils.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/sls_fsa1_parameters.o alp/sls_fsa1_parameters.cpp g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o Alignment.o Alignment.cc Alignment.cc: In member function ‘cbrc::Alignment::extend(std::vector >&, std::vector >&, cbrc::Aligners&, bool, bool, mcf::BigSeq, unsigned char const*, unsigned long, unsigned long, bool, int, int const (*) [66], int, int, double const* const*, double, int, mcf::GapCosts const&, unsigned long, int const (*) [66], cbrc::TwoQualityScoreMatrix const&, unsigned char const*, unsigned char const*, cbrc::Alphabet const&, cbrc::AlignmentExtras&, double, int)’: Alignment.cc:423:33: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized] 423 | centroid.addExpectedCounts(start2, isForward, probMat, gap, alph.size, | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 424 | subsCounts, tranCounts); | ~~~~~~~~~~~~~~~~~~~~~~~ Alignment.cc:282:11: note: ‘tranCounts’ was declared here 282 | double *tranCounts; | ^~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o AlignmentPot.o AlignmentPot.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o AlignmentWrite.o AlignmentWrite.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o Centroid.o Centroid.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o DiagonalTable.o DiagonalTable.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o SegmentPair.o SegmentPair.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o SegmentPairPot.o SegmentPairPot.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o SubsetSuffixArraySearch.o SubsetSuffixArraySearch.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o lastal.o lastal.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o split/cbrc_split_aligner.o split/cbrc_split_aligner.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o split/mcf_last_splitter.o split/mcf_last_splitter.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o split/last-split-main.o split/last-split-main.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o split/last-split.o split/last-split.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o MultiSequence.o5 MultiSequence.cc lastal.cc: In function ‘alignGapless1(LastAligner&, cbrc::SegmentPairPot&, cbrc::MultiSequence const&, SeqData const&, Dispatcher const&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, cbrc::SubsetSuffixArray const&, unsigned char const*, unsigned int)’: lastal.cc:640:78: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:22: note: ‘fwdLen’ was declared here 637 | size_t revLen, fwdLen; | ^~~~~~ lastal.cc:640:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:14: note: ‘revLen’ was declared here 637 | size_t revLen, fwdLen; | ^~~~~~ g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o MultiSequenceQual.o5 MultiSequenceQual.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o SubsetSuffixArray.o5 SubsetSuffixArray.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o SubsetSuffixArraySort.o5 SubsetSuffixArraySort.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o lastdb.o5 lastdb.cc lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int)’: lastdb.cc:343:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual] 343 | std::cout.write((char *)m.qualityReader() + m.seqBeg(i), m.seqLen(i)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o Alignment.o5 Alignment.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o AlignmentPot.o5 AlignmentPot.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o AlignmentWrite.o5 AlignmentWrite.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o Centroid.o5 Centroid.cc Alignment.cc: In member function ‘cbrc::Alignment::extend(std::vector >&, std::vector >&, cbrc::Aligners&, bool, bool, mcf::BigSeq, unsigned char const*, unsigned long, unsigned long, bool, int, int const (*) [66], int, int, double const* const*, double, int, mcf::GapCosts const&, unsigned long, int const (*) [66], cbrc::TwoQualityScoreMatrix const&, unsigned char const*, unsigned char const*, cbrc::Alphabet const&, cbrc::AlignmentExtras&, double, int)’: Alignment.cc:423:33: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized] 423 | centroid.addExpectedCounts(start2, isForward, probMat, gap, alph.size, | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 424 | subsCounts, tranCounts); | ~~~~~~~~~~~~~~~~~~~~~~~ Alignment.cc:282:11: note: ‘tranCounts’ was declared here 282 | double *tranCounts; | ^~~~~~~~~~ g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o DiagonalTable.o5 DiagonalTable.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o SegmentPair.o5 SegmentPair.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o SegmentPairPot.o5 SegmentPairPot.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o SubsetSuffixArraySearch.o5 SubsetSuffixArraySearch.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o lastal.o5 lastal.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o split/cbrc_split_aligner.o5 split/cbrc_split_aligner.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o split/mcf_last_splitter.o5 split/mcf_last_splitter.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o split/last-split.o5 split/last-split.cc cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -msse4.1 -c -o last-merge-batches.o last-merge-batches.c g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o last-pair-probs.o last-pair-probs.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o last-pair-probs-main.o last-pair-probs-main.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o LastdbArguments.o LastdbArguments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/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_aligment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.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 split/cbrc_split_aligner.o split/mcf_last_splitter.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/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_options.o split/last-split-main.o MultiSequence.o split/cbrc_split_aligner.o split/mcf_last_splitter.o split/last-split.o alp/sls_alp_data.hpp:101:36: warning: type ‘struct array_positive’ violates the C++ One Definition Rule [-Wodr] 101 | template class array_positive{ | ^ alp/sls_fsa1_utils.hpp:555:36: note: a different type is defined in another translation unit 555 | template class array_positive{ | ^ alp/sls_alp_data.hpp:163:27: note: the first difference of corresponding definitions is field ‘d_alp_data’ 163 | alp_data *d_alp_data;//initial data | ^ alp/sls_fsa1_utils.hpp:641:23: note: a field with different name is defined in another translation unit 641 | void *d_fsa;//initial data | ^ alp/sls_alp_data.hpp:101:36: warning: type ‘struct array_positive’ violates the C++ One Definition Rule [-Wodr] 101 | template class array_positive{ | ^ alp/sls_fsa1_utils.hpp:555:36: note: a different type is defined in another translation unit 555 | template class array_positive{ | ^ alp/sls_alp_data.hpp:163:27: note: the first difference of corresponding definitions is field ‘d_alp_data’ 163 | alp_data *d_alp_data;//initial data | ^ alp/sls_fsa1_utils.hpp:641:23: note: a field with different name is defined in another translation unit 641 | void *d_fsa;//initial data | ^ alp/sls_alp_sim.hpp:54:16: warning: type ‘struct struct_for_lambda_calculation’ violates the C++ One Definition Rule [-Wodr] 54 | struct struct_for_lambda_calculation | ^ alp/sls_fsa1_parameters.hpp:47:16: note: a different type is defined in another translation unit 47 | struct struct_for_lambda_calculation | ^ alp/sls_alp_sim.hpp:64:22: note: the first difference of corresponding definitions is field ‘d_calculate_alp_number’ 64 | bool d_calculate_alp_number; | ^ alp/sls_fsa1_parameters.hpp:57:24: note: a field with different name is defined in another translation unit 57 | double d_before_last_sum; | ^ In file included from Centroid.hh:9, from Alignment.hh:8, from AlignmentPot.hh:8, from lastal.cc:14: In member function ‘cbrc::SegmentPair::end2() const’, inlined from ‘alignGapless1(LastAligner&, cbrc::SegmentPairPot&, cbrc::MultiSequence const&, SeqData const&, Dispatcher const&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, cbrc::SubsetSuffixArray const&, unsigned char const*, unsigned int)’ at lastal.cc:641:21: SegmentPair.hh:36:40: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 36 | indexT end2() const{ return start2 + size; } // end in sequence 2 | ^~~~ lastal.cc: In function ‘alignGapless1(LastAligner&, cbrc::SegmentPairPot&, cbrc::MultiSequence const&, SeqData const&, Dispatcher const&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, cbrc::SubsetSuffixArray const&, unsigned char const*, unsigned int)’: lastal.cc:637:22: note: ‘fwdLen’ was declared here 637 | size_t revLen, fwdLen; | ^~~~~~ lastal.cc:640:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:14: note: ‘revLen’ was declared here 637 | size_t revLen, fwdLen; | ^~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split5-sse4.1 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/last-split-main.o MultiSequence.o5 split/cbrc_split_aligner.o5 split/mcf_last_splitter.o5 split/last-split.o5 cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -msse4.1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-merge-batches-sse4.1 last-merge-batches.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-pair-probs-sse4.1 last-pair-probs.o last-pair-probs-main.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/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 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastdb5-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.o5 MultiSequenceQual.o5 SubsetSuffixArray.o5 SubsetSuffixArraySort.o5 lastdb.o5 -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastal5-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_aligment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.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.o5 AlignmentPot.o5 AlignmentWrite.o5 Centroid.o5 DiagonalTable.o5 MultiSequence.o5 MultiSequenceQual.o5 SegmentPair.o5 SegmentPairPot.o5 SubsetSuffixArray.o5 SubsetSuffixArraySearch.o5 lastal.o5 split/cbrc_split_aligner.o5 split/mcf_last_splitter.o5 -lz alp/sls_alp_data.hpp:101:36: warning: type ‘struct array_positive’ violates the C++ One Definition Rule [-Wodr] 101 | template class array_positive{ | ^ alp/sls_fsa1_utils.hpp:555:36: note: a different type is defined in another translation unit 555 | template class array_positive{ | ^ alp/sls_alp_data.hpp:163:27: note: the first difference of corresponding definitions is field ‘d_alp_data’ 163 | alp_data *d_alp_data;//initial data | ^ alp/sls_fsa1_utils.hpp:641:23: note: a field with different name is defined in another translation unit 641 | void *d_fsa;//initial data | ^ alp/sls_alp_data.hpp:101:36: warning: type ‘struct array_positive’ violates the C++ One Definition Rule [-Wodr] 101 | template class array_positive{ | ^ alp/sls_fsa1_utils.hpp:555:36: note: a different type is defined in another translation unit 555 | template class array_positive{ | ^ alp/sls_alp_data.hpp:163:27: note: the first difference of corresponding definitions is field ‘d_alp_data’ 163 | alp_data *d_alp_data;//initial data | ^ alp/sls_fsa1_utils.hpp:641:23: note: a field with different name is defined in another translation unit 641 | void *d_fsa;//initial data | ^ alp/sls_alp_sim.hpp:54:16: warning: type ‘struct struct_for_lambda_calculation’ violates the C++ One Definition Rule [-Wodr] 54 | struct struct_for_lambda_calculation | ^ alp/sls_fsa1_parameters.hpp:47:16: note: a different type is defined in another translation unit 47 | struct struct_for_lambda_calculation | ^ alp/sls_alp_sim.hpp:64:22: note: the first difference of corresponding definitions is field ‘d_calculate_alp_number’ 64 | bool d_calculate_alp_number; | ^ alp/sls_fsa1_parameters.hpp:57:24: note: a field with different name is defined in another translation unit 57 | double d_before_last_sum; | ^ lastal.cc: In function ‘alignGapless1’: lastal.cc:640:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:14: note: ‘revLen’ was declared here 637 | size_t revLen, fwdLen; | ^ lastal.cc:640:78: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:22: note: ‘fwdLen’ was declared here 637 | size_t revLen, fwdLen; | ^ In member function ‘addExpectedCounts’, inlined from ‘extend.constprop.isra’ at Alignment.cc:423:33: Centroid.cc:606:23: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized] 606 | transitionCounts[2] += insCount; // inserted letter count | ^ Alignment.cc: In member function ‘extend.constprop.isra’: Alignment.cc:282:11: note: ‘tranCounts’ was declared here 282 | double *tranCounts; | ^ lastal.cc: In function ‘alignGapless1’: lastal.cc:640:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:14: note: ‘revLen’ was declared here 637 | size_t revLen, fwdLen; | ^ In member function ‘end2’, inlined from ‘alignGapless1’ at lastal.cc:641:21: SegmentPair.hh:36:40: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 36 | indexT end2() const{ return start2 + size; } // end in sequence 2 | ^ lastal.cc: In function ‘alignGapless1’: lastal.cc:637:22: note: ‘fwdLen’ was declared here 637 | size_t revLen, fwdLen; | ^ In member function ‘addExpectedCounts’, inlined from ‘extend.constprop.isra’ at Alignment.cc:423:33: Centroid.cc:606:23: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized] 606 | transitionCounts[2] += insCount; // inserted letter count | ^ Alignment.cc: In member function ‘extend.constprop.isra’: Alignment.cc:282:11: note: ‘tranCounts’ was declared here 282 | double *tranCounts; | ^ make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' make -j4 "INSTALL=install --strip-program=true" all SFX=-ssse3 "CFLAGS=-g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -mssse3" "CXXFLAGS=-g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3" make[2]: Entering directory '/<>' make[3]: Entering directory '/<>/src' g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o Alphabet.o Alphabet.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o CyclicSubsetSeed.o CyclicSubsetSeed.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o LambdaCalculator.o LambdaCalculator.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o ScoreMatrix.o ScoreMatrix.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o SubsetMinimizerFinder.o SubsetMinimizerFinder.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o TantanMasker.o TantanMasker.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o dna_words_finder.o dna_words_finder.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o cbrc_linalg.o cbrc_linalg.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o mcf_substitution_matrix_stats.o mcf_substitution_matrix_stats.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o tantan.o tantan.cc echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1447) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" | cmp -s version.hh - || echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1447) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" > version.hh g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o MultiSequence.o MultiSequence.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from tantan.cc:4: /usr/include/simde/x86/avx.h: In function ‘__vector(4) double simde__m256d_from_private(simde__m256d_private)’: /usr/include/simde/x86/avx.h:290:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 290 | simde__m256d_from_private(simde__m256d_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o lastdb.o lastdb.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o LastalArguments.o LastalArguments.cc lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int)’: lastdb.cc:343:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual] 343 | std::cout.write((char *)m.qualityReader() + m.seqBeg(i), m.seqLen(i)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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:52, 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:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | 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:52, 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:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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:52, 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:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | 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:52, 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:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o mcf_aligment_path_adder.o mcf_aligment_path_adder.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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:52, 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:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o mcf_gap_costs.o mcf_gap_costs.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o GeneticCode.o GeneticCode.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o GreedyXdropAligner.o GreedyXdropAligner.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o LastEvaluer.o LastEvaluer.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o OneQualityScoreMatrix.o OneQualityScoreMatrix.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o QualityPssmMaker.o QualityPssmMaker.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o TwoQualityScoreMatrix.o TwoQualityScoreMatrix.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o split/cbrc_unsplit_alignment.o split/cbrc_unsplit_alignment.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o split/last_split_options.o split/last_split_options.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_alp.o alp/sls_alp.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_basic.o alp/sls_basic.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/njn_localmaxstatutil.o alp/njn_localmaxstatutil.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/njn_dynprogprob.o alp/njn_dynprogprob.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/njn_dynprogprobproto.o alp/njn_dynprogprobproto.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/njn_dynprogproblim.o alp/njn_dynprogproblim.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/njn_ioutil.o alp/njn_ioutil.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/njn_random.o alp/njn_random.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_falp_alignment_evaluer.o alp/sls_falp_alignment_evaluer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_fsa1_pvalues.o alp/sls_fsa1_pvalues.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_fsa1_utils.o alp/sls_fsa1_utils.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/sls_fsa1_parameters.o alp/sls_fsa1_parameters.cpp g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o Alignment.o Alignment.cc Alignment.cc: In member function ‘cbrc::Alignment::extend(std::vector >&, std::vector >&, cbrc::Aligners&, bool, bool, mcf::BigSeq, unsigned char const*, unsigned long, unsigned long, bool, int, int const (*) [66], int, int, double const* const*, double, int, mcf::GapCosts const&, unsigned long, int const (*) [66], cbrc::TwoQualityScoreMatrix const&, unsigned char const*, unsigned char const*, cbrc::Alphabet const&, cbrc::AlignmentExtras&, double, int)’: Alignment.cc:423:33: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized] 423 | centroid.addExpectedCounts(start2, isForward, probMat, gap, alph.size, | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 424 | subsCounts, tranCounts); | ~~~~~~~~~~~~~~~~~~~~~~~ Alignment.cc:282:11: note: ‘tranCounts’ was declared here 282 | double *tranCounts; | ^~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o AlignmentPot.o AlignmentPot.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o AlignmentWrite.o AlignmentWrite.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o Centroid.o Centroid.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o DiagonalTable.o DiagonalTable.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o SegmentPair.o SegmentPair.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o SegmentPairPot.o SegmentPairPot.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o SubsetSuffixArraySearch.o SubsetSuffixArraySearch.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o lastal.o lastal.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o split/cbrc_split_aligner.o split/cbrc_split_aligner.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o split/mcf_last_splitter.o split/mcf_last_splitter.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o split/last-split-main.o split/last-split-main.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o split/last-split.o split/last-split.cc lastal.cc: In function ‘alignGapless1(LastAligner&, cbrc::SegmentPairPot&, cbrc::MultiSequence const&, SeqData const&, Dispatcher const&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, cbrc::SubsetSuffixArray const&, unsigned char const*, unsigned int)’: lastal.cc:640:78: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:22: note: ‘fwdLen’ was declared here 637 | size_t revLen, fwdLen; | ^~~~~~ lastal.cc:640:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:14: note: ‘revLen’ was declared here 637 | size_t revLen, fwdLen; | ^~~~~~ g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o MultiSequence.o5 MultiSequence.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o MultiSequenceQual.o5 MultiSequenceQual.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o SubsetSuffixArray.o5 SubsetSuffixArray.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o SubsetSuffixArraySort.o5 SubsetSuffixArraySort.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o lastdb.o5 lastdb.cc lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int)’: lastdb.cc:343:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual] 343 | std::cout.write((char *)m.qualityReader() + m.seqBeg(i), m.seqLen(i)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o Alignment.o5 Alignment.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o AlignmentPot.o5 AlignmentPot.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o AlignmentWrite.o5 AlignmentWrite.cc Alignment.cc: In member function ‘cbrc::Alignment::extend(std::vector >&, std::vector >&, cbrc::Aligners&, bool, bool, mcf::BigSeq, unsigned char const*, unsigned long, unsigned long, bool, int, int const (*) [66], int, int, double const* const*, double, int, mcf::GapCosts const&, unsigned long, int const (*) [66], cbrc::TwoQualityScoreMatrix const&, unsigned char const*, unsigned char const*, cbrc::Alphabet const&, cbrc::AlignmentExtras&, double, int)’: Alignment.cc:423:33: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized] 423 | centroid.addExpectedCounts(start2, isForward, probMat, gap, alph.size, | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 424 | subsCounts, tranCounts); | ~~~~~~~~~~~~~~~~~~~~~~~ Alignment.cc:282:11: note: ‘tranCounts’ was declared here 282 | double *tranCounts; | ^~~~~~~~~~ g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o Centroid.o5 Centroid.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o DiagonalTable.o5 DiagonalTable.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o SegmentPair.o5 SegmentPair.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o SegmentPairPot.o5 SegmentPairPot.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o SubsetSuffixArraySearch.o5 SubsetSuffixArraySearch.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o lastal.o5 lastal.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o split/cbrc_split_aligner.o5 split/cbrc_split_aligner.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o split/mcf_last_splitter.o5 split/mcf_last_splitter.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o split/last-split.o5 split/last-split.cc cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -mssse3 -c -o last-merge-batches.o last-merge-batches.c g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o last-pair-probs.o last-pair-probs.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o last-pair-probs-main.o last-pair-probs-main.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o LastdbArguments.o LastdbArguments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/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_aligment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.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 split/cbrc_split_aligner.o split/mcf_last_splitter.o -lz alp/sls_alp_data.hpp:101:36: warning: type ‘struct array_positive’ violates the C++ One Definition Rule [-Wodr] 101 | template class array_positive{ | ^ alp/sls_fsa1_utils.hpp:555:36: note: a different type is defined in another translation unit 555 | template class array_positive{ | ^ alp/sls_alp_data.hpp:163:27: note: the first difference of corresponding definitions is field ‘d_alp_data’ 163 | alp_data *d_alp_data;//initial data | ^ alp/sls_fsa1_utils.hpp:641:23: note: a field with different name is defined in another translation unit 641 | void *d_fsa;//initial data | ^ alp/sls_alp_data.hpp:101:36: warning: type ‘struct array_positive’ violates the C++ One Definition Rule [-Wodr] 101 | template class array_positive{ | ^ alp/sls_fsa1_utils.hpp:555:36: note: a different type is defined in another translation unit 555 | template class array_positive{ | ^ alp/sls_alp_data.hpp:163:27: note: the first difference of corresponding definitions is field ‘d_alp_data’ 163 | alp_data *d_alp_data;//initial data | ^ alp/sls_fsa1_utils.hpp:641:23: note: a field with different name is defined in another translation unit 641 | void *d_fsa;//initial data | ^ alp/sls_alp_sim.hpp:54:16: warning: type ‘struct struct_for_lambda_calculation’ violates the C++ One Definition Rule [-Wodr] 54 | struct struct_for_lambda_calculation | ^ alp/sls_fsa1_parameters.hpp:47:16: note: a different type is defined in another translation unit 47 | struct struct_for_lambda_calculation | ^ alp/sls_alp_sim.hpp:64:22: note: the first difference of corresponding definitions is field ‘d_calculate_alp_number’ 64 | bool d_calculate_alp_number; | ^ alp/sls_fsa1_parameters.hpp:57:24: note: a field with different name is defined in another translation unit 57 | double d_before_last_sum; | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/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_options.o split/last-split-main.o MultiSequence.o split/cbrc_split_aligner.o split/mcf_last_splitter.o split/last-split.o In file included from Centroid.hh:9, from Alignment.hh:8, from AlignmentPot.hh:8, from lastal.cc:14: In member function ‘cbrc::SegmentPair::end2() const’, inlined from ‘alignGapless1(LastAligner&, cbrc::SegmentPairPot&, cbrc::MultiSequence const&, SeqData const&, Dispatcher const&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, cbrc::SubsetSuffixArray const&, unsigned char const*, unsigned int)’ at lastal.cc:641:21: SegmentPair.hh:36:40: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 36 | indexT end2() const{ return start2 + size; } // end in sequence 2 | ^~~~ lastal.cc: In function ‘alignGapless1(LastAligner&, cbrc::SegmentPairPot&, cbrc::MultiSequence const&, SeqData const&, Dispatcher const&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, cbrc::SubsetSuffixArray const&, unsigned char const*, unsigned int)’: lastal.cc:637:22: note: ‘fwdLen’ was declared here 637 | size_t revLen, fwdLen; | ^~~~~~ lastal.cc:640:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:14: note: ‘revLen’ was declared here 637 | size_t revLen, fwdLen; | ^~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split5-ssse3 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/last-split-main.o MultiSequence.o5 split/cbrc_split_aligner.o5 split/mcf_last_splitter.o5 split/last-split.o5 lastal.cc: In function ‘alignGapless1’: lastal.cc:640:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:14: note: ‘revLen’ was declared here 637 | size_t revLen, fwdLen; | ^ lastal.cc:640:78: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:22: note: ‘fwdLen’ was declared here 637 | size_t revLen, fwdLen; | ^ cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -mssse3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-merge-batches-ssse3 last-merge-batches.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-pair-probs-ssse3 last-pair-probs.o last-pair-probs-main.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/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 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastdb5-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.o5 MultiSequenceQual.o5 SubsetSuffixArray.o5 SubsetSuffixArraySort.o5 lastdb.o5 -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastal5-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_aligment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.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.o5 AlignmentPot.o5 AlignmentWrite.o5 Centroid.o5 DiagonalTable.o5 MultiSequence.o5 MultiSequenceQual.o5 SegmentPair.o5 SegmentPairPot.o5 SubsetSuffixArray.o5 SubsetSuffixArraySearch.o5 lastal.o5 split/cbrc_split_aligner.o5 split/mcf_last_splitter.o5 -lz alp/sls_alp_data.hpp:101:36: warning: type ‘struct array_positive’ violates the C++ One Definition Rule [-Wodr] 101 | template class array_positive{ | ^ alp/sls_fsa1_utils.hpp:555:36: note: a different type is defined in another translation unit 555 | template class array_positive{ | ^ alp/sls_alp_data.hpp:163:27: note: the first difference of corresponding definitions is field ‘d_alp_data’ 163 | alp_data *d_alp_data;//initial data | ^ alp/sls_fsa1_utils.hpp:641:23: note: a field with different name is defined in another translation unit 641 | void *d_fsa;//initial data | ^ alp/sls_alp_data.hpp:101:36: warning: type ‘struct array_positive’ violates the C++ One Definition Rule [-Wodr] 101 | template class array_positive{ | ^ alp/sls_fsa1_utils.hpp:555:36: note: a different type is defined in another translation unit 555 | template class array_positive{ | ^ alp/sls_alp_data.hpp:163:27: note: the first difference of corresponding definitions is field ‘d_alp_data’ 163 | alp_data *d_alp_data;//initial data | ^ alp/sls_fsa1_utils.hpp:641:23: note: a field with different name is defined in another translation unit 641 | void *d_fsa;//initial data | ^ alp/sls_alp_sim.hpp:54:16: warning: type ‘struct struct_for_lambda_calculation’ violates the C++ One Definition Rule [-Wodr] 54 | struct struct_for_lambda_calculation | ^ alp/sls_fsa1_parameters.hpp:47:16: note: a different type is defined in another translation unit 47 | struct struct_for_lambda_calculation | ^ alp/sls_alp_sim.hpp:64:22: note: the first difference of corresponding definitions is field ‘d_calculate_alp_number’ 64 | bool d_calculate_alp_number; | ^ alp/sls_fsa1_parameters.hpp:57:24: note: a field with different name is defined in another translation unit 57 | double d_before_last_sum; | ^ In member function ‘addExpectedCounts’, inlined from ‘extend.constprop.isra’ at Alignment.cc:423:33: Centroid.cc:606:23: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized] 606 | transitionCounts[2] += insCount; // inserted letter count | ^ Alignment.cc: In member function ‘extend.constprop.isra’: Alignment.cc:282:11: note: ‘tranCounts’ was declared here 282 | double *tranCounts; | ^ lastal.cc: In function ‘alignGapless1’: lastal.cc:640:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:14: note: ‘revLen’ was declared here 637 | size_t revLen, fwdLen; | ^ In member function ‘end2’, inlined from ‘alignGapless1’ at lastal.cc:641:21: SegmentPair.hh:36:40: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 36 | indexT end2() const{ return start2 + size; } // end in sequence 2 | ^ lastal.cc: In function ‘alignGapless1’: lastal.cc:637:22: note: ‘fwdLen’ was declared here 637 | size_t revLen, fwdLen; | ^ In member function ‘addExpectedCounts’, inlined from ‘extend.constprop.isra’ at Alignment.cc:423:33: Centroid.cc:606:23: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized] 606 | transitionCounts[2] += insCount; // inserted letter count | ^ Alignment.cc: In member function ‘extend.constprop.isra’: Alignment.cc:282:11: note: ‘tranCounts’ was declared here 282 | double *tranCounts; | ^ make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' make -j4 "INSTALL=install --strip-program=true" all SFX=-sse3 "CFLAGS=-g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -msse3" "CXXFLAGS=-g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3" make[2]: Entering directory '/<>' make[3]: Entering directory '/<>/src' g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o Alphabet.o Alphabet.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o CyclicSubsetSeed.o CyclicSubsetSeed.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o LambdaCalculator.o LambdaCalculator.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o ScoreMatrix.o ScoreMatrix.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o SubsetMinimizerFinder.o SubsetMinimizerFinder.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o TantanMasker.o TantanMasker.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o dna_words_finder.o dna_words_finder.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o cbrc_linalg.o cbrc_linalg.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o mcf_substitution_matrix_stats.o mcf_substitution_matrix_stats.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o tantan.o tantan.cc echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1447) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" | cmp -s version.hh - || echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1447) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" > version.hh g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o MultiSequence.o MultiSequence.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from tantan.cc:4: /usr/include/simde/x86/avx.h: In function ‘__vector(4) double simde__m256d_from_private(simde__m256d_private)’: /usr/include/simde/x86/avx.h:290:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 290 | simde__m256d_from_private(simde__m256d_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o lastdb.o lastdb.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o LastalArguments.o LastalArguments.cc lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int)’: lastdb.cc:343:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual] 343 | std::cout.write((char *)m.qualityReader() + m.seqBeg(i), m.seqLen(i)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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:52, 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:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | 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:52, 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:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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:52, 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:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | 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:52, 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:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o mcf_aligment_path_adder.o mcf_aligment_path_adder.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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:52, 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:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o GeneticCode.o GeneticCode.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o GreedyXdropAligner.o GreedyXdropAligner.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o LastEvaluer.o LastEvaluer.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o OneQualityScoreMatrix.o OneQualityScoreMatrix.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o QualityPssmMaker.o QualityPssmMaker.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o TwoQualityScoreMatrix.o TwoQualityScoreMatrix.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o split/cbrc_unsplit_alignment.o split/cbrc_unsplit_alignment.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o split/last_split_options.o split/last_split_options.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_alp.o alp/sls_alp.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_basic.o alp/sls_basic.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/njn_localmaxstatutil.o alp/njn_localmaxstatutil.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/njn_dynprogprob.o alp/njn_dynprogprob.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/njn_dynprogprobproto.o alp/njn_dynprogprobproto.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/njn_dynprogproblim.o alp/njn_dynprogproblim.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/njn_ioutil.o alp/njn_ioutil.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/njn_random.o alp/njn_random.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_falp_alignment_evaluer.o alp/sls_falp_alignment_evaluer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_fsa1_pvalues.o alp/sls_fsa1_pvalues.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_fsa1_utils.o alp/sls_fsa1_utils.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_fsa1_parameters.o alp/sls_fsa1_parameters.cpp g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o Alignment.o Alignment.cc Alignment.cc: In member function ‘cbrc::Alignment::extend(std::vector >&, std::vector >&, cbrc::Aligners&, bool, bool, mcf::BigSeq, unsigned char const*, unsigned long, unsigned long, bool, int, int const (*) [66], int, int, double const* const*, double, int, mcf::GapCosts const&, unsigned long, int const (*) [66], cbrc::TwoQualityScoreMatrix const&, unsigned char const*, unsigned char const*, cbrc::Alphabet const&, cbrc::AlignmentExtras&, double, int)’: Alignment.cc:423:33: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized] 423 | centroid.addExpectedCounts(start2, isForward, probMat, gap, alph.size, | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 424 | subsCounts, tranCounts); | ~~~~~~~~~~~~~~~~~~~~~~~ Alignment.cc:282:11: note: ‘tranCounts’ was declared here 282 | double *tranCounts; | ^~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o AlignmentPot.o AlignmentPot.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o AlignmentWrite.o AlignmentWrite.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o Centroid.o Centroid.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o DiagonalTable.o DiagonalTable.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o SegmentPair.o SegmentPair.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o SegmentPairPot.o SegmentPairPot.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o SubsetSuffixArraySearch.o SubsetSuffixArraySearch.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o lastal.o lastal.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o split/cbrc_split_aligner.o split/cbrc_split_aligner.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o split/mcf_last_splitter.o split/mcf_last_splitter.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o split/last-split-main.o split/last-split-main.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o split/last-split.o split/last-split.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o MultiSequence.o5 MultiSequence.cc lastal.cc: In function ‘alignGapless1(LastAligner&, cbrc::SegmentPairPot&, cbrc::MultiSequence const&, SeqData const&, Dispatcher const&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, cbrc::SubsetSuffixArray const&, unsigned char const*, unsigned int)’: lastal.cc:640:78: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:22: note: ‘fwdLen’ was declared here 637 | size_t revLen, fwdLen; | ^~~~~~ lastal.cc:640:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:14: note: ‘revLen’ was declared here 637 | size_t revLen, fwdLen; | ^~~~~~ g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o MultiSequenceQual.o5 MultiSequenceQual.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o SubsetSuffixArray.o5 SubsetSuffixArray.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o SubsetSuffixArraySort.o5 SubsetSuffixArraySort.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o lastdb.o5 lastdb.cc lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int)’: lastdb.cc:343:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual] 343 | std::cout.write((char *)m.qualityReader() + m.seqBeg(i), m.seqLen(i)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o Alignment.o5 Alignment.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o AlignmentPot.o5 AlignmentPot.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o AlignmentWrite.o5 AlignmentWrite.cc Alignment.cc: In member function ‘cbrc::Alignment::extend(std::vector >&, std::vector >&, cbrc::Aligners&, bool, bool, mcf::BigSeq, unsigned char const*, unsigned long, unsigned long, bool, int, int const (*) [66], int, int, double const* const*, double, int, mcf::GapCosts const&, unsigned long, int const (*) [66], cbrc::TwoQualityScoreMatrix const&, unsigned char const*, unsigned char const*, cbrc::Alphabet const&, cbrc::AlignmentExtras&, double, int)’: Alignment.cc:423:33: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized] 423 | centroid.addExpectedCounts(start2, isForward, probMat, gap, alph.size, | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 424 | subsCounts, tranCounts); | ~~~~~~~~~~~~~~~~~~~~~~~ Alignment.cc:282:11: note: ‘tranCounts’ was declared here 282 | double *tranCounts; | ^~~~~~~~~~ g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o Centroid.o5 Centroid.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o DiagonalTable.o5 DiagonalTable.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o SegmentPair.o5 SegmentPair.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o SegmentPairPot.o5 SegmentPairPot.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o SubsetSuffixArraySearch.o5 SubsetSuffixArraySearch.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o lastal.o5 lastal.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o split/cbrc_split_aligner.o5 split/cbrc_split_aligner.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o split/mcf_last_splitter.o5 split/mcf_last_splitter.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o split/last-split.o5 split/last-split.cc cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -msse3 -c -o last-merge-batches.o last-merge-batches.c g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o last-pair-probs.o last-pair-probs.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o last-pair-probs-main.o last-pair-probs-main.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o LastdbArguments.o LastdbArguments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/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_aligment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.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 split/cbrc_split_aligner.o split/mcf_last_splitter.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/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_options.o split/last-split-main.o MultiSequence.o split/cbrc_split_aligner.o split/mcf_last_splitter.o split/last-split.o alp/sls_alp_data.hpp:101:36: warning: type ‘struct array_positive’ violates the C++ One Definition Rule [-Wodr] 101 | template class array_positive{ | ^ alp/sls_fsa1_utils.hpp:555:36: note: a different type is defined in another translation unit 555 | template class array_positive{ | ^ alp/sls_alp_data.hpp:163:27: note: the first difference of corresponding definitions is field ‘d_alp_data’ 163 | alp_data *d_alp_data;//initial data | ^ alp/sls_fsa1_utils.hpp:641:23: note: a field with different name is defined in another translation unit 641 | void *d_fsa;//initial data | ^ alp/sls_alp_data.hpp:101:36: warning: type ‘struct array_positive’ violates the C++ One Definition Rule [-Wodr] 101 | template class array_positive{ | ^ alp/sls_fsa1_utils.hpp:555:36: note: a different type is defined in another translation unit 555 | template class array_positive{ | ^ alp/sls_alp_data.hpp:163:27: note: the first difference of corresponding definitions is field ‘d_alp_data’ 163 | alp_data *d_alp_data;//initial data | ^ alp/sls_fsa1_utils.hpp:641:23: note: a field with different name is defined in another translation unit 641 | void *d_fsa;//initial data | ^ alp/sls_alp_sim.hpp:54:16: warning: type ‘struct struct_for_lambda_calculation’ violates the C++ One Definition Rule [-Wodr] 54 | struct struct_for_lambda_calculation | ^ alp/sls_fsa1_parameters.hpp:47:16: note: a different type is defined in another translation unit 47 | struct struct_for_lambda_calculation | ^ alp/sls_alp_sim.hpp:64:22: note: the first difference of corresponding definitions is field ‘d_calculate_alp_number’ 64 | bool d_calculate_alp_number; | ^ alp/sls_fsa1_parameters.hpp:57:24: note: a field with different name is defined in another translation unit 57 | double d_before_last_sum; | ^ In file included from Centroid.hh:9, from Alignment.hh:8, from AlignmentPot.hh:8, from lastal.cc:14: In member function ‘cbrc::SegmentPair::end2() const’, inlined from ‘alignGapless1(LastAligner&, cbrc::SegmentPairPot&, cbrc::MultiSequence const&, SeqData const&, Dispatcher const&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, cbrc::SubsetSuffixArray const&, unsigned char const*, unsigned int)’ at lastal.cc:641:21: SegmentPair.hh:36:40: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 36 | indexT end2() const{ return start2 + size; } // end in sequence 2 | ^~~~ lastal.cc: In function ‘alignGapless1(LastAligner&, cbrc::SegmentPairPot&, cbrc::MultiSequence const&, SeqData const&, Dispatcher const&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, cbrc::SubsetSuffixArray const&, unsigned char const*, unsigned int)’: lastal.cc:637:22: note: ‘fwdLen’ was declared here 637 | size_t revLen, fwdLen; | ^~~~~~ lastal.cc:640:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:14: note: ‘revLen’ was declared here 637 | size_t revLen, fwdLen; | ^~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split5-sse3 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/last-split-main.o MultiSequence.o5 split/cbrc_split_aligner.o5 split/mcf_last_splitter.o5 split/last-split.o5 lastal.cc: In function ‘alignGapless1’: lastal.cc:640:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:14: note: ‘revLen’ was declared here 637 | size_t revLen, fwdLen; | ^ lastal.cc:640:78: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:22: note: ‘fwdLen’ was declared here 637 | size_t revLen, fwdLen; | ^ GappedXdropAlignerDna.cc: In function ‘simdChoose1’: GappedXdropAlignerDna.cc:104:34: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 104 | SimdUint1 s = simdChoose1(scorer4x4, j); | ^ cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -msse3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-merge-batches-sse3 last-merge-batches.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-pair-probs-sse3 last-pair-probs.o last-pair-probs-main.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/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 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastdb5-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.o5 MultiSequenceQual.o5 SubsetSuffixArray.o5 SubsetSuffixArraySort.o5 lastdb.o5 -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastal5-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_aligment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.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.o5 AlignmentPot.o5 AlignmentWrite.o5 Centroid.o5 DiagonalTable.o5 MultiSequence.o5 MultiSequenceQual.o5 SegmentPair.o5 SegmentPairPot.o5 SubsetSuffixArray.o5 SubsetSuffixArraySearch.o5 lastal.o5 split/cbrc_split_aligner.o5 split/mcf_last_splitter.o5 -lz alp/sls_alp_data.hpp:101:36: warning: type ‘struct array_positive’ violates the C++ One Definition Rule [-Wodr] 101 | template class array_positive{ | ^ alp/sls_fsa1_utils.hpp:555:36: note: a different type is defined in another translation unit 555 | template class array_positive{ | ^ alp/sls_alp_data.hpp:163:27: note: the first difference of corresponding definitions is field ‘d_alp_data’ 163 | alp_data *d_alp_data;//initial data | ^ alp/sls_fsa1_utils.hpp:641:23: note: a field with different name is defined in another translation unit 641 | void *d_fsa;//initial data | ^ alp/sls_alp_data.hpp:101:36: warning: type ‘struct array_positive’ violates the C++ One Definition Rule [-Wodr] 101 | template class array_positive{ | ^ alp/sls_fsa1_utils.hpp:555:36: note: a different type is defined in another translation unit 555 | template class array_positive{ | ^ alp/sls_alp_data.hpp:163:27: note: the first difference of corresponding definitions is field ‘d_alp_data’ 163 | alp_data *d_alp_data;//initial data | ^ alp/sls_fsa1_utils.hpp:641:23: note: a field with different name is defined in another translation unit 641 | void *d_fsa;//initial data | ^ alp/sls_alp_sim.hpp:54:16: warning: type ‘struct struct_for_lambda_calculation’ violates the C++ One Definition Rule [-Wodr] 54 | struct struct_for_lambda_calculation | ^ alp/sls_fsa1_parameters.hpp:47:16: note: a different type is defined in another translation unit 47 | struct struct_for_lambda_calculation | ^ alp/sls_alp_sim.hpp:64:22: note: the first difference of corresponding definitions is field ‘d_calculate_alp_number’ 64 | bool d_calculate_alp_number; | ^ alp/sls_fsa1_parameters.hpp:57:24: note: a field with different name is defined in another translation unit 57 | double d_before_last_sum; | ^ In member function ‘addExpectedCounts’, inlined from ‘extend.constprop.isra’ at Alignment.cc:423:33: Centroid.cc:606:23: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized] 606 | transitionCounts[2] += insCount; // inserted letter count | ^ Alignment.cc: In member function ‘extend.constprop.isra’: Alignment.cc:282:11: note: ‘tranCounts’ was declared here 282 | double *tranCounts; | ^ lastal.cc: In function ‘alignGapless1’: lastal.cc:640:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:14: note: ‘revLen’ was declared here 637 | size_t revLen, fwdLen; | ^ In member function ‘end2’, inlined from ‘alignGapless1’ at lastal.cc:641:21: SegmentPair.hh:36:40: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 36 | indexT end2() const{ return start2 + size; } // end in sequence 2 | ^ lastal.cc: In function ‘alignGapless1’: lastal.cc:637:22: note: ‘fwdLen’ was declared here 637 | size_t revLen, fwdLen; | ^ GappedXdropAlignerDna.cc: In function ‘simdChoose1’: GappedXdropAlignerDna.cc:104:34: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 104 | SimdUint1 s = simdChoose1(scorer4x4, j); | ^ In member function ‘addExpectedCounts’, inlined from ‘extend.constprop.isra’ at Alignment.cc:423:33: Centroid.cc:606:23: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized] 606 | transitionCounts[2] += insCount; // inserted letter count | ^ Alignment.cc: In member function ‘extend.constprop.isra’: Alignment.cc:282:11: note: ‘tranCounts’ was declared here 282 | double *tranCounts; | ^ make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' make -j4 "INSTALL=install --strip-program=true" all SFX=-sse2 "CFLAGS=-g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -msse2" "CXXFLAGS=-g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2" make[2]: Entering directory '/<>' make[3]: Entering directory '/<>/src' g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o Alphabet.o Alphabet.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o CyclicSubsetSeed.o CyclicSubsetSeed.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o LambdaCalculator.o LambdaCalculator.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o ScoreMatrix.o ScoreMatrix.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o SubsetMinimizerFinder.o SubsetMinimizerFinder.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o TantanMasker.o TantanMasker.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o dna_words_finder.o dna_words_finder.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o cbrc_linalg.o cbrc_linalg.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o mcf_substitution_matrix_stats.o mcf_substitution_matrix_stats.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o tantan.o tantan.cc echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1447) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" | cmp -s version.hh - || echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1447) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" > version.hh g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o MultiSequence.o MultiSequence.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from tantan.cc:4: /usr/include/simde/x86/avx.h: In function ‘__vector(4) double simde__m256d_from_private(simde__m256d_private)’: /usr/include/simde/x86/avx.h:290:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 290 | simde__m256d_from_private(simde__m256d_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o lastdb.o lastdb.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o LastalArguments.o LastalArguments.cc lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int)’: lastdb.cc:343:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual] 343 | std::cout.write((char *)m.qualityReader() + m.seqBeg(i), m.seqLen(i)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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:52, 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:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | 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:52, 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:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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:52, 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:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | 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:52, 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:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o mcf_aligment_path_adder.o mcf_aligment_path_adder.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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:52, 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:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o GeneticCode.o GeneticCode.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o GreedyXdropAligner.o GreedyXdropAligner.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o LastEvaluer.o LastEvaluer.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o OneQualityScoreMatrix.o OneQualityScoreMatrix.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o QualityPssmMaker.o QualityPssmMaker.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o TwoQualityScoreMatrix.o TwoQualityScoreMatrix.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o split/cbrc_unsplit_alignment.o split/cbrc_unsplit_alignment.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o split/last_split_options.o split/last_split_options.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_alp.o alp/sls_alp.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_basic.o alp/sls_basic.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/njn_localmaxstatutil.o alp/njn_localmaxstatutil.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/njn_dynprogprob.o alp/njn_dynprogprob.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/njn_dynprogprobproto.o alp/njn_dynprogprobproto.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/njn_dynprogproblim.o alp/njn_dynprogproblim.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/njn_ioutil.o alp/njn_ioutil.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/njn_random.o alp/njn_random.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_falp_alignment_evaluer.o alp/sls_falp_alignment_evaluer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_fsa1_pvalues.o alp/sls_fsa1_pvalues.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_fsa1_utils.o alp/sls_fsa1_utils.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/sls_fsa1_parameters.o alp/sls_fsa1_parameters.cpp g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o Alignment.o Alignment.cc Alignment.cc: In member function ‘cbrc::Alignment::extend(std::vector >&, std::vector >&, cbrc::Aligners&, bool, bool, mcf::BigSeq, unsigned char const*, unsigned long, unsigned long, bool, int, int const (*) [66], int, int, double const* const*, double, int, mcf::GapCosts const&, unsigned long, int const (*) [66], cbrc::TwoQualityScoreMatrix const&, unsigned char const*, unsigned char const*, cbrc::Alphabet const&, cbrc::AlignmentExtras&, double, int)’: Alignment.cc:423:33: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized] 423 | centroid.addExpectedCounts(start2, isForward, probMat, gap, alph.size, | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 424 | subsCounts, tranCounts); | ~~~~~~~~~~~~~~~~~~~~~~~ Alignment.cc:282:11: note: ‘tranCounts’ was declared here 282 | double *tranCounts; | ^~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o AlignmentPot.o AlignmentPot.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o AlignmentWrite.o AlignmentWrite.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o Centroid.o Centroid.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o DiagonalTable.o DiagonalTable.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o SegmentPair.o SegmentPair.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o SegmentPairPot.o SegmentPairPot.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o SubsetSuffixArraySearch.o SubsetSuffixArraySearch.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o lastal.o lastal.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o split/cbrc_split_aligner.o split/cbrc_split_aligner.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o split/mcf_last_splitter.o split/mcf_last_splitter.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o split/last-split-main.o split/last-split-main.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o split/last-split.o split/last-split.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o MultiSequence.o5 MultiSequence.cc lastal.cc: In function ‘alignGapless1(LastAligner&, cbrc::SegmentPairPot&, cbrc::MultiSequence const&, SeqData const&, Dispatcher const&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, cbrc::SubsetSuffixArray const&, unsigned char const*, unsigned int)’: lastal.cc:640:78: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:22: note: ‘fwdLen’ was declared here 637 | size_t revLen, fwdLen; | ^~~~~~ lastal.cc:640:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:14: note: ‘revLen’ was declared here 637 | size_t revLen, fwdLen; | ^~~~~~ g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o MultiSequenceQual.o5 MultiSequenceQual.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o SubsetSuffixArray.o5 SubsetSuffixArray.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o SubsetSuffixArraySort.o5 SubsetSuffixArraySort.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o lastdb.o5 lastdb.cc lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int)’: lastdb.cc:343:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual] 343 | std::cout.write((char *)m.qualityReader() + m.seqBeg(i), m.seqLen(i)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o Alignment.o5 Alignment.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o AlignmentPot.o5 AlignmentPot.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o AlignmentWrite.o5 AlignmentWrite.cc Alignment.cc: In member function ‘cbrc::Alignment::extend(std::vector >&, std::vector >&, cbrc::Aligners&, bool, bool, mcf::BigSeq, unsigned char const*, unsigned long, unsigned long, bool, int, int const (*) [66], int, int, double const* const*, double, int, mcf::GapCosts const&, unsigned long, int const (*) [66], cbrc::TwoQualityScoreMatrix const&, unsigned char const*, unsigned char const*, cbrc::Alphabet const&, cbrc::AlignmentExtras&, double, int)’: Alignment.cc:423:33: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized] 423 | centroid.addExpectedCounts(start2, isForward, probMat, gap, alph.size, | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 424 | subsCounts, tranCounts); | ~~~~~~~~~~~~~~~~~~~~~~~ Alignment.cc:282:11: note: ‘tranCounts’ was declared here 282 | double *tranCounts; | ^~~~~~~~~~ g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o Centroid.o5 Centroid.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o DiagonalTable.o5 DiagonalTable.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o SegmentPair.o5 SegmentPair.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o SegmentPairPot.o5 SegmentPairPot.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o SubsetSuffixArraySearch.o5 SubsetSuffixArraySearch.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o lastal.o5 lastal.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o split/cbrc_split_aligner.o5 split/cbrc_split_aligner.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o split/mcf_last_splitter.o5 split/mcf_last_splitter.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o split/last-split.o5 split/last-split.cc cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -msse2 -c -o last-merge-batches.o last-merge-batches.c g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o last-pair-probs.o last-pair-probs.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o last-pair-probs-main.o last-pair-probs-main.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o LastdbArguments.o LastdbArguments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/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_aligment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.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 split/cbrc_split_aligner.o split/mcf_last_splitter.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/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_options.o split/last-split-main.o MultiSequence.o split/cbrc_split_aligner.o split/mcf_last_splitter.o split/last-split.o alp/sls_alp_data.hpp:101:36: warning: type ‘struct array_positive’ violates the C++ One Definition Rule [-Wodr] 101 | template class array_positive{ | ^ alp/sls_fsa1_utils.hpp:555:36: note: a different type is defined in another translation unit 555 | template class array_positive{ | ^ alp/sls_alp_data.hpp:163:27: note: the first difference of corresponding definitions is field ‘d_alp_data’ 163 | alp_data *d_alp_data;//initial data | ^ alp/sls_fsa1_utils.hpp:641:23: note: a field with different name is defined in another translation unit 641 | void *d_fsa;//initial data | ^ alp/sls_alp_data.hpp:101:36: warning: type ‘struct array_positive’ violates the C++ One Definition Rule [-Wodr] 101 | template class array_positive{ | ^ alp/sls_fsa1_utils.hpp:555:36: note: a different type is defined in another translation unit 555 | template class array_positive{ | ^ alp/sls_alp_data.hpp:163:27: note: the first difference of corresponding definitions is field ‘d_alp_data’ 163 | alp_data *d_alp_data;//initial data | ^ alp/sls_fsa1_utils.hpp:641:23: note: a field with different name is defined in another translation unit 641 | void *d_fsa;//initial data | ^ alp/sls_alp_sim.hpp:54:16: warning: type ‘struct struct_for_lambda_calculation’ violates the C++ One Definition Rule [-Wodr] 54 | struct struct_for_lambda_calculation | ^ alp/sls_fsa1_parameters.hpp:47:16: note: a different type is defined in another translation unit 47 | struct struct_for_lambda_calculation | ^ alp/sls_alp_sim.hpp:64:22: note: the first difference of corresponding definitions is field ‘d_calculate_alp_number’ 64 | bool d_calculate_alp_number; | ^ alp/sls_fsa1_parameters.hpp:57:24: note: a field with different name is defined in another translation unit 57 | double d_before_last_sum; | ^ In file included from Centroid.hh:9, from Alignment.hh:8, from AlignmentPot.hh:8, from lastal.cc:14: In member function ‘cbrc::SegmentPair::end2() const’, inlined from ‘alignGapless1(LastAligner&, cbrc::SegmentPairPot&, cbrc::MultiSequence const&, SeqData const&, Dispatcher const&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, cbrc::SubsetSuffixArray const&, unsigned char const*, unsigned int)’ at lastal.cc:641:21: SegmentPair.hh:36:40: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 36 | indexT end2() const{ return start2 + size; } // end in sequence 2 | ^~~~ lastal.cc: In function ‘alignGapless1(LastAligner&, cbrc::SegmentPairPot&, cbrc::MultiSequence const&, SeqData const&, Dispatcher const&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, cbrc::SubsetSuffixArray const&, unsigned char const*, unsigned int)’: lastal.cc:637:22: note: ‘fwdLen’ was declared here 637 | size_t revLen, fwdLen; | ^~~~~~ lastal.cc:640:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:14: note: ‘revLen’ was declared here 637 | size_t revLen, fwdLen; | ^~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split5-sse2 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/last-split-main.o MultiSequence.o5 split/cbrc_split_aligner.o5 split/mcf_last_splitter.o5 split/last-split.o5 lastal.cc: In function ‘alignGapless1’: lastal.cc:640:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:14: note: ‘revLen’ was declared here 637 | size_t revLen, fwdLen; | ^ lastal.cc:640:78: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:22: note: ‘fwdLen’ was declared here 637 | size_t revLen, fwdLen; | ^ GappedXdropAlignerDna.cc: In function ‘simdChoose1’: GappedXdropAlignerDna.cc:104:34: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 104 | SimdUint1 s = simdChoose1(scorer4x4, j); | ^ cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -msse2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-merge-batches-sse2 last-merge-batches.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-pair-probs-sse2 last-pair-probs.o last-pair-probs-main.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/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 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastdb5-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.o5 MultiSequenceQual.o5 SubsetSuffixArray.o5 SubsetSuffixArraySort.o5 lastdb.o5 -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastal5-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_aligment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.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.o5 AlignmentPot.o5 AlignmentWrite.o5 Centroid.o5 DiagonalTable.o5 MultiSequence.o5 MultiSequenceQual.o5 SegmentPair.o5 SegmentPairPot.o5 SubsetSuffixArray.o5 SubsetSuffixArraySearch.o5 lastal.o5 split/cbrc_split_aligner.o5 split/mcf_last_splitter.o5 -lz alp/sls_alp_data.hpp:101:36: warning: type ‘struct array_positive’ violates the C++ One Definition Rule [-Wodr] 101 | template class array_positive{ | ^ alp/sls_fsa1_utils.hpp:555:36: note: a different type is defined in another translation unit 555 | template class array_positive{ | ^ alp/sls_alp_data.hpp:163:27: note: the first difference of corresponding definitions is field ‘d_alp_data’ 163 | alp_data *d_alp_data;//initial data | ^ alp/sls_fsa1_utils.hpp:641:23: note: a field with different name is defined in another translation unit 641 | void *d_fsa;//initial data | ^ alp/sls_alp_data.hpp:101:36: warning: type ‘struct array_positive’ violates the C++ One Definition Rule [-Wodr] 101 | template class array_positive{ | ^ alp/sls_fsa1_utils.hpp:555:36: note: a different type is defined in another translation unit 555 | template class array_positive{ | ^ alp/sls_alp_data.hpp:163:27: note: the first difference of corresponding definitions is field ‘d_alp_data’ 163 | alp_data *d_alp_data;//initial data | ^ alp/sls_fsa1_utils.hpp:641:23: note: a field with different name is defined in another translation unit 641 | void *d_fsa;//initial data | ^ alp/sls_alp_sim.hpp:54:16: warning: type ‘struct struct_for_lambda_calculation’ violates the C++ One Definition Rule [-Wodr] 54 | struct struct_for_lambda_calculation | ^ alp/sls_fsa1_parameters.hpp:47:16: note: a different type is defined in another translation unit 47 | struct struct_for_lambda_calculation | ^ alp/sls_alp_sim.hpp:64:22: note: the first difference of corresponding definitions is field ‘d_calculate_alp_number’ 64 | bool d_calculate_alp_number; | ^ alp/sls_fsa1_parameters.hpp:57:24: note: a field with different name is defined in another translation unit 57 | double d_before_last_sum; | ^ In member function ‘addExpectedCounts’, inlined from ‘extend.constprop.isra’ at Alignment.cc:423:33: Centroid.cc:606:23: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized] 606 | transitionCounts[2] += insCount; // inserted letter count | ^ Alignment.cc: In member function ‘extend.constprop.isra’: Alignment.cc:282:11: note: ‘tranCounts’ was declared here 282 | double *tranCounts; | ^ lastal.cc: In function ‘alignGapless1’: lastal.cc:640:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:14: note: ‘revLen’ was declared here 637 | size_t revLen, fwdLen; | ^ In member function ‘end2’, inlined from ‘alignGapless1’ at lastal.cc:641:21: SegmentPair.hh:36:40: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 36 | indexT end2() const{ return start2 + size; } // end in sequence 2 | ^ lastal.cc: In function ‘alignGapless1’: lastal.cc:637:22: note: ‘fwdLen’ was declared here 637 | size_t revLen, fwdLen; | ^ GappedXdropAlignerDna.cc: In function ‘simdChoose1’: GappedXdropAlignerDna.cc:104:34: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 104 | SimdUint1 s = simdChoose1(scorer4x4, j); | ^ In member function ‘addExpectedCounts’, inlined from ‘extend.constprop.isra’ at Alignment.cc:423:33: Centroid.cc:606:23: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized] 606 | transitionCounts[2] += insCount; // inserted letter count | ^ Alignment.cc: In member function ‘extend.constprop.isra’: Alignment.cc:282:11: note: ‘tranCounts’ was declared here 282 | double *tranCounts; | ^ make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' dh_auto_build -- all SFX=-plain CFLAGS="-g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1" CXXFLAGS="-g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3" make -j4 "INSTALL=install --strip-program=true" all SFX=-plain "CFLAGS=-g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1" "CXXFLAGS=-g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3" make[2]: Entering directory '/<>' make[3]: Entering directory '/<>/src' g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o Alphabet.o Alphabet.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o CyclicSubsetSeed.o CyclicSubsetSeed.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o LambdaCalculator.o LambdaCalculator.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o ScoreMatrix.o ScoreMatrix.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o SubsetMinimizerFinder.o SubsetMinimizerFinder.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o TantanMasker.o TantanMasker.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o dna_words_finder.o dna_words_finder.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -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_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o cbrc_linalg.o cbrc_linalg.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o mcf_substitution_matrix_stats.o mcf_substitution_matrix_stats.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o tantan.o tantan.cc echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1447) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" | cmp -s version.hh - || echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1447) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" > version.hh g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o MultiSequence.o MultiSequence.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from tantan.cc:4: /usr/include/simde/x86/avx.h: In function ‘__vector(4) double simde__m256d_from_private(simde__m256d_private)’: /usr/include/simde/x86/avx.h:290:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 290 | simde__m256d_from_private(simde__m256d_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o lastdb.o lastdb.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o LastalArguments.o LastalArguments.cc lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int)’: lastdb.cc:343:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual] 343 | std::cout.write((char *)m.qualityReader() + m.seqBeg(i), m.seqLen(i)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -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:52, 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:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | 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:52, 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:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -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:52, 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:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | 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:52, 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:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o mcf_aligment_path_adder.o mcf_aligment_path_adder.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -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:52, 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:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o GeneticCode.o GeneticCode.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o GreedyXdropAligner.o GreedyXdropAligner.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o LastEvaluer.o LastEvaluer.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o OneQualityScoreMatrix.o OneQualityScoreMatrix.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o QualityPssmMaker.o QualityPssmMaker.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o TwoQualityScoreMatrix.o TwoQualityScoreMatrix.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o split/cbrc_unsplit_alignment.o split/cbrc_unsplit_alignment.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o split/last_split_options.o split/last_split_options.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_alp.o alp/sls_alp.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_basic.o alp/sls_basic.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/njn_localmaxstatutil.o alp/njn_localmaxstatutil.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/njn_dynprogprob.o alp/njn_dynprogprob.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/njn_dynprogprobproto.o alp/njn_dynprogprobproto.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/njn_dynprogproblim.o alp/njn_dynprogproblim.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/njn_ioutil.o alp/njn_ioutil.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/njn_random.o alp/njn_random.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_falp_alignment_evaluer.o alp/sls_falp_alignment_evaluer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_fsa1_pvalues.o alp/sls_fsa1_pvalues.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_fsa1_utils.o alp/sls_fsa1_utils.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_fsa1_parameters.o alp/sls_fsa1_parameters.cpp g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o Alignment.o Alignment.cc Alignment.cc: In member function ‘cbrc::Alignment::extend(std::vector >&, std::vector >&, cbrc::Aligners&, bool, bool, mcf::BigSeq, unsigned char const*, unsigned long, unsigned long, bool, int, int const (*) [66], int, int, double const* const*, double, int, mcf::GapCosts const&, unsigned long, int const (*) [66], cbrc::TwoQualityScoreMatrix const&, unsigned char const*, unsigned char const*, cbrc::Alphabet const&, cbrc::AlignmentExtras&, double, int)’: Alignment.cc:423:33: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized] 423 | centroid.addExpectedCounts(start2, isForward, probMat, gap, alph.size, | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 424 | subsCounts, tranCounts); | ~~~~~~~~~~~~~~~~~~~~~~~ Alignment.cc:282:11: note: ‘tranCounts’ was declared here 282 | double *tranCounts; | ^~~~~~~~~~ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o AlignmentPot.o AlignmentPot.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o AlignmentWrite.o AlignmentWrite.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o Centroid.o Centroid.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o DiagonalTable.o DiagonalTable.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o SegmentPair.o SegmentPair.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o SegmentPairPot.o SegmentPairPot.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o SubsetSuffixArraySearch.o SubsetSuffixArraySearch.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o lastal.o lastal.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o split/cbrc_split_aligner.o split/cbrc_split_aligner.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o split/mcf_last_splitter.o split/mcf_last_splitter.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o split/last-split-main.o split/last-split-main.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o split/last-split.o split/last-split.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o MultiSequence.o5 MultiSequence.cc lastal.cc: In function ‘alignGapless1(LastAligner&, cbrc::SegmentPairPot&, cbrc::MultiSequence const&, SeqData const&, Dispatcher const&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, cbrc::SubsetSuffixArray const&, unsigned char const*, unsigned int)’: lastal.cc:640:78: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:22: note: ‘fwdLen’ was declared here 637 | size_t revLen, fwdLen; | ^~~~~~ lastal.cc:640:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:14: note: ‘revLen’ was declared here 637 | size_t revLen, fwdLen; | ^~~~~~ g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o MultiSequenceQual.o5 MultiSequenceQual.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o SubsetSuffixArray.o5 SubsetSuffixArray.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o SubsetSuffixArraySort.o5 SubsetSuffixArraySort.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o lastdb.o5 lastdb.cc lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int)’: lastdb.cc:343:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual] 343 | std::cout.write((char *)m.qualityReader() + m.seqBeg(i), m.seqLen(i)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o Alignment.o5 Alignment.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o AlignmentPot.o5 AlignmentPot.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o AlignmentWrite.o5 AlignmentWrite.cc Alignment.cc: In member function ‘cbrc::Alignment::extend(std::vector >&, std::vector >&, cbrc::Aligners&, bool, bool, mcf::BigSeq, unsigned char const*, unsigned long, unsigned long, bool, int, int const (*) [66], int, int, double const* const*, double, int, mcf::GapCosts const&, unsigned long, int const (*) [66], cbrc::TwoQualityScoreMatrix const&, unsigned char const*, unsigned char const*, cbrc::Alphabet const&, cbrc::AlignmentExtras&, double, int)’: Alignment.cc:423:33: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized] 423 | centroid.addExpectedCounts(start2, isForward, probMat, gap, alph.size, | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 424 | subsCounts, tranCounts); | ~~~~~~~~~~~~~~~~~~~~~~~ Alignment.cc:282:11: note: ‘tranCounts’ was declared here 282 | double *tranCounts; | ^~~~~~~~~~ g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o Centroid.o5 Centroid.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o DiagonalTable.o5 DiagonalTable.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o SegmentPair.o5 SegmentPair.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o SegmentPairPot.o5 SegmentPairPot.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o SubsetSuffixArraySearch.o5 SubsetSuffixArraySearch.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o lastal.o5 lastal.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o split/cbrc_split_aligner.o5 split/cbrc_split_aligner.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o split/mcf_last_splitter.o5 split/mcf_last_splitter.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o split/last-split.o5 split/last-split.cc cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -c -o last-merge-batches.o last-merge-batches.c g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o last-pair-probs.o last-pair-probs.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o last-pair-probs-main.o last-pair-probs-main.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o LastdbArguments.o LastdbArguments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastal-plain 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_aligment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.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 split/cbrc_split_aligner.o split/mcf_last_splitter.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split-plain Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/last-split-main.o MultiSequence.o split/cbrc_split_aligner.o split/mcf_last_splitter.o split/last-split.o alp/sls_alp_data.hpp:101:36: warning: type ‘struct array_positive’ violates the C++ One Definition Rule [-Wodr] 101 | template class array_positive{ | ^ alp/sls_fsa1_utils.hpp:555:36: note: a different type is defined in another translation unit 555 | template class array_positive{ | ^ alp/sls_alp_data.hpp:163:27: note: the first difference of corresponding definitions is field ‘d_alp_data’ 163 | alp_data *d_alp_data;//initial data | ^ alp/sls_fsa1_utils.hpp:641:23: note: a field with different name is defined in another translation unit 641 | void *d_fsa;//initial data | ^ alp/sls_alp_data.hpp:101:36: warning: type ‘struct array_positive’ violates the C++ One Definition Rule [-Wodr] 101 | template class array_positive{ | ^ alp/sls_fsa1_utils.hpp:555:36: note: a different type is defined in another translation unit 555 | template class array_positive{ | ^ alp/sls_alp_data.hpp:163:27: note: the first difference of corresponding definitions is field ‘d_alp_data’ 163 | alp_data *d_alp_data;//initial data | ^ alp/sls_fsa1_utils.hpp:641:23: note: a field with different name is defined in another translation unit 641 | void *d_fsa;//initial data | ^ alp/sls_alp_sim.hpp:54:16: warning: type ‘struct struct_for_lambda_calculation’ violates the C++ One Definition Rule [-Wodr] 54 | struct struct_for_lambda_calculation | ^ alp/sls_fsa1_parameters.hpp:47:16: note: a different type is defined in another translation unit 47 | struct struct_for_lambda_calculation | ^ alp/sls_alp_sim.hpp:64:22: note: the first difference of corresponding definitions is field ‘d_calculate_alp_number’ 64 | bool d_calculate_alp_number; | ^ alp/sls_fsa1_parameters.hpp:57:24: note: a field with different name is defined in another translation unit 57 | double d_before_last_sum; | ^ In file included from Centroid.hh:9, from Alignment.hh:8, from AlignmentPot.hh:8, from lastal.cc:14: In member function ‘cbrc::SegmentPair::end2() const’, inlined from ‘alignGapless1(LastAligner&, cbrc::SegmentPairPot&, cbrc::MultiSequence const&, SeqData const&, Dispatcher const&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, cbrc::SubsetSuffixArray const&, unsigned char const*, unsigned int)’ at lastal.cc:641:21: SegmentPair.hh:36:40: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 36 | indexT end2() const{ return start2 + size; } // end in sequence 2 | ^~~~ lastal.cc: In function ‘alignGapless1(LastAligner&, cbrc::SegmentPairPot&, cbrc::MultiSequence const&, SeqData const&, Dispatcher const&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, cbrc::SubsetSuffixArray const&, unsigned char const*, unsigned int)’: lastal.cc:637:22: note: ‘fwdLen’ was declared here 637 | size_t revLen, fwdLen; | ^~~~~~ lastal.cc:640:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:14: note: ‘revLen’ was declared here 637 | size_t revLen, fwdLen; | ^~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split5-plain Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/last-split-main.o MultiSequence.o5 split/cbrc_split_aligner.o5 split/mcf_last_splitter.o5 split/last-split.o5 lastal.cc: In function ‘alignGapless1’: lastal.cc:640:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:14: note: ‘revLen’ was declared here 637 | size_t revLen, fwdLen; | ^ lastal.cc:640:78: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:22: note: ‘fwdLen’ was declared here 637 | size_t revLen, fwdLen; | ^ GappedXdropAlignerDna.cc: In function ‘simdChoose1’: GappedXdropAlignerDna.cc:104:34: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 104 | SimdUint1 s = simdChoose1(scorer4x4, j); | ^ cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-merge-batches-plain last-merge-batches.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-pair-probs-plain last-pair-probs.o last-pair-probs-main.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastdb-plain 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 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastdb5-plain 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.o5 MultiSequenceQual.o5 SubsetSuffixArray.o5 SubsetSuffixArraySort.o5 lastdb.o5 -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/last-align-1447-1 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastal5-plain 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_aligment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.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.o5 AlignmentPot.o5 AlignmentWrite.o5 Centroid.o5 DiagonalTable.o5 MultiSequence.o5 MultiSequenceQual.o5 SegmentPair.o5 SegmentPairPot.o5 SubsetSuffixArray.o5 SubsetSuffixArraySearch.o5 lastal.o5 split/cbrc_split_aligner.o5 split/mcf_last_splitter.o5 -lz alp/sls_alp_data.hpp:101:36: warning: type ‘struct array_positive’ violates the C++ One Definition Rule [-Wodr] 101 | template class array_positive{ | ^ alp/sls_fsa1_utils.hpp:555:36: note: a different type is defined in another translation unit 555 | template class array_positive{ | ^ alp/sls_alp_data.hpp:163:27: note: the first difference of corresponding definitions is field ‘d_alp_data’ 163 | alp_data *d_alp_data;//initial data | ^ alp/sls_fsa1_utils.hpp:641:23: note: a field with different name is defined in another translation unit 641 | void *d_fsa;//initial data | ^ alp/sls_alp_data.hpp:101:36: warning: type ‘struct array_positive’ violates the C++ One Definition Rule [-Wodr] 101 | template class array_positive{ | ^ alp/sls_fsa1_utils.hpp:555:36: note: a different type is defined in another translation unit 555 | template class array_positive{ | ^ alp/sls_alp_data.hpp:163:27: note: the first difference of corresponding definitions is field ‘d_alp_data’ 163 | alp_data *d_alp_data;//initial data | ^ alp/sls_fsa1_utils.hpp:641:23: note: a field with different name is defined in another translation unit 641 | void *d_fsa;//initial data | ^ alp/sls_alp_sim.hpp:54:16: warning: type ‘struct struct_for_lambda_calculation’ violates the C++ One Definition Rule [-Wodr] 54 | struct struct_for_lambda_calculation | ^ alp/sls_fsa1_parameters.hpp:47:16: note: a different type is defined in another translation unit 47 | struct struct_for_lambda_calculation | ^ alp/sls_alp_sim.hpp:64:22: note: the first difference of corresponding definitions is field ‘d_calculate_alp_number’ 64 | bool d_calculate_alp_number; | ^ alp/sls_fsa1_parameters.hpp:57:24: note: a field with different name is defined in another translation unit 57 | double d_before_last_sum; | ^ In member function ‘addExpectedCounts’, inlined from ‘extend.constprop.isra’ at Alignment.cc:423:33: Centroid.cc:606:23: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized] 606 | transitionCounts[2] += insCount; // inserted letter count | ^ Alignment.cc: In member function ‘extend.constprop.isra’: Alignment.cc:282:11: note: ‘tranCounts’ was declared here 282 | double *tranCounts; | ^ lastal.cc: In function ‘alignGapless1’: lastal.cc:640:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 640 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:637:14: note: ‘revLen’ was declared here 637 | size_t revLen, fwdLen; | ^ In member function ‘end2’, inlined from ‘alignGapless1’ at lastal.cc:641:21: SegmentPair.hh:36:40: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 36 | indexT end2() const{ return start2 + size; } // end in sequence 2 | ^ lastal.cc: In function ‘alignGapless1’: lastal.cc:637:22: note: ‘fwdLen’ was declared here 637 | size_t revLen, fwdLen; | ^ GappedXdropAlignerDna.cc: In function ‘simdChoose1’: GappedXdropAlignerDna.cc:104:34: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 104 | SimdUint1 s = simdChoose1(scorer4x4, j); | ^ In member function ‘addExpectedCounts’, inlined from ‘extend.constprop.isra’ at Alignment.cc:423:33: Centroid.cc:606:23: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized] 606 | transitionCounts[2] += insCount; // inserted letter count | ^ Alignment.cc: In member function ‘extend.constprop.isra’: Alignment.cc:282:11: note: ‘tranCounts’ was declared here 282 | double *tranCounts; | ^ make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_install debian/bin/simd-dispatch /usr/lib/last-align/ dh_install bin/lastdb-* bin/lastal-* bin/last-split-* bin/last-merge-batches-* bin/last-pair-probs-* bin/lastdb5-* bin/lastal5-* bin/last-split5-* usr/lib/last-align dh_install bin/fastq-* bin/fasta-* bin/last-dotplot bin/last-map-probs bin/last-postmask bin/last-train bin/maf-* bin/parallel-fast* usr/bin mkdir -p /<>/debian/last-align/usr/bin cd /<>/debian/last-align/usr/bin \ && for prog in lastdb lastal last-split last-merge-batches last-pair-probs lastdb5 lastal5 last-split5 ; do \ ln -s ../lib/last-align/simd-dispatch ${prog} ; done make[1]: Leaving directory '/<>' dh_installdocs dh_installchangelogs dh_installexamples debian/rules override_dh_installman make[1]: Entering directory '/<>' dh_installman help2man --no-info --version-string="1447" \ --name='make a dotplot, a.k.a. Oxford Grid, of alignments in LAST tabular format' \ /<>/bin/last-dotplot > /<>/debian/last-align/usr/share/man/man1/last-dotplot.1 help2man --no-info --version-string="1447" \ --name="genome-scale comparison of biological sequences" \ --help-option="-h" \ /<>/debian/last-align/usr/bin/lastal > /<>/debian/last-align/usr/share/man/man1/lastal.1 help2man --no-info --version-string="1447" \ --name="genome-scale comparison of biological sequences" \ --help-option="-h" \ /<>/debian/last-align/usr/bin/lastal5 > /<>/debian/last-align/usr/share/man/man1/lastal5.1 # help2man output needs manual postprocessing - see debian/mans #help2man --no-info --version-string="1447" \ # --name="genome-scale comparison of biological sequences" \ # --help-option="-h" \ # /<>/debian/last-align/usr/bin/lastdb > /<>/debian/last-align/usr/share/man/man1/lastdb.1 help2man --no-info --version-string="1447" \ --name="Sort MAF-format alignments by sequence name" \ /<>/bin/maf-sort > /<>/debian/last-align/usr/share/man/man1/maf-sort.1 help2man --no-info --version-string="1447" \ --name="changes the order of the sequences in MAF-format alignments" \ /<>/bin/maf-swap > /<>/debian/last-align/usr/share/man/man1/maf-swap.1 # help2man output needs manual postprocessing - see debian/mans #help2man --no-info --version-string="1447" \ # --name="Add extra column with mapping probabilities" \ # /<>/bin/last-map-probs > /<>/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="1447" \ # --name="Read files of lastal output, merge corresponding batches, and write them." \ # /<>/bin/last-merge-batches > /<>/debian/last-align/usr/share/man/man1/last-merge-batches.1 # # These bin were droped #help2man --no-info --version-string="1447" \ # --name="Clean up MAF-format alignments" \ # /<>/bin/last-reduce-alignments > /<>/debian/last-align/usr/share/man/man1/last-reduce-alignments.1 #help2man --no-info --version-string="1447" \ # --name='Remove MAF-format alignments which are "dominated" by others' \ # /<>/bin/last-remove-dominated > /<>/debian/last-align/usr/share/man/man1/last-remove-dominated.1 help2man --no-info --version-string="1447" \ --name='Estimates "split" or "spliced" alignments.' \ /<>/debian/last-align/usr/bin/last-split > /<>/debian/last-align/usr/share/man/man1/last-split.1 help2man --no-info --version-string="1447" \ --name='Estimates "split" or "spliced" alignments.' \ /<>/debian/last-align/usr/bin/last-split5 > /<>/debian/last-align/usr/share/man/man1/last-split5.1 help2man --no-info --version-string="1447" \ --name="Join two or more sets of MAF-format multiple alignments" \ /<>/bin/maf-join > /<>/debian/last-align/usr/share/man/man1/maf-join.1 help2man --no-info --version-string="1447" \ --help-option="-h" \ /<>/bin/maf-cut > /<>/debian/last-align/usr/share/man/man1/maf-cut.1 help2man --no-info --version-string="1447" \ --name="Convert MAF-format alignments to tabular format" \ /<>/bin/maf-convert > /<>/debian/last-align/usr/share/man/man1/maf-convert.1 help2man --no-info --version-string="1447" \ --name="Read 2 fastq files, and write them interleaved" \ /<>/bin/fastq-interleave > /<>/debian/last-align/usr/share/man/man1/fastq-interleave.1 help2man --no-info --version-string="1447" \ --name="Read files of lastal output, merge corresponding batches, and write them" \ /<>/debian/last-align/usr/bin/last-merge-batches > /<>/debian/last-align/usr/share/man/man1/last-merge-batches.1 # help2man output needs manual postprocessing - see debian/mans #help2man --no-info --version-string="1447" \ # --name="Read alignments of paired DNA reads to a genome, and do estimations" \ # /<>/debian/last-align/usr/bin/last-pair-probs > /<>/debian/last-align/usr/share/man/man1/last-pair-probs.1 help2man --no-info --version-string="1447" \ --name="Get alignments that have a segment with score >= threshold, with gentle masking of lowercase letters" \ /<>/bin/last-postmask > /<>/debian/last-align/usr/share/man/man1/last-postmask.1 help2man --no-info --version-string="1447" \ --name="Try to find suitable score parameters for aligning the given sequences" \ /<>/bin/last-train > /<>/debian/last-align/usr/share/man/man1/last-train.1 help2man --no-info --version-string="1447" \ --name="Keep the first of identical sequences" \ --help-option="-h" \ /<>/debian/last-align/usr/bin/fasta-nr > /<>/debian/last-align/usr/share/man/man1/fasta-nr.1 make[1]: Leaving directory '/<>' dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a debugedit: debian/last-align/usr/lib/last-align/lastal5-sse4.1: Unknown DWARF DW_FORM_0x1f20 6ec4947abf5489d3ea302c15136f9da70d8258fb debugedit: debian/last-align/usr/lib/last-align/lastdb5-sse4.1: Unknown DWARF DW_FORM_0x1f20 4a325a3a73fe0b48555b956acab1419a580da2dd debugedit: debian/last-align/usr/lib/last-align/last-split-plain: Unknown DWARF DW_FORM_0x1f21 adc51221564a1dc42e3a9f670528487ee7a664a1 debugedit: debian/last-align/usr/lib/last-align/last-merge-batches-plain: Unknown DWARF DW_FORM_0x1f20 5e9eb1c31fe30f6add328dbbac5a152b93ee7290 debugedit: debian/last-align/usr/lib/last-align/lastal-avx: Unknown DWARF DW_FORM_0x1f21 1ee0ece2185bff01e20d98d9cf4fa94598025817 debugedit: debian/last-align/usr/lib/last-align/lastdb-avx: Unknown DWARF DW_FORM_0x1f21 80be6613ab5b35401d5a7354b4c2919bc983e558 debugedit: debian/last-align/usr/lib/last-align/last-merge-batches-sse4.1: Unknown DWARF DW_FORM_0x1f20 fab28caed00067f94992ddcb26d0ee0f92ba2263 debugedit: debian/last-align/usr/lib/last-align/lastdb5-plain: Unknown DWARF DW_FORM_0x1f20 32ae5b4ba49099092bdc95dba446f7b066de1a22 debugedit: debian/last-align/usr/lib/last-align/last-split5-sse3: Unknown DWARF DW_FORM_0x1f21 cafe848536ba4930ec852df66be58b7027f6ec1b debugedit: debian/last-align/usr/lib/last-align/lastal-sse3: Unknown DWARF DW_FORM_0x1f21 80aa470e64c4bb952ccd50374d93bbf164a1666f debugedit: debian/last-align/usr/lib/last-align/last-merge-batches-ssse3: Unknown DWARF DW_FORM_0x1f20 b9258fdab73daa715534c0ed1644f751118c39a7 debugedit: debian/last-align/usr/lib/last-align/lastdb5-ssse3: Unknown DWARF DW_FORM_0x1f20 113f16129aa74c0b5963112f09109d0c5dfdaa34 debugedit: debian/last-align/usr/lib/last-align/lastal5-sse3: Unknown DWARF DW_FORM_0x1f20 243363e861523db9c8c56f17d5dcb3272e37df06 debugedit: debian/last-align/usr/lib/last-align/lastal-plain: Unknown DWARF DW_FORM_0x1f20 efb93e06cc550b96287628004892dd6ad016aa6c debugedit: debian/last-align/usr/lib/last-align/lastal5-sse2: Unknown DWARF DW_FORM_0x1f21 48fc8cb6b1ccd4a15826b134a6e9294624489ef9 debugedit: debian/last-align/usr/lib/last-align/last-split5-sse2: Unknown DWARF DW_FORM_0x1f21 281bcfca0d99eaf77b4aaf555cd49abf0be22cc9 debugedit: debian/last-align/usr/lib/last-align/lastdb-sse4.1: Unknown DWARF DW_FORM_0x1f20 6de1ef5a645e0c9fe93cce7cf0e527d1933cf73b debugedit: debian/last-align/usr/lib/last-align/last-pair-probs-sse4.1: Unknown DWARF DW_FORM_0x1f20 a187f995a9389d6ad41d129d2d01d131bd6718fb debugedit: debian/last-align/usr/lib/last-align/last-split-avx: Unknown DWARF DW_FORM_0x1f21 3eba0ec277de8e8c44093641f19cbcc87d2a8108 debugedit: debian/last-align/usr/lib/last-align/last-split5-sse4.1: Unknown DWARF DW_FORM_0x1f21 113a76f6d1f63e297aed3e641520e6490eb2bb5e debugedit: debian/last-align/usr/lib/last-align/lastdb5-sse2: Unknown DWARF DW_FORM_0x1f20 3adc9cfe04489e9efea7db53289c350e2d1f17d6 debugedit: debian/last-align/usr/lib/last-align/lastal-sse2: Unknown DWARF DW_FORM_0x1f20 bbdb1c1cd5ce121efce8bdc73fa3f3eaf7784597 debugedit: debian/last-align/usr/lib/last-align/lastdb-ssse3: Unknown DWARF DW_FORM_0x1f20 718be18e35969479121b90f95135ad1eb33081ea debugedit: debian/last-align/usr/lib/last-align/lastal-sse4.1: Unknown DWARF DW_FORM_0x1f21 01c72bf98ad7f44c716d7ad9156df161e3c37f61 debugedit: debian/last-align/usr/lib/last-align/last-split5-plain: Unknown DWARF DW_FORM_0x1f21 95bc40453dbbf5ee24ada1b027520a0ed64f772c debugedit: debian/last-align/usr/lib/last-align/lastal5-avx2: Unknown DWARF DW_FORM_0x1f20 697e0ccbbb12110b5ca428ea3265fb9033db091a debugedit: debian/last-align/usr/lib/last-align/last-split-ssse3: Unknown DWARF DW_FORM_0x1f21 045dce7c9ac9b501aa998541a2955de9a1f9d8e4 debugedit: debian/last-align/usr/lib/last-align/lastal5-avx: Unknown DWARF DW_FORM_0x1f20 d892564471c62b0e74978c5ccfd38bace7d50e4a debugedit: debian/last-align/usr/lib/last-align/last-pair-probs-sse2: Unknown DWARF DW_FORM_0x1f20 b9cee2e7f8468fa6ba8f6f06b955bd5056fa4d71 debugedit: debian/last-align/usr/lib/last-align/last-split-sse2: Unknown DWARF DW_FORM_0x1f21 68dbda6bb8c60a2a139251ae0859001deacced1a debugedit: debian/last-align/usr/lib/last-align/lastdb5-avx2: Unknown DWARF DW_FORM_0x1f20 36ffc8c2fda1a165c6fcd30f99d9f1b2ed2ed513 debugedit: debian/last-align/usr/lib/last-align/lastdb5-avx: Unknown DWARF DW_FORM_0x1f20 231ce33314308c1640c82f8040a721c5a9db4782 debugedit: debian/last-align/usr/lib/last-align/last-split-avx2: Unknown DWARF DW_FORM_0x1f21 149532427bbc1edf673d80933650039a92986d41 debugedit: debian/last-align/usr/lib/last-align/lastal-ssse3: Unknown DWARF DW_FORM_0x1f21 51baad750a9352024b6ae8d4e670242e99e585c7 debugedit: debian/last-align/usr/lib/last-align/last-pair-probs-avx2: Unknown DWARF DW_FORM_0x1f20 99f79d05e7c09251cecad302df3c72e71b41152a debugedit: debian/last-align/usr/lib/last-align/last-split5-avx: Unknown DWARF DW_FORM_0x1f21 620f517895e5e5a91a12cce202929a212248b4ec debugedit: debian/last-align/usr/lib/last-align/last-split5-ssse3: Unknown DWARF DW_FORM_0x1f21 4197b6e6531fa9fdf9c117432b46371863a92cfa debugedit: debian/last-align/usr/lib/last-align/lastdb-sse2: Unknown DWARF DW_FORM_0x1f20 d6ee6756ff5618ae68a2743f8a7a5eba624d7eeb debugedit: debian/last-align/usr/lib/last-align/last-merge-batches-avx2: Unknown DWARF DW_FORM_0x1f20 5483424f14751bd23597f10db3b07da996a33e3e debugedit: debian/last-align/usr/lib/last-align/lastdb5-sse3: Unknown DWARF DW_FORM_0x1f20 1d5823f9c3d15d66e64c80646883ae3115515081 debugedit: debian/last-align/usr/lib/last-align/last-pair-probs-plain: Unknown DWARF DW_FORM_0x1f20 bc797206d6890127c1d17ce9bbfe0596902864d4 debugedit: debian/last-align/usr/lib/last-align/lastal-avx2: Unknown DWARF DW_FORM_0x1f21 dc8e10d1feb3fcc32302bb6209c8f0ecf436faa4 debugedit: debian/last-align/usr/lib/last-align/lastdb-avx2: Unknown DWARF DW_FORM_0x1f20 ecd3aa4974b0f46401a4374ffa9e70741550e54d debugedit: debian/last-align/usr/lib/last-align/lastal5-plain: Unknown DWARF DW_FORM_0x1f21 b1565fdc89116d34767c99e6ad1ae20051958678 debugedit: debian/last-align/usr/lib/last-align/last-pair-probs-ssse3: Unknown DWARF DW_FORM_0x1f20 30ccc5307931744fb8e0191cb0e5e8d53f91001f debugedit: debian/last-align/usr/lib/last-align/lastdb-plain: Unknown DWARF DW_FORM_0x1f20 91b7f80e60458d0a83675d4aa7feceef0a8b625a debugedit: debian/last-align/usr/lib/last-align/lastdb-sse3: Unknown DWARF DW_FORM_0x1f20 e5e62111b8fbd2147f8d929670dee9bc4c74392f debugedit: debian/last-align/usr/lib/last-align/last-pair-probs-avx: Unknown DWARF DW_FORM_0x1f20 bfad9a4db482ce0a84b469975946a3d1c9b910ac debugedit: debian/last-align/usr/lib/last-align/last-merge-batches-avx: Unknown DWARF DW_FORM_0x1f20 b4892d3bd72ac78a9554cf74cedb0e96a0828e54 debugedit: debian/last-align/usr/lib/last-align/last-pair-probs-sse3: Unknown DWARF DW_FORM_0x1f20 d4982d1a7f5393be0bb2c34efb3698c30993f9dc debugedit: debian/last-align/usr/lib/last-align/last-split-sse4.1: Unknown DWARF DW_FORM_0x1f21 8b5412422dfa97ccf5eae4a26ae4e1c24b683a1d debugedit: debian/last-align/usr/lib/last-align/last-merge-batches-sse3: Unknown DWARF DW_FORM_0x1f20 39e96cadf211a0c59a1b8221fc4976ac045f2333 debugedit: debian/last-align/usr/lib/last-align/last-split-sse3: Unknown DWARF DW_FORM_0x1f21 03fe471872aedeced10068fd89816be231b145cc debugedit: debian/last-align/usr/lib/last-align/lastal5-ssse3: Unknown DWARF DW_FORM_0x1f20 4f4d56960fdd1678ebde6c32de75c1cab247e214 debugedit: debian/last-align/usr/lib/last-align/last-merge-batches-sse2: Unknown DWARF DW_FORM_0x1f20 d6bef8cfc38be4221a254b287c12157edbd030c8 debugedit: debian/last-align/usr/lib/last-align/last-split5-avx2: Unknown DWARF DW_FORM_0x1f21 84242bafed14f5f192dc2ef9413d40008a9c0569 dh_makeshlibs -a dh_shlibdeps -a dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/<>' dh_gencontrol -- -VBuilt-Using="simde (= 0.7.4~rc1-1), " make[1]: Leaving directory '/<>' dh_md5sums dh_builddeb INFO: pkgstriptranslations version 151 INFO: pkgstriptranslations version 151 pkgstriptranslations: processing last-align (in debian/last-align); do_strip: , oemstrip: pkgstriptranslations: processing last-align-dbgsym (in debian/.debhelper/last-align/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/last-align/DEBIAN/control, package last-align, directory debian/last-align pkgstripfiles: Truncating usr/share/doc/last-align/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package last-align ... pkgstripfiles: No PNG files. dpkg-deb: building package 'last-align' in '../last-align_1447-1_amd64.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/last-align/dbgsym-root/DEBIAN/control, package last-align-dbgsym, directory debian/.debhelper/last-align/dbgsym-root dpkg-deb: building package 'last-align-dbgsym' in 'debian/.debhelper/scratch-space/build-last-align/last-align-dbgsym_1447-1_amd64.deb'. Renaming last-align-dbgsym_1447-1_amd64.deb to last-align-dbgsym_1447-1_amd64.ddeb dpkg-genbuildinfo --build=binary -O../last-align_1447-1_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../last-align_1447-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2023-02-06T05:39:28Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ last-align_1447-1_amd64.changes: -------------------------------- Format: 1.8 Date: Sun, 05 Feb 2023 21:03:18 +0100 Source: last-align Binary: last-align Built-For-Profiles: noudeb Architecture: amd64 Version: 1447-1 Distribution: lunar-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: last-align - genome-scale comparison of biological sequences Changes: last-align (1447-1) unstable; urgency=medium . * New upstream version Checksums-Sha1: 4fd735d7fd41f63b6196618dee396db0246c2e47 49186840 last-align-dbgsym_1447-1_amd64.ddeb 3a6e52b00af7a793c21dc44798219ac8f943d45a 7025 last-align_1447-1_amd64.buildinfo 2723289ab831f4d85bf5675b004013b49879f65a 2181762 last-align_1447-1_amd64.deb Checksums-Sha256: bbfb91799b76c1e376b4c1cdddc9d63d9ff729284022e267bf145b5831290aba 49186840 last-align-dbgsym_1447-1_amd64.ddeb ce392a3566e69e3bc52cb6a1bab4fbc7662a98faff836f9e4417cc31757869ba 7025 last-align_1447-1_amd64.buildinfo d7701bb54c506450125ab42abc2c6aee5dab88e8fb35003f2b501bcc5662873f 2181762 last-align_1447-1_amd64.deb Files: 78f342e9079e268e06bf05efad1d416b 49186840 debug optional last-align-dbgsym_1447-1_amd64.ddeb bcc64a369d40179d3050f4a9b5ed7792 7025 science optional last-align_1447-1_amd64.buildinfo 57020878af4620f47a3cb75d80e319d9 2181762 science optional last-align_1447-1_amd64.deb /<>/last-align_1447-1_amd64.changes.new could not be renamed to /<>/last-align_1447-1_amd64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: last-align Binary: last-align last-align-dbgsym Architecture: amd64 Version: 1447-1 Checksums-Md5: 78f342e9079e268e06bf05efad1d416b 49186840 last-align-dbgsym_1447-1_amd64.ddeb 57020878af4620f47a3cb75d80e319d9 2181762 last-align_1447-1_amd64.deb Checksums-Sha1: 4fd735d7fd41f63b6196618dee396db0246c2e47 49186840 last-align-dbgsym_1447-1_amd64.ddeb 2723289ab831f4d85bf5675b004013b49879f65a 2181762 last-align_1447-1_amd64.deb Checksums-Sha256: bbfb91799b76c1e376b4c1cdddc9d63d9ff729284022e267bf145b5831290aba 49186840 last-align-dbgsym_1447-1_amd64.ddeb d7701bb54c506450125ab42abc2c6aee5dab88e8fb35003f2b501bcc5662873f 2181762 last-align_1447-1_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Mon, 06 Feb 2023 05:39:28 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-11), autotools-dev (= 20220109.1), base-files (= 12.3ubuntu1), base-passwd (= 3.6.1), bash (= 5.2.15-2ubuntu1), binutils (= 2.40-2ubuntu1), binutils-common (= 2.40-2ubuntu1), binutils-x86-64-linux-gnu (= 2.40-2ubuntu1), bsdextrautils (= 2.38.1-4ubuntu1), bsdutils (= 1:2.38.1-4ubuntu1), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), coreutils (= 9.1-1ubuntu2), cpp (= 4:12.2.0-1ubuntu1), cpp-12 (= 12.2.0-14ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-9ubuntu1), debconf (= 1.5.82), debhelper (= 13.11.4ubuntu3), debianutils (= 5.7-0.4), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.8-4), dpkg (= 1.21.19ubuntu3), dpkg-dev (= 1.21.19ubuntu3), dwz (= 0.15-1), file (= 1:5.44-3), findutils (= 4.9.0-3ubuntu1), g++ (= 4:12.2.0-1ubuntu1), g++-12 (= 12.2.0-14ubuntu1), gcc (= 4:12.2.0-1ubuntu1), gcc-12 (= 12.2.0-14ubuntu1), gcc-12-base (= 12.2.0-14ubuntu1), gettext (= 0.21-11), gettext-base (= 0.21-11), grep (= 3.8-5), groff-base (= 1.22.4-9), gzip (= 1.12-1ubuntu1), help2man (= 1.49.3), hostname (= 3.23ubuntu2), init-system-helpers (= 1.65.2), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-3), libarchive-zip-perl (= 1.68-1), libasan8 (= 12.2.0-14ubuntu1), libatomic1 (= 12.2.0-14ubuntu1), libattr1 (= 1:2.5.1-4), libaudit-common (= 1:3.0.7-1.1), libaudit1 (= 1:3.0.7-1.1), libbinutils (= 2.40-2ubuntu1), libblkid1 (= 2.38.1-4ubuntu1), libbrotli1 (= 1.0.9-2build7), libbsd0 (= 0.11.7-2), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.37-0ubuntu1), libc-dev-bin (= 2.37-0ubuntu1), libc6 (= 2.37-0ubuntu1), libc6-dev 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2.38.1-4ubuntu1), xz-utils (= 5.4.1-0.1), zlib1g (= 1:1.2.13.dfsg-1ubuntu4), zlib1g-dev (= 1:1.2.13.dfsg-1ubuntu4) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1675627398" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ last-align_1447-1_amd64.deb --------------------------- new Debian package, version 2.0. size 2181762 bytes: control archive=4276 bytes. 1313 bytes, 26 lines control 9266 bytes, 131 lines md5sums Package: last-align Version: 1447-1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 20667 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.3.1), libstdc++6 (>= 11), zlib1g (>= 1:1.1.4), python3 Recommends: python3-pil, parallel Built-Using: simde (= 0.7.4~rc1-1) Section: science Priority: optional Homepage: https://gitlab.com/mcfrith/last Description: genome-scale comparison of biological sequences LAST is software for comparing and aligning sequences, typically DNA or protein sequences. LAST is similar to BLAST, but it copes better with very large amounts of sequence data. Here are two things LAST is good at: . * Comparing large (e.g. mammalian) genomes. * Mapping lots of sequence tags onto a genome. . The main technical innovation is that LAST finds initial matches based on their multiplicity, instead of using a fixed size (e.g. BLAST uses 10-mers). This allows one to map tags to genomes without repeat-masking, without becoming overwhelmed by repetitive hits. To find these variable-sized matches, it uses a suffix array (inspired by Vmatch). To achieve high sensitivity, it uses a discontiguous suffix array, analogous to spaced seeds. drwxr-xr-x root/root 0 2023-02-05 20:03 ./ drwxr-xr-x root/root 0 2023-02-05 20:03 ./usr/ drwxr-xr-x root/root 0 2023-02-05 20:03 ./usr/bin/ -rwxr-xr-x root/root 2586 2023-02-05 20:03 ./usr/bin/fasta-nr -rwxr-xr-x root/root 518 2023-01-30 05:09 ./usr/bin/fastq-interleave -rwxr-xr-x root/root 48302 2023-02-05 20:03 ./usr/bin/last-dotplot -rwxr-xr-x root/root 4905 2023-02-05 20:03 ./usr/bin/last-map-probs lrwxrwxrwx root/root 0 2023-02-05 20:03 ./usr/bin/last-merge-batches -> ../lib/last-align/simd-dispatch lrwxrwxrwx root/root 0 2023-02-05 20:03 ./usr/bin/last-pair-probs -> ../lib/last-align/simd-dispatch -rwxr-xr-x root/root 5538 2023-02-05 20:03 ./usr/bin/last-postmask lrwxrwxrwx root/root 0 2023-02-05 20:03 ./usr/bin/last-split -> ../lib/last-align/simd-dispatch lrwxrwxrwx root/root 0 2023-02-05 20:03 ./usr/bin/last-split5 -> ../lib/last-align/simd-dispatch -rwxr-xr-x root/root 39928 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+------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 524796 Build-Time: 438 Distribution: lunar-proposed Host Architecture: amd64 Install-Time: 11 Job: last-align_1447-1.dsc Machine Architecture: amd64 Package: last-align Package-Time: 451 Source-Version: 1447-1 Space: 524796 Status: successful Version: 1447-1 -------------------------------------------------------------------------------- Finished at 2023-02-06T05:39:28Z Build needed 00:07:31, 524796k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-25558855 Scanning for processes to kill in build PACKAGEBUILD-25558855