Fri Oct 24 08:29:19 UTC 2025 I: starting to build last-align/forky/amd64 on jenkins on '2025-10-24 08:29' Fri Oct 24 08:29:19 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_4/72586/console.log Fri Oct 24 08:29:19 UTC 2025 I: Downloading source for forky/last-align=1645-1 --2025-10-24 08:29:20-- http://deb.debian.org/debian/pool/main/l/last-align/last-align_1645-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1515 (1.5K) [text/prs.lines.tag] Saving to: ‘last-align_1645-1.dsc’ 0K . 100% 162M=0s 2025-10-24 08:29:20 (162 MB/s) - ‘last-align_1645-1.dsc’ saved [1515/1515] Fri Oct 24 08:29:20 UTC 2025 I: last-align_1645-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: last-align Binary: last-align Architecture: any Version: 1645-1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Homepage: https://gitlab.com/mcfrith/last Standards-Version: 4.7.2 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, architecture-is-64-bit Package-List: last-align deb science optional arch=any Checksums-Sha1: 703474f6dfffd892f2fdab0604a770391898057e 2231972 last-align_1645.orig.tar.bz2 9e7c71d3237717310d0ec124e8d4359b71dd889c 17092 last-align_1645-1.debian.tar.xz Checksums-Sha256: 037d4edd590bc7886b60ea87710148548ef71b9cc17b13c807b5767ff2ca05c4 2231972 last-align_1645.orig.tar.bz2 f384b8884d32037c0270c79d43e4efb01ed182a8f18e42506cdf184c838565f8 17092 last-align_1645-1.debian.tar.xz Files: a44d8a800a3c909539b1e772d169a153 2231972 last-align_1645.orig.tar.bz2 50223fb79ea0668d8025cf29ccd9a28b 17092 last-align_1645-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iIgEARYKADAWIQSglbZu4JAkvuai8HIqJ5BL1yQ+2gUCaNkJaxIcbmlsZXNoQGRl Ymlhbi5vcmcACgkQKieQS9ckPtpJdgEAiAan/W7nrjKfigH0YKPuPN1mKHlh3ydG z8M+rg12fHcBAJsBxODb8LzLkXPZeRneoMZBowhULazHr3s3oftSmk8F =8Wy7 -----END PGP SIGNATURE----- Fri Oct 24 08:29:20 UTC 2025 I: Checking whether the package is not for us Fri Oct 24 08:29:20 UTC 2025 I: Starting 1st build on remote node ionos15-amd64.debian.net. Fri Oct 24 08:29:20 UTC 2025 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Fri Oct 24 08:33:15 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Nov 26 02:52:20 -12 2026 I: pbuilder-time-stamp: 1795704740 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [last-align_1645-1.dsc] I: copying [./last-align_1645.orig.tar.bz2] I: copying [./last-align_1645-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./last-align_1645-1.dsc: no acceptable signature found dpkg-source: info: extracting last-align in last-align-1645 dpkg-source: info: unpacking last-align_1645.orig.tar.bz2 dpkg-source: info: unpacking last-align_1645-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying helpMakefiles.patch dpkg-source: info: applying simde I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2955330/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='46016786c8744f45bbc6423b95f7d90f' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2955330' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ZTxVM3CB/pbuilderrc_2Mf2 --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ZTxVM3CB/b1 --logfile b1/build.log last-align_1645-1.dsc' SUDO_GID='111' SUDO_HOME='/var/lib/jenkins' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2955330/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), help2man, python3-pil, zlib1g-dev, libsimde-dev, architecture-is-64-bit dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19900 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on python3-pil; however: Package python3-pil is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev is not installed. pbuilder-satisfydepends-dummy depends on architecture-is-64-bit; however: Package architecture-is-64-bit is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libabsl20240722{a} libaom3{a} libarchive-zip-perl{a} libavif16{a} libbrotli1{a} libdav1d7{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libglib2.0-0t64{a} libgraphite2-3{a} libharfbuzz0b{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} liblcms2-2{a} liblerc4{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libopenjp2-7{a} libpipeline1{a} libpng16-16t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraqm0{a} librav1e0.8{a} libreadline8t64{a} libsharpyuv0{a} libsimde-dev{a} libsvtav1enc2{a} libtiff6{a} libtool{a} libuchardet0{a} libunistring5{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxml2-16{a} libyuv0{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-minimal{a} python3-pil{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx python3-olefile shared-mime-info wget xdg-user-dirs 0 packages upgraded, 80 newly installed, 0 to remove and 0 not upgraded. Need to get 32.6 MB of archives. After unpacking 119 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 libexpat1 amd64 2.7.3-1 [112 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 libpython3.13-minimal amd64 3.13.9-1 [865 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 python3.13-minimal amd64 3.13.9-1 [2257 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 media-types all 14.0.0 [30.8 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 netbase all 6.5 [12.4 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 tzdata all 2025b-5 [260 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 libpython3.13-stdlib amd64 3.13.9-1 [1965 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 python3.13 amd64 3.13.9-1 [764 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 22 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.2-1 [95.2 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 architecture-properties amd64 0.2.6 [2336 B] Get: 27 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-2 [325 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.28 [92.4 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 35 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 37 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 38 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 39 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 40 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 41 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.6+dfsg-0.1 [651 kB] Get: 42 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 43 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian forky/main amd64 debhelper all 13.28 [941 kB] Get: 46 http://deb.debian.org/debian forky/main amd64 help2man amd64 1.49.3 [198 kB] Get: 47 http://deb.debian.org/debian forky/main amd64 libabsl20240722 amd64 20240722.0-4 [492 kB] Get: 48 http://deb.debian.org/debian forky/main amd64 libaom3 amd64 3.13.1-1 [1905 kB] Get: 49 http://deb.debian.org/debian forky/main amd64 libdav1d7 amd64 1.5.1-1 [559 kB] Get: 50 http://deb.debian.org/debian forky/main amd64 libgav1-1 amd64 0.19.0-3+b1 [353 kB] Get: 51 http://deb.debian.org/debian forky/main amd64 librav1e0.8 amd64 0.8.1-5 [976 kB] Get: 52 http://deb.debian.org/debian forky/main amd64 libsvtav1enc2 amd64 2.3.0+dfsg-1 [2489 kB] Get: 53 http://deb.debian.org/debian forky/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get: 54 http://deb.debian.org/debian forky/main amd64 libyuv0 amd64 0.0.1919.20250919-1 [175 kB] Get: 55 http://deb.debian.org/debian forky/main amd64 libavif16 amd64 1.3.0-1+b1 [137 kB] Get: 56 http://deb.debian.org/debian forky/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 57 http://deb.debian.org/debian forky/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 58 http://deb.debian.org/debian forky/main amd64 libpng16-16t64 amd64 1.6.50-1 [282 kB] Get: 59 http://deb.debian.org/debian forky/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 60 http://deb.debian.org/debian forky/main amd64 libfribidi0 amd64 1.0.16-3 [26.6 kB] Get: 61 http://deb.debian.org/debian forky/main amd64 libglib2.0-0t64 amd64 2.86.1-1 [1546 kB] Get: 62 http://deb.debian.org/debian forky/main amd64 libgraphite2-3 amd64 1.3.14-11 [76.7 kB] Get: 63 http://deb.debian.org/debian forky/main amd64 libharfbuzz0b amd64 12.1.0-1 [530 kB] Get: 64 http://deb.debian.org/debian forky/main amd64 libimagequant0 amd64 4.4.0-3 [251 kB] Get: 65 http://deb.debian.org/debian forky/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 66 http://deb.debian.org/debian forky/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 67 http://deb.debian.org/debian forky/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 68 http://deb.debian.org/debian forky/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [204 kB] Get: 69 http://deb.debian.org/debian forky/main amd64 libraqm0 amd64 0.10.3-1 [14.0 kB] Get: 70 http://deb.debian.org/debian forky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 71 http://deb.debian.org/debian forky/main amd64 libsimde-dev all 0.8.2-3 [467 kB] Get: 72 http://deb.debian.org/debian forky/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 73 http://deb.debian.org/debian forky/main amd64 libtiff6 amd64 4.7.1-1 [361 kB] Get: 74 http://deb.debian.org/debian forky/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get: 75 http://deb.debian.org/debian forky/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get: 76 http://deb.debian.org/debian forky/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 77 http://deb.debian.org/debian forky/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 78 http://deb.debian.org/debian forky/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 79 http://deb.debian.org/debian forky/main amd64 python3-pil amd64 11.3.0-1 [526 kB] Get: 80 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 32.6 MB in 0s (140 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19900 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.3-1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../liblocale-gettext-perl_1.07-7+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.9-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.9-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.9-1_amd64.deb ... Unpacking python3.13-minimal (3.13.9-1) ... Setting up libpython3.13-minimal:amd64 (3.13.9-1) ... Setting up libexpat1:amd64 (2.7.3-1) ... Setting up python3.13-minimal (3.13.9-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20249 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_amd64.deb ... Unpacking python3-minimal (3.13.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_14.0.0_all.deb ... Unpacking media-types (14.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.9-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.9-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.9-1_amd64.deb ... Unpacking python3.13 (3.13.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Current default time zone: 'Etc/UTC' Local time is now: Thu Nov 26 14:53:12 UTC 2026. Universal Time is now: Thu Nov 26 14:53:12 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-4) ... Setting up libsvtav1enc2:amd64 (2.3.0+dfsg-1) ... Setting up libfribidi0:amd64 (1.0.16-3) ... Setting up libimagequant0:amd64 (4.4.0-3) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up libpng16-16t64:amd64 (1.6.50-1) ... Setting up autopoint (0.23.1-2) ... Setting up libgav1-1:amd64 (0.19.0-3+b1) ... Setting up autoconf (2.72-3.1) ... Setting up libwebp7:amd64 (1.5.0-0.1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up libdav1d7:amd64 (1.5.1-1) ... Setting up sensible-utils (0.0.26) ... Setting up libtiff6:amd64 (4.7.1-1) ... Setting up libuchardet0:amd64 (0.0.8-2) ... 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Setting up groff-base (1.23.0-9) ... Setting up libharfbuzz0b:amd64 (12.1.0-1) ... Setting up libpython3.13-stdlib:amd64 (3.13.9-1) ... Setting up libpython3-stdlib:amd64 (3.13.7-1) ... Setting up python3.13 (3.13.9-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.7-1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libraqm0:amd64 (0.10.3-1) ... Setting up debhelper (13.28) ... Setting up python3-pil:amd64 (11.3.0-1) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.37.1.2-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/reproducible-path/last-align-1645/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../last-align_1645-1_source.changes dpkg-buildpackage: info: source package last-align dpkg-buildpackage: info: source version 1645-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/last-align-1645' for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \ dh_auto_clean -- SFX=-${SIMD} ; done make -j42 clean SFX=-avx2 make[2]: Entering directory '/build/reproducible-path/last-align-1645' make[3]: Entering directory '/build/reproducible-path/last-align-1645/src' rm -f ../bin/lastdb-avx2 ../bin/lastal-avx2 ../bin/last-split-avx2 ../bin/last-merge-batches-avx2 ../bin/last-pair-probs-avx2 *.o* */*.o* make[3]: Leaving directory '/build/reproducible-path/last-align-1645/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1645' make -j42 clean SFX=-avx make[2]: Entering directory '/build/reproducible-path/last-align-1645' make[3]: Entering directory '/build/reproducible-path/last-align-1645/src' rm -f ../bin/lastdb-avx ../bin/lastal-avx ../bin/last-split-avx ../bin/last-merge-batches-avx ../bin/last-pair-probs-avx *.o* */*.o* make[3]: Leaving directory '/build/reproducible-path/last-align-1645/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1645' make -j42 clean SFX=-sse4.1 make[2]: Entering directory '/build/reproducible-path/last-align-1645' make[3]: Entering directory '/build/reproducible-path/last-align-1645/src' rm -f ../bin/lastdb-sse4.1 ../bin/lastal-sse4.1 ../bin/last-split-sse4.1 ../bin/last-merge-batches-sse4.1 ../bin/last-pair-probs-sse4.1 *.o* */*.o* make[3]: Leaving directory '/build/reproducible-path/last-align-1645/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1645' make -j42 clean SFX=-ssse3 make[2]: Entering directory '/build/reproducible-path/last-align-1645' make[3]: Entering directory '/build/reproducible-path/last-align-1645/src' rm -f ../bin/lastdb-ssse3 ../bin/lastal-ssse3 ../bin/last-split-ssse3 ../bin/last-merge-batches-ssse3 ../bin/last-pair-probs-ssse3 *.o* */*.o* make[3]: Leaving directory '/build/reproducible-path/last-align-1645/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1645' make -j42 clean SFX=-sse3 make[2]: Entering directory '/build/reproducible-path/last-align-1645' make[3]: Entering directory '/build/reproducible-path/last-align-1645/src' rm -f ../bin/lastdb-sse3 ../bin/lastal-sse3 ../bin/last-split-sse3 ../bin/last-merge-batches-sse3 ../bin/last-pair-probs-sse3 *.o* */*.o* make[3]: Leaving directory '/build/reproducible-path/last-align-1645/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1645' make -j42 clean SFX=-sse2 make[2]: Entering directory '/build/reproducible-path/last-align-1645' make[3]: Entering directory '/build/reproducible-path/last-align-1645/src' rm -f ../bin/lastdb-sse2 ../bin/lastal-sse2 ../bin/last-split-sse2 ../bin/last-merge-batches-sse2 ../bin/last-pair-probs-sse2 *.o* */*.o* make[3]: Leaving directory '/build/reproducible-path/last-align-1645/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1645' for i in last-merge-batches last-pair-probs last-split lastal lastdb ; \ do \ for j in avx avx2 plain sse2 sse3 sse4.1 ssse3 sse3 sse2 sse ; \ do \ rm -f bin/$i-$j ; \ done ; \ done make[1]: Leaving directory '/build/reproducible-path/last-align-1645' 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 '/build/reproducible-path/last-align-1645' mkdir -p /build/reproducible-path/last-align-1645/debian/last-align/usr mkdir -p /build/reproducible-path/last-align-1645/debian/last-align/usr/lib/last-align for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \ dh_auto_build -- all SFX=-${SIMD} CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -m${SIMD}" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -j42 INSTALL="install --strip-program=true" all SFX=-avx2 CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mavx2" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 '/build/reproducible-path/last-align-1645' make[3]: Entering directory '/build/reproducible-path/last-align-1645/src' g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 ../build/mat-inc.sh ../data/*.mat > ScoreMatrixData.hh g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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: 1645) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" | cmp -s version.hh - || echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1645) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" > version.hh g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_alignment_path_adder.o mcf_alignment_path_adder.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 SubsetSuffixArray.cc: In function ‘void makeSomeBuckets(const cbrc::uchar*, const cbrc::CyclicSubsetSeed&, const size_t*, int, mcf::PackedArray, size_t, size_t, size_t, mcf::ConstPackedArray, size_t, size_t)’: SubsetSuffixArray.cc:190:50: warning: unused parameter ‘saEnd’ [-Wunused-parameter] 190 | size_t saBeg, size_t saEnd) { | ~~~~~~~^~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from alp/njn_dynprogproblim.hpp:39, from alp/njn_dynprogproblim.cpp:37: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 116 | virtual inline void copy (const DynProgProb &dynProgProb_) | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] 124 | virtual void copy ( | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from alp/njn_dynprogproblim.hpp:39, from alp/njn_localmaxstat.cpp:39: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] 124 | virtual void copy ( | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 116 | virtual inline void copy (const DynProgProb &dynProgProb_) | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mavx2 -c -o last-merge-batches.o last-merge-batches.c g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from alp/njn_dynprogproblim.hpp:39, from alp/njn_localmaxstatutil.cpp:39: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 116 | virtual inline void copy (const DynProgProb &dynProgProb_) | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] 124 | virtual void copy ( | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mavx2 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-merge-batches-avx2 last-merge-batches.o lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int, int)’: lastdb.cc:372:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual] 372 | std::cout.write((char *)m.qualityReader() + b, e - b); | ^~~~~~~~~~~~~~~~~~~~~~~~~ alp/sls_alp_data.cpp: In constructor ‘Sls::alp_data::alp_data(long int, std::string, long int, long int, long int, long int, long int, long int, std::string, std::string, std::string, double, double, double, double, double, bool)’: alp/sls_alp_data.cpp:418:17: warning: ‘*this.Sls::alp_data::d_memory_size_in_MB’ is used uninitialized [-Wuninitialized] 418 | d_memory_size_in_MB+=sizeof(struct_for_randomization)/mb_bytes; | ^~~~~~~~~~~~~~~~~~~ last-pair-probs.cc: In function ‘Alignment parseMaf(const char* const*, const char* const*, char, double, const std::set >&)’: last-pair-probs.cc:438:19: warning: ‘qName’ may be used uninitialized [-Wmaybe-uninitialized] 438 | parseAlignment(score, rName, rStart, rSpan, rStrand, rSize, qName, qStrand, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 439 | linesBeg, linesEnd, strand, scale, circularChroms); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ last-pair-probs.cc:411:17: note: ‘qName’ was declared here 411 | String rName, qName; | ^~~~~ last-pair-probs.cc:438:19: warning: ‘qStrand’ may be used uninitialized [-Wmaybe-uninitialized] 438 | parseAlignment(score, rName, rStart, rSpan, rStrand, rSize, qName, qStrand, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 439 | linesBeg, linesEnd, strand, scale, circularChroms); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ last-pair-probs.cc:412:17: note: ‘qStrand’ was declared here 412 | char rStrand, qStrand; | ^~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split-avx2 Alphabet.o LambdaCalculator.o MultiSequence.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 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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastdb-avx2 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySort.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o lastdb.o -lz lastal.cc: In function ‘void alignGapless1(LastAligner&, cbrc::SegmentPairPot&, const cbrc::MultiSequence&, const SeqData&, const Dispatcher&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, const cbrc::SubsetSuffixArray&, const cbrc::uchar*, unsigned int)’: lastal.cc:657:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 657 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:654:14: note: ‘revLen’ was declared here 654 | size_t revLen, fwdLen; | ^~~~~~ lastal.cc:657:78: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 657 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:654:22: note: ‘fwdLen’ was declared here 654 | size_t revLen, fwdLen; | ^~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastal-avx2 Alphabet.o Centroid.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySearch.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o lastal.o Alignment.o AlignmentPot.o AlignmentWrite.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_alignment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o SegmentPair.o SegmentPairPot.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_split_aligner.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/mcf_last_splitter.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 -lz make[3]: Leaving directory '/build/reproducible-path/last-align-1645/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1645' make -j42 INSTALL="install --strip-program=true" all SFX=-avx CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mavx" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 '/build/reproducible-path/last-align-1645' make[3]: Entering directory '/build/reproducible-path/last-align-1645/src' g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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: 1645) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" | cmp -s version.hh - || echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1645) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" > version.hh g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_alignment_path_adder.o mcf_alignment_path_adder.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 SubsetSuffixArray.cc: In function ‘void makeSomeBuckets(const cbrc::uchar*, const cbrc::CyclicSubsetSeed&, const size_t*, int, mcf::PackedArray, size_t, size_t, size_t, mcf::ConstPackedArray, size_t, size_t)’: SubsetSuffixArray.cc:190:50: warning: unused parameter ‘saEnd’ [-Wunused-parameter] 190 | size_t saBeg, size_t saEnd) { | ~~~~~~~^~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from alp/njn_dynprogproblim.hpp:39, from alp/njn_dynprogproblim.cpp:37: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 116 | virtual inline void copy (const DynProgProb &dynProgProb_) | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] 124 | virtual void copy ( | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from alp/njn_dynprogproblim.hpp:39, from alp/njn_localmaxstat.cpp:39: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 116 | virtual inline void copy (const DynProgProb &dynProgProb_) | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] 124 | virtual void copy ( | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ In file included from alp/njn_dynprogproblim.hpp:39, from alp/njn_localmaxstatutil.cpp:39: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] 124 | virtual void copy ( | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 116 | virtual inline void copy (const DynProgProb &dynProgProb_) | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mavx -c -o last-merge-batches.o last-merge-batches.c g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mavx -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-merge-batches-avx last-merge-batches.o lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int, int)’: lastdb.cc:372:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual] 372 | std::cout.write((char *)m.qualityReader() + b, e - b); | ^~~~~~~~~~~~~~~~~~~~~~~~~ alp/sls_alp_data.cpp: In constructor ‘Sls::alp_data::alp_data(long int, std::string, long int, long int, long int, long int, long int, long int, std::string, std::string, std::string, double, double, double, double, double, bool)’: alp/sls_alp_data.cpp:418:17: warning: ‘*this.Sls::alp_data::d_memory_size_in_MB’ is used uninitialized [-Wuninitialized] 418 | d_memory_size_in_MB+=sizeof(struct_for_randomization)/mb_bytes; | ^~~~~~~~~~~~~~~~~~~ last-pair-probs.cc: In function ‘Alignment parseMaf(const char* const*, const char* const*, char, double, const std::set >&)’: last-pair-probs.cc:438:19: warning: ‘qName’ may be used uninitialized [-Wmaybe-uninitialized] 438 | parseAlignment(score, rName, rStart, rSpan, rStrand, rSize, qName, qStrand, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 439 | linesBeg, linesEnd, strand, scale, circularChroms); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ last-pair-probs.cc:411:17: note: ‘qName’ was declared here 411 | String rName, qName; | ^~~~~ last-pair-probs.cc:438:19: warning: ‘qStrand’ may be used uninitialized [-Wmaybe-uninitialized] 438 | parseAlignment(score, rName, rStart, rSpan, rStrand, rSize, qName, qStrand, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 439 | linesBeg, linesEnd, strand, scale, circularChroms); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ last-pair-probs.cc:412:17: note: ‘qStrand’ was declared here 412 | char rStrand, qStrand; | ^~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split-avx Alphabet.o LambdaCalculator.o MultiSequence.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 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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastdb-avx Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySort.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o lastdb.o -lz lastal.cc: In function ‘void alignGapless1(LastAligner&, cbrc::SegmentPairPot&, const cbrc::MultiSequence&, const SeqData&, const Dispatcher&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, const cbrc::SubsetSuffixArray&, const cbrc::uchar*, unsigned int)’: lastal.cc:657:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 657 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:654:14: note: ‘revLen’ was declared here 654 | size_t revLen, fwdLen; | ^~~~~~ lastal.cc:657:78: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 657 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:654:22: note: ‘fwdLen’ was declared here 654 | size_t revLen, fwdLen; | ^~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastal-avx Alphabet.o Centroid.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySearch.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o lastal.o Alignment.o AlignmentPot.o AlignmentWrite.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_alignment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o SegmentPair.o SegmentPairPot.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_split_aligner.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/mcf_last_splitter.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 -lz make[3]: Leaving directory '/build/reproducible-path/last-align-1645/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1645' make -j42 INSTALL="install --strip-program=true" all SFX=-sse4.1 CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -msse4.1" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 '/build/reproducible-path/last-align-1645' make[3]: Entering directory '/build/reproducible-path/last-align-1645/src' g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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: 1645) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" | cmp -s version.hh - || echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1645) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" > version.hh g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_alignment_path_adder.o mcf_alignment_path_adder.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from tantan.cc:5: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from GappedXdropAligner.hh:52, from GappedXdropAlignerFrame.cc:4: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from GappedXdropAlignerPssm.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from GappedXdropAlignerDna.cc:4: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from GappedXdropAligner3frame.cc:53: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Centroid.cc:4: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Alignment.hh:8, from Alignment.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Alignment.hh:8, from AlignmentPot.hh:8, from AlignmentPot.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ SubsetSuffixArray.cc: In function ‘void makeSomeBuckets(const cbrc::uchar*, const cbrc::CyclicSubsetSeed&, const size_t*, int, mcf::PackedArray, size_t, size_t, size_t, mcf::ConstPackedArray, size_t, size_t)’: SubsetSuffixArray.cc:190:50: warning: unused parameter ‘saEnd’ [-Wunused-parameter] 190 | size_t saBeg, size_t saEnd) { | ~~~~~~~^~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Alignment.hh:8, from AlignmentWrite.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from GappedXdropAligner2qual.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from GappedXdropAligner.cc:49: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256d simde__m256d_from_private(simde__m256d_private)’: /usr/include/simde/x86/avx.h:297:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 297 | simde__m256d_from_private(simde__m256d_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from alp/njn_dynprogproblim.hpp:39, from alp/njn_dynprogproblim.cpp:37: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 116 | virtual inline void copy (const DynProgProb &dynProgProb_) | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] 124 | virtual void copy ( | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from alp/njn_dynprogproblim.hpp:39, from alp/njn_localmaxstat.cpp:39: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] 124 | virtual void copy ( | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 116 | virtual inline void copy (const DynProgProb &dynProgProb_) | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -msse4.1 -c -o last-merge-batches.o last-merge-batches.c g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from alp/njn_dynprogproblim.hpp:39, from alp/njn_localmaxstatutil.cpp:39: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 116 | virtual inline void copy (const DynProgProb &dynProgProb_) | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] 124 | virtual void copy ( | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -msse4.1 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-merge-batches-sse4.1 last-merge-batches.o lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int, int)’: lastdb.cc:372:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual] 372 | std::cout.write((char *)m.qualityReader() + b, e - b); | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Alignment.hh:8, from AlignmentPot.hh:8, from lastal.cc:13: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ last-pair-probs.cc: In function ‘Alignment parseMaf(const char* const*, const char* const*, char, double, const std::set >&)’: last-pair-probs.cc:438:19: warning: ‘qName’ may be used uninitialized [-Wmaybe-uninitialized] 438 | parseAlignment(score, rName, rStart, rSpan, rStrand, rSize, qName, qStrand, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 439 | linesBeg, linesEnd, strand, scale, circularChroms); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ last-pair-probs.cc:411:17: note: ‘qName’ was declared here 411 | String rName, qName; | ^~~~~ last-pair-probs.cc:438:19: warning: ‘qStrand’ may be used uninitialized [-Wmaybe-uninitialized] 438 | parseAlignment(score, rName, rStart, rSpan, rStrand, rSize, qName, qStrand, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 439 | linesBeg, linesEnd, strand, scale, circularChroms); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ last-pair-probs.cc:412:17: note: ‘qStrand’ was declared here 412 | char rStrand, qStrand; | ^~~~~~~ alp/sls_alp_data.cpp: In constructor ‘Sls::alp_data::alp_data(long int, std::string, long int, long int, long int, long int, long int, long int, std::string, std::string, std::string, double, double, double, double, double, bool)’: alp/sls_alp_data.cpp:418:17: warning: ‘*this.Sls::alp_data::d_memory_size_in_MB’ is used uninitialized [-Wuninitialized] 418 | d_memory_size_in_MB+=sizeof(struct_for_randomization)/mb_bytes; | ^~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split-sse4.1 Alphabet.o LambdaCalculator.o MultiSequence.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 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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastdb-sse4.1 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySort.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o lastdb.o -lz lastal.cc: In function ‘void alignGapless1(LastAligner&, cbrc::SegmentPairPot&, const cbrc::MultiSequence&, const SeqData&, const Dispatcher&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, const cbrc::SubsetSuffixArray&, const cbrc::uchar*, unsigned int)’: lastal.cc:657:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 657 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:654:14: note: ‘revLen’ was declared here 654 | size_t revLen, fwdLen; | ^~~~~~ lastal.cc:657:78: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 657 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:654:22: note: ‘fwdLen’ was declared here 654 | size_t revLen, fwdLen; | ^~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastal-sse4.1 Alphabet.o Centroid.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySearch.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o lastal.o Alignment.o AlignmentPot.o AlignmentWrite.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_alignment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o SegmentPair.o SegmentPairPot.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_split_aligner.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/mcf_last_splitter.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 -lz make[3]: Leaving directory '/build/reproducible-path/last-align-1645/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1645' make -j42 INSTALL="install --strip-program=true" all SFX=-ssse3 CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mssse3" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 '/build/reproducible-path/last-align-1645' make[3]: Entering directory '/build/reproducible-path/last-align-1645/src' g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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: 1645) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" | cmp -s version.hh - || echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1645) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" > version.hh g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_alignment_path_adder.o mcf_alignment_path_adder.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from tantan.cc:5: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from GappedXdropAligner.hh:52, from GappedXdropAligner2qual.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from GappedXdropAlignerFrame.cc:4: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from GappedXdropAligner3frame.cc:53: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from GappedXdropAlignerDna.cc:4: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Centroid.cc:4: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from GappedXdropAlignerPssm.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from GappedXdropAligner.cc:49: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Alignment.hh:8, from AlignmentPot.hh:8, from AlignmentPot.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Alignment.hh:8, from AlignmentWrite.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ SubsetSuffixArray.cc: In function ‘void makeSomeBuckets(const cbrc::uchar*, const cbrc::CyclicSubsetSeed&, const size_t*, int, mcf::PackedArray, size_t, size_t, size_t, mcf::ConstPackedArray, size_t, size_t)’: SubsetSuffixArray.cc:190:50: warning: unused parameter ‘saEnd’ [-Wunused-parameter] 190 | size_t saBeg, size_t saEnd) { | ~~~~~~~^~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Alignment.hh:8, from Alignment.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256d simde__m256d_from_private(simde__m256d_private)’: /usr/include/simde/x86/avx.h:297:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 297 | simde__m256d_from_private(simde__m256d_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from alp/njn_dynprogproblim.hpp:39, from alp/njn_dynprogproblim.cpp:37: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] 124 | virtual void copy ( | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 116 | virtual inline void copy (const DynProgProb &dynProgProb_) | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ In file included from alp/njn_dynprogproblim.hpp:39, from alp/njn_localmaxstatutil.cpp:39: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 116 | virtual inline void copy (const DynProgProb &dynProgProb_) | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] 124 | virtual void copy ( | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ In file included from alp/njn_dynprogproblim.hpp:39, from alp/njn_localmaxstat.cpp:39: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] 124 | virtual void copy ( | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 116 | virtual inline void copy (const DynProgProb &dynProgProb_) | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mssse3 -c -o last-merge-batches.o last-merge-batches.c g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mssse3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-merge-batches-ssse3 last-merge-batches.o lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int, int)’: lastdb.cc:372:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual] 372 | std::cout.write((char *)m.qualityReader() + b, e - b); | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Alignment.hh:8, from AlignmentPot.hh:8, from lastal.cc:13: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ alp/sls_alp_data.cpp: In constructor ‘Sls::alp_data::alp_data(long int, std::string, long int, long int, long int, long int, long int, long int, std::string, std::string, std::string, double, double, double, double, double, bool)’: alp/sls_alp_data.cpp:418:17: warning: ‘*this.Sls::alp_data::d_memory_size_in_MB’ is used uninitialized [-Wuninitialized] 418 | d_memory_size_in_MB+=sizeof(struct_for_randomization)/mb_bytes; | ^~~~~~~~~~~~~~~~~~~ last-pair-probs.cc: In function ‘Alignment parseMaf(const char* const*, const char* const*, char, double, const std::set >&)’: last-pair-probs.cc:438:19: warning: ‘qName’ may be used uninitialized [-Wmaybe-uninitialized] 438 | parseAlignment(score, rName, rStart, rSpan, rStrand, rSize, qName, qStrand, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 439 | linesBeg, linesEnd, strand, scale, circularChroms); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ last-pair-probs.cc:411:17: note: ‘qName’ was declared here 411 | String rName, qName; | ^~~~~ last-pair-probs.cc:438:19: warning: ‘qStrand’ may be used uninitialized [-Wmaybe-uninitialized] 438 | parseAlignment(score, rName, rStart, rSpan, rStrand, rSize, qName, qStrand, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 439 | linesBeg, linesEnd, strand, scale, circularChroms); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ last-pair-probs.cc:412:17: note: ‘qStrand’ was declared here 412 | char rStrand, qStrand; | ^~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split-ssse3 Alphabet.o LambdaCalculator.o MultiSequence.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 split/cbrc_split_aligner.o split/mcf_last_splitter.o split/last-split.o lastal.cc: In function ‘void alignGapless1(LastAligner&, cbrc::SegmentPairPot&, const cbrc::MultiSequence&, const SeqData&, const Dispatcher&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, const cbrc::SubsetSuffixArray&, const cbrc::uchar*, unsigned int)’: lastal.cc:657:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 657 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:654:14: note: ‘revLen’ was declared here 654 | size_t revLen, fwdLen; | ^~~~~~ lastal.cc:657:78: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 657 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:654:22: note: ‘fwdLen’ was declared here 654 | size_t revLen, fwdLen; | ^~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastdb-ssse3 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySort.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o lastdb.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastal-ssse3 Alphabet.o Centroid.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySearch.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o lastal.o Alignment.o AlignmentPot.o AlignmentWrite.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_alignment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o SegmentPair.o SegmentPairPot.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_split_aligner.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/mcf_last_splitter.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 -lz make[3]: Leaving directory '/build/reproducible-path/last-align-1645/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1645' make -j42 INSTALL="install --strip-program=true" all SFX=-sse3 CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -msse3" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 '/build/reproducible-path/last-align-1645' make[3]: Entering directory '/build/reproducible-path/last-align-1645/src' g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. 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mcf_substitution_matrix_stats.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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: 1645) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" | cmp -s version.hh - || echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1645) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" > version.hh g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong 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-Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o TwoQualityScoreMatrix.o TwoQualityScoreMatrix.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from tantan.cc:5: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from GappedXdropAlignerFrame.cc:4: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from GappedXdropAlignerPssm.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from GappedXdropAlignerDna.cc:4: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from GappedXdropAligner3frame.cc:53: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from GappedXdropAligner2qual.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Centroid.cc:4: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from GappedXdropAligner.cc:49: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Alignment.hh:8, from AlignmentPot.hh:8, from AlignmentPot.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Alignment.hh:8, from Alignment.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ SubsetSuffixArray.cc: In function ‘void makeSomeBuckets(const cbrc::uchar*, const cbrc::CyclicSubsetSeed&, const size_t*, int, mcf::PackedArray, size_t, size_t, size_t, mcf::ConstPackedArray, size_t, size_t)’: SubsetSuffixArray.cc:190:50: warning: unused parameter ‘saEnd’ [-Wunused-parameter] 190 | size_t saBeg, size_t saEnd) { | ~~~~~~~^~~~~ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Alignment.hh:8, from AlignmentWrite.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256d simde__m256d_from_private(simde__m256d_private)’: /usr/include/simde/x86/avx.h:297:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 297 | simde__m256d_from_private(simde__m256d_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from alp/njn_dynprogproblim.hpp:39, from alp/njn_dynprogproblim.cpp:37: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] 124 | virtual void copy ( | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 116 | virtual inline void copy (const DynProgProb &dynProgProb_) | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from alp/njn_dynprogproblim.hpp:39, from alp/njn_localmaxstatutil.cpp:39: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 116 | virtual inline void copy (const DynProgProb &dynProgProb_) | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] 124 | virtual void copy ( | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ In file included from alp/njn_dynprogproblim.hpp:39, from alp/njn_localmaxstat.cpp:39: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] 124 | virtual void copy ( | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 116 | virtual inline void copy (const DynProgProb &dynProgProb_) | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -msse3 -c -o last-merge-batches.o last-merge-batches.c g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -msse3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-merge-batches-sse3 last-merge-batches.o lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int, int)’: lastdb.cc:372:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual] 372 | std::cout.write((char *)m.qualityReader() + b, e - b); | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Alignment.hh:8, from AlignmentPot.hh:8, from lastal.cc:13: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ alp/sls_alp_data.cpp: In constructor ‘Sls::alp_data::alp_data(long int, std::string, long int, long int, long int, long int, long int, long int, std::string, std::string, std::string, double, double, double, double, double, bool)’: alp/sls_alp_data.cpp:418:17: warning: ‘*this.Sls::alp_data::d_memory_size_in_MB’ is used uninitialized [-Wuninitialized] 418 | d_memory_size_in_MB+=sizeof(struct_for_randomization)/mb_bytes; | ^~~~~~~~~~~~~~~~~~~ last-pair-probs.cc: In function ‘Alignment parseMaf(const char* const*, const char* const*, char, double, const std::set >&)’: last-pair-probs.cc:438:19: warning: ‘qName’ may be used uninitialized [-Wmaybe-uninitialized] 438 | parseAlignment(score, rName, rStart, rSpan, rStrand, rSize, qName, qStrand, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 439 | linesBeg, linesEnd, strand, scale, circularChroms); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ last-pair-probs.cc:411:17: note: ‘qName’ was declared here 411 | String rName, qName; | ^~~~~ last-pair-probs.cc:438:19: warning: ‘qStrand’ may be used uninitialized [-Wmaybe-uninitialized] 438 | parseAlignment(score, rName, rStart, rSpan, rStrand, rSize, qName, qStrand, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 439 | linesBeg, linesEnd, strand, scale, circularChroms); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ last-pair-probs.cc:412:17: note: ‘qStrand’ was declared here 412 | char rStrand, qStrand; | ^~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split-sse3 Alphabet.o LambdaCalculator.o MultiSequence.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 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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastdb-sse3 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySort.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o lastdb.o -lz lastal.cc: In function ‘void alignGapless1(LastAligner&, cbrc::SegmentPairPot&, const cbrc::MultiSequence&, const SeqData&, const Dispatcher&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, const cbrc::SubsetSuffixArray&, const cbrc::uchar*, unsigned int)’: lastal.cc:657:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 657 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:654:14: note: ‘revLen’ was declared here 654 | size_t revLen, fwdLen; | ^~~~~~ lastal.cc:657:78: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 657 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:654:22: note: ‘fwdLen’ was declared here 654 | size_t revLen, fwdLen; | ^~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastal-sse3 Alphabet.o Centroid.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySearch.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o lastal.o Alignment.o AlignmentPot.o AlignmentWrite.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_alignment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o SegmentPair.o SegmentPairPot.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_split_aligner.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/mcf_last_splitter.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 -lz make[3]: Leaving directory '/build/reproducible-path/last-align-1645/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1645' make -j42 INSTALL="install --strip-program=true" all SFX=-sse2 CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -msse2" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 '/build/reproducible-path/last-align-1645' make[3]: Entering directory '/build/reproducible-path/last-align-1645/src' g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 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-Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o mcf_alignment_path_adder.o mcf_alignment_path_adder.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from tantan.cc:5: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from GappedXdropAlignerDna.cc:4: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from GappedXdropAlignerFrame.cc:4: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from GappedXdropAligner2qual.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from GappedXdropAlignerPssm.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from GappedXdropAligner3frame.cc:53: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Centroid.cc:4: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Alignment.hh:8, from AlignmentPot.hh:8, from AlignmentPot.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Alignment.hh:8, from Alignment.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Alignment.hh:8, from AlignmentWrite.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from GappedXdropAligner.hh:52, from GappedXdropAligner.cc:49: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ SubsetSuffixArray.cc: In function ‘void makeSomeBuckets(const cbrc::uchar*, const cbrc::CyclicSubsetSeed&, const size_t*, int, mcf::PackedArray, size_t, size_t, size_t, mcf::ConstPackedArray, size_t, size_t)’: SubsetSuffixArray.cc:190:50: warning: unused parameter ‘saEnd’ [-Wunused-parameter] 190 | size_t saBeg, size_t saEnd) { | ~~~~~~~^~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256d simde__m256d_from_private(simde__m256d_private)’: /usr/include/simde/x86/avx.h:297:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 297 | simde__m256d_from_private(simde__m256d_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from alp/njn_dynprogproblim.hpp:39, from alp/njn_dynprogproblim.cpp:37: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 116 | virtual inline void copy (const DynProgProb &dynProgProb_) | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] 124 | virtual void copy ( | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ In file included from alp/njn_dynprogproblim.hpp:39, from alp/njn_localmaxstatutil.cpp:39: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] 124 | virtual void copy ( | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 116 | virtual inline void copy (const DynProgProb &dynProgProb_) | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from alp/njn_dynprogproblim.hpp:39, from alp/njn_localmaxstat.cpp:39: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 116 | virtual inline void copy (const DynProgProb &dynProgProb_) | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] 124 | virtual void copy ( | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -msse2 -c -o last-merge-batches.o last-merge-batches.c g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -msse2 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-merge-batches-sse2 last-merge-batches.o lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int, int)’: lastdb.cc:372:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual] 372 | std::cout.write((char *)m.qualityReader() + b, e - b); | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Alignment.hh:8, from AlignmentPot.hh:8, from lastal.cc:13: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ alp/sls_alp_data.cpp: In constructor ‘Sls::alp_data::alp_data(long int, std::string, long int, long int, long int, long int, long int, long int, std::string, std::string, std::string, double, double, double, double, double, bool)’: alp/sls_alp_data.cpp:418:17: warning: ‘*this.Sls::alp_data::d_memory_size_in_MB’ is used uninitialized [-Wuninitialized] 418 | d_memory_size_in_MB+=sizeof(struct_for_randomization)/mb_bytes; | ^~~~~~~~~~~~~~~~~~~ last-pair-probs.cc: In function ‘Alignment parseMaf(const char* const*, const char* const*, char, double, const std::set >&)’: last-pair-probs.cc:438:19: warning: ‘qName’ may be used uninitialized [-Wmaybe-uninitialized] 438 | parseAlignment(score, rName, rStart, rSpan, rStrand, rSize, qName, qStrand, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 439 | linesBeg, linesEnd, strand, scale, circularChroms); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ last-pair-probs.cc:411:17: note: ‘qName’ was declared here 411 | String rName, qName; | ^~~~~ last-pair-probs.cc:438:19: warning: ‘qStrand’ may be used uninitialized [-Wmaybe-uninitialized] 438 | parseAlignment(score, rName, rStart, rSpan, rStrand, rSize, qName, qStrand, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 439 | linesBeg, linesEnd, strand, scale, circularChroms); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ last-pair-probs.cc:412:17: note: ‘qStrand’ was declared here 412 | char rStrand, qStrand; | ^~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastdb-sse2 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySort.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o lastdb.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split-sse2 Alphabet.o LambdaCalculator.o MultiSequence.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 split/cbrc_split_aligner.o split/mcf_last_splitter.o split/last-split.o lastal.cc: In function ‘void alignGapless1(LastAligner&, cbrc::SegmentPairPot&, const cbrc::MultiSequence&, const SeqData&, const Dispatcher&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, const cbrc::SubsetSuffixArray&, const cbrc::uchar*, unsigned int)’: lastal.cc:657:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 657 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:654:14: note: ‘revLen’ was declared here 654 | size_t revLen, fwdLen; | ^~~~~~ lastal.cc:657:78: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 657 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:654:22: note: ‘fwdLen’ was declared here 654 | size_t revLen, fwdLen; | ^~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastal-sse2 Alphabet.o Centroid.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySearch.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o lastal.o Alignment.o AlignmentPot.o AlignmentWrite.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_alignment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o SegmentPair.o SegmentPairPot.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_split_aligner.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/mcf_last_splitter.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 -lz make[3]: Leaving directory '/build/reproducible-path/last-align-1645/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1645' dh_auto_build -- all SFX=-plain CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3" make -j42 INSTALL="install --strip-program=true" all SFX=-plain CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3" make[2]: Entering directory '/build/reproducible-path/last-align-1645' make[3]: Entering directory '/build/reproducible-path/last-align-1645/src' g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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: 1645) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" | cmp -s version.hh - || echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1645) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" > version.hh g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o mcf_alignment_path_adder.o mcf_alignment_path_adder.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from tantan.cc:5: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from GappedXdropAligner2qual.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from GappedXdropAligner3frame.cc:53: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from GappedXdropAlignerDna.cc:4: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from GappedXdropAlignerPssm.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from GappedXdropAlignerFrame.cc:4: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Alignment.hh:8, from AlignmentPot.hh:8, from AlignmentPot.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Alignment.hh:8, from Alignment.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Centroid.cc:4: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from GappedXdropAligner.cc:49: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Alignment.hh:8, from AlignmentWrite.cc:3: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 SubsetSuffixArray.cc: In function ‘void makeSomeBuckets(const cbrc::uchar*, const cbrc::CyclicSubsetSeed&, const size_t*, int, mcf::PackedArray, size_t, size_t, size_t, mcf::ConstPackedArray, size_t, size_t)’: SubsetSuffixArray.cc:190:50: warning: unused parameter ‘saEnd’ [-Wunused-parameter] 190 | size_t saBeg, size_t saEnd) { | ~~~~~~~^~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256d simde__m256d_from_private(simde__m256d_private)’: /usr/include/simde/x86/avx.h:297:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 297 | simde__m256d_from_private(simde__m256d_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8: /usr/include/simde/x86/avx.h: In function ‘simde__m256i simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:281:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 281 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from alp/njn_dynprogproblim.hpp:39, from alp/njn_dynprogproblim.cpp:37: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 116 | virtual inline void copy (const DynProgProb &dynProgProb_) | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] 124 | virtual void copy ( | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from alp/njn_dynprogproblim.hpp:39, from alp/njn_localmaxstat.cpp:39: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 116 | virtual inline void copy (const DynProgProb &dynProgProb_) | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] 124 | virtual void copy ( | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from alp/njn_dynprogproblim.hpp:39, from alp/njn_localmaxstatutil.cpp:39: alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 110 | virtual inline DynProgProb &operator= (const DynProgProb &dynProgProb_) | ^~~~~~~~ alp/njn_dynprogproblim.hpp:90:40: note: by ‘virtual Njn::DynProgProbLim& Njn::DynProgProbLim::operator=(const Njn::DynProgProbLim&)’ 90 | virtual inline DynProgProbLim &operator= (const DynProgProbLim &dynProgProbLim_) | ^~~~~~~~ alp/njn_dynprogprob.hpp:124:22: warning: ‘virtual void Njn::DynProgProb::copy(size_t, const double* const*, size_t, long int, long int, long int, long int (*)(long int, size_t), size_t, const double*)’ was hidden [-Woverloaded-virtual=] 124 | virtual void copy ( | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ alp/njn_dynprogprob.hpp:116:29: warning: ‘virtual void Njn::DynProgProb::copy(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] 116 | virtual inline void copy (const DynProgProb &dynProgProb_) | ^~~~ alp/njn_dynprogproblim.hpp:96:29: note: by ‘virtual void Njn::DynProgProbLim::copy(const Njn::DynProgProbLim&)’ 96 | virtual inline void copy (const DynProgProbLim &dynProgProbLim_) | ^~~~ g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o last-merge-batches.o last-merge-batches.c g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-merge-batches-plain last-merge-batches.o lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int, int)’: lastdb.cc:372:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual] 372 | std::cout.write((char *)m.qualityReader() + b, e - b); | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from GappedXdropAligner.hh:52, from Centroid.hh:7, from Alignment.hh:8, from AlignmentPot.hh:8, from lastal.cc:13: mcf_simd.hh: In function ‘mcf::SimdInt mcf::simdZero()’: mcf_simd.hh:20:32: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 20 | static inline SimdInt simdZero() { | ^ alp/sls_alp_data.cpp: In constructor ‘Sls::alp_data::alp_data(long int, std::string, long int, long int, long int, long int, long int, long int, std::string, std::string, std::string, double, double, double, double, double, bool)’: alp/sls_alp_data.cpp:418:17: warning: ‘*this.Sls::alp_data::d_memory_size_in_MB’ is used uninitialized [-Wuninitialized] 418 | d_memory_size_in_MB+=sizeof(struct_for_randomization)/mb_bytes; | ^~~~~~~~~~~~~~~~~~~ last-pair-probs.cc: In function ‘Alignment parseMaf(const char* const*, const char* const*, char, double, const std::set >&)’: last-pair-probs.cc:438:19: warning: ‘qName’ may be used uninitialized [-Wmaybe-uninitialized] 438 | parseAlignment(score, rName, rStart, rSpan, rStrand, rSize, qName, qStrand, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 439 | linesBeg, linesEnd, strand, scale, circularChroms); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ last-pair-probs.cc:411:17: note: ‘qName’ was declared here 411 | String rName, qName; | ^~~~~ last-pair-probs.cc:438:19: warning: ‘qStrand’ may be used uninitialized [-Wmaybe-uninitialized] 438 | parseAlignment(score, rName, rStart, rSpan, rStrand, rSize, qName, qStrand, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 439 | linesBeg, linesEnd, strand, scale, circularChroms); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ last-pair-probs.cc:412:17: note: ‘qStrand’ was declared here 412 | char rStrand, qStrand; | ^~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -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=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastdb-plain Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySort.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o lastdb.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split-plain Alphabet.o LambdaCalculator.o MultiSequence.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 split/cbrc_split_aligner.o split/mcf_last_splitter.o split/last-split.o lastal.cc: In function ‘void alignGapless1(LastAligner&, cbrc::SegmentPairPot&, const cbrc::MultiSequence&, const SeqData&, const Dispatcher&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, const cbrc::SubsetSuffixArray&, const cbrc::uchar*, unsigned int)’: lastal.cc:657:78: warning: ‘revLen’ may be used uninitialized [-Wmaybe-uninitialized] 657 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:654:14: note: ‘revLen’ was declared here 654 | size_t revLen, fwdLen; | ^~~~~~ lastal.cc:657:78: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized] 657 | SegmentPair sp(refPos - revLen, qryPos - revLen, revLen + fwdLen, score); | ^ lastal.cc:654:22: note: ‘fwdLen’ was declared here 654 | size_t revLen, fwdLen; | ^~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1645=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastal-plain Alphabet.o Centroid.o CyclicSubsetSeed.o LambdaCalculator.o MultiSequence.o MultiSequenceQual.o ScoreMatrix.o SubsetMinimizerFinder.o SubsetSuffixArray.o SubsetSuffixArraySearch.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o lastal.o Alignment.o AlignmentPot.o AlignmentWrite.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_alignment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o SegmentPair.o SegmentPairPot.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_split_aligner.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/mcf_last_splitter.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 -lz make[3]: Leaving directory '/build/reproducible-path/last-align-1645/src' make[2]: Leaving directory '/build/reproducible-path/last-align-1645' make[1]: Leaving directory '/build/reproducible-path/last-align-1645' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/last-align-1645' 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-* 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 /build/reproducible-path/last-align-1645/debian/last-align/usr/bin cd /build/reproducible-path/last-align-1645/debian/last-align/usr/bin \ && for prog in lastdb lastal last-split last-merge-batches last-pair-probs ; do \ ln -s ../lib/last-align/simd-dispatch ${prog} ; done make[1]: Leaving directory '/build/reproducible-path/last-align-1645' dh_installdocs dh_installchangelogs dh_installexamples debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/last-align-1645' dh_installman help2man --no-info --version-string="1645" \ --name='make a dotplot, a.k.a. Oxford Grid, of alignments in LAST tabular format' \ /build/reproducible-path/last-align-1645/bin/last-dotplot > /build/reproducible-path/last-align-1645/debian/last-align/usr/share/man/man1/last-dotplot.1 help2man --no-info --version-string="1645" \ --name="genome-scale comparison of biological sequences" \ --help-option="-h" \ /build/reproducible-path/last-align-1645/debian/last-align/usr/bin/lastal > /build/reproducible-path/last-align-1645/debian/last-align/usr/share/man/man1/lastal.1 # help2man output needs manual postprocessing - see debian/mans #help2man --no-info --version-string="1645" \ # --name="genome-scale comparison of biological sequences" \ # --help-option="-h" \ # /build/reproducible-path/last-align-1645/debian/last-align/usr/bin/lastdb > /build/reproducible-path/last-align-1645/debian/last-align/usr/share/man/man1/lastdb.1 help2man --no-info --version-string="1645" \ --name="Sort MAF-format alignments by sequence name" \ /build/reproducible-path/last-align-1645/bin/maf-sort > /build/reproducible-path/last-align-1645/debian/last-align/usr/share/man/man1/maf-sort.1 help2man --no-info --version-string="1645" \ --name="changes the order of the sequences in MAF-format alignments" \ /build/reproducible-path/last-align-1645/bin/maf-swap > /build/reproducible-path/last-align-1645/debian/last-align/usr/share/man/man1/maf-swap.1 # help2man output needs manual postprocessing - see debian/mans #help2man --no-info --version-string="1645" \ # --name="Add extra column with mapping probabilities" \ # /build/reproducible-path/last-align-1645/bin/last-map-probs > /build/reproducible-path/last-align-1645/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="1645" \ # --name="Read files of lastal output, merge corresponding batches, and write them." \ # /build/reproducible-path/last-align-1645/bin/last-merge-batches > /build/reproducible-path/last-align-1645/debian/last-align/usr/share/man/man1/last-merge-batches.1 # # These bin were droped #help2man --no-info --version-string="1645" \ # --name="Clean up MAF-format alignments" \ # /build/reproducible-path/last-align-1645/bin/last-reduce-alignments > /build/reproducible-path/last-align-1645/debian/last-align/usr/share/man/man1/last-reduce-alignments.1 #help2man --no-info --version-string="1645" \ # --name='Remove MAF-format alignments which are "dominated" by others' \ # /build/reproducible-path/last-align-1645/bin/last-remove-dominated > /build/reproducible-path/last-align-1645/debian/last-align/usr/share/man/man1/last-remove-dominated.1 help2man --no-info --version-string="1645" \ --name='Estimates "split" or "spliced" alignments.' \ /build/reproducible-path/last-align-1645/debian/last-align/usr/bin/last-split > /build/reproducible-path/last-align-1645/debian/last-align/usr/share/man/man1/last-split.1 help2man --no-info --version-string="1645" \ --name="Join two or more sets of MAF-format multiple alignments" \ /build/reproducible-path/last-align-1645/bin/maf-join > /build/reproducible-path/last-align-1645/debian/last-align/usr/share/man/man1/maf-join.1 help2man --no-info --version-string="1645" \ --help-option="-h" \ /build/reproducible-path/last-align-1645/bin/maf-cut > /build/reproducible-path/last-align-1645/debian/last-align/usr/share/man/man1/maf-cut.1 help2man --no-info --version-string="1645" \ --name="Convert MAF-format alignments to tabular format" \ /build/reproducible-path/last-align-1645/bin/maf-convert > /build/reproducible-path/last-align-1645/debian/last-align/usr/share/man/man1/maf-convert.1 help2man --no-info --version-string="1645" \ --name="Read 2 fastq files, and write them interleaved" \ /build/reproducible-path/last-align-1645/bin/fastq-interleave > /build/reproducible-path/last-align-1645/debian/last-align/usr/share/man/man1/fastq-interleave.1 help2man --no-info --version-string="1645" \ --name="Read files of lastal output, merge corresponding batches, and write them" \ /build/reproducible-path/last-align-1645/debian/last-align/usr/bin/last-merge-batches > /build/reproducible-path/last-align-1645/debian/last-align/usr/share/man/man1/last-merge-batches.1 # help2man output needs manual postprocessing - see debian/mans #help2man --no-info --version-string="1645" \ # --name="Read alignments of paired DNA reads to a genome, and do estimations" \ # /build/reproducible-path/last-align-1645/debian/last-align/usr/bin/last-pair-probs > /build/reproducible-path/last-align-1645/debian/last-align/usr/share/man/man1/last-pair-probs.1 help2man --no-info --version-string="1645" \ --name="Get alignments that have a segment with score >= threshold, with gentle masking of lowercase letters" \ /build/reproducible-path/last-align-1645/bin/last-postmask > /build/reproducible-path/last-align-1645/debian/last-align/usr/share/man/man1/last-postmask.1 help2man --no-info --version-string="1645" \ --name="Try to find suitable score parameters for aligning the given sequences" \ /build/reproducible-path/last-align-1645/bin/last-train > /build/reproducible-path/last-align-1645/debian/last-align/usr/share/man/man1/last-train.1 help2man --no-info --version-string="1645" \ --name="Keep the first of identical sequences" \ --help-option="-h" \ /build/reproducible-path/last-align-1645/debian/last-align/usr/bin/fasta-nr > /build/reproducible-path/last-align-1645/debian/last-align/usr/share/man/man1/fasta-nr.1 make[1]: Leaving directory '/build/reproducible-path/last-align-1645' dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/build/reproducible-path/last-align-1645' dh_gencontrol -- -VBuilt-Using="simde (= 0.8.2-3), " make[1]: Leaving directory '/build/reproducible-path/last-align-1645' dh_md5sums dh_builddeb dpkg-deb: building package 'last-align' in '../last-align_1645-1_amd64.deb'. dpkg-deb: building package 'last-align-dbgsym' in '../last-align-dbgsym_1645-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../last-align_1645-1_amd64.buildinfo dpkg-genchanges --build=binary -O../last-align_1645-1_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) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2955330 and its subdirectories I: Current time: Thu Nov 26 02:56:12 -12 2026 I: pbuilder-time-stamp: 1795704972 Fri Oct 24 08:33:15 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Fri Oct 24 08:33:15 UTC 2025 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Fri Oct 24 08:42:48 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Fri Oct 24 08:42:48 UTC 2025 I: last-align_1645-1_amd64.changes: Format: 1.8 Date: Sun, 28 Sep 2025 15:32:21 +0530 Source: last-align Binary: last-align last-align-dbgsym Architecture: amd64 Version: 1645-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: last-align - genome-scale comparison of biological sequences Changes: last-align (1645-1) unstable; urgency=medium . * Team Upload. * New upstream version 1645 * Drop myself from uploaders * Drop Rules-Requires-Root field * Drop Redundant B-D on debhelper Checksums-Sha1: 9c39037b485e4e3889932941fdb63cd9872518d9 45327076 last-align-dbgsym_1645-1_amd64.deb 7d2536a66ecfd9a4465ac6a7e4c66337edb8bfc6 6327 last-align_1645-1_amd64.buildinfo 4f5be0b6711f3074b9907571c3a05d672b6f6ba5 1902136 last-align_1645-1_amd64.deb Checksums-Sha256: d57966cf5687edcb12ab08dc38b728b1686ca851ca604df905aa4c82692b180e 45327076 last-align-dbgsym_1645-1_amd64.deb 1560d0bb18853ba08f51b0cca30a26707c95ce35c237b47b294e932988d1e62c 6327 last-align_1645-1_amd64.buildinfo 74f7099d460d31ad78474fe6291ac5e33890c9b0c77c70665bf7e92e4a0a1ed9 1902136 last-align_1645-1_amd64.deb Files: 559c3ad6c9a33ea97516c61d8844eb6a 45327076 debug optional last-align-dbgsym_1645-1_amd64.deb 2ecf0e4502b51fc7162841f069398491 6327 science optional last-align_1645-1_amd64.buildinfo 90c017aa8c7dd9c1e5dfb21001587e48 1902136 science optional last-align_1645-1_amd64.deb Fri Oct 24 08:42:49 UTC 2025 I: diffoscope 306 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_4-72586.service; invocation ID: 986cf2721531495c869424e508a6e9e1 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.ZTxVM3CB/last-align_1645-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.ZTxVM3CB/last-align_1645-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.ZTxVM3CB/last-align_1645-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.ZTxVM3CB/b1/last-align_1645-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.ZTxVM3CB/b2/last-align_1645-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 205ms CPU time consumed: 171ms Memory peak: 17.5M (swap: 0B) Fri Oct 24 08:42:49 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Fri Oct 24 08:42:49 UTC 2025 I: last-align from forky built successfully and reproducibly on amd64. Fri Oct 24 08:42:50 UTC 2025 I: Removing signed last-align_1645-1_amd64.buildinfo.asc files: removed './b1/last-align_1645-1_amd64.buildinfo.asc' removed './b2/last-align_1645-1_amd64.buildinfo.asc'