I: pbuilder: network access will be disabled during build
I: Current time: Tue Feb 25 13:27:59 +14 2025
I: pbuilder-time-stamp: 1740439679
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-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: using eatmydata during job
I: Copying source file
I: copying [last-align_1542-1.dsc]
I: copying [./last-align_1542.orig.tar.xz]
I: copying [./last-align_1542-1.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./last-align_1542-1.dsc: unsupported subcommand
dpkg-source: info: extracting last-align in last-align-1542
dpkg-source: info: unpacking last-align_1542.orig.tar.xz
dpkg-source: info: unpacking last-align_1542-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying helpMakefiles.patch
dpkg-source: info: applying simde
dpkg-source: info: applying fix-shebang.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/23349/tmp/hooks/D01_modify_environment starting
debug: Running on ionos2-i386.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Feb 24 23:28 /bin/sh -> /bin/bash
I: Setting pbuilder2's login shell to /bin/bash
I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
I: user script /srv/workspace/pbuilder/23349/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/23349/tmp/hooks/D02_print_environment starting
I: set
  BASH=/bin/sh
  BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
  BASH_ALIASES=()
  BASH_ARGC=()
  BASH_ARGV=()
  BASH_CMDS=()
  BASH_LINENO=([0]="12" [1]="0")
  BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
  BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
  BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="i686-pc-linux-gnu")
  BASH_VERSION='5.2.37(1)-release'
  BUILDDIR=/build/reproducible-path
  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
  BUILDUSERNAME=pbuilder2
  BUILD_ARCH=i386
  DEBIAN_FRONTEND=noninteractive
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 '
  DIRSTACK=()
  DISTRIBUTION=trixie
  EUID=0
  FUNCNAME=([0]="Echo" [1]="main")
  GROUPS=()
  HOME=/root
  HOSTNAME=i-capture-the-hostname
  HOSTTYPE=i686
  HOST_ARCH=i386
  IFS=' 	
  '
  INVOCATION_ID=c60ec0bd84024c8ab5e1f35a5e498557
  LANG=C
  LANGUAGE=de_CH:de
  LC_ALL=C
  LD_LIBRARY_PATH=/usr/lib/libeatmydata
  LD_PRELOAD=libeatmydata.so
  MACHTYPE=i686-pc-linux-gnu
  MAIL=/var/mail/root
  OPTERR=1
  OPTIND=1
  OSTYPE=linux-gnu
  PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
  PBCURRENTCOMMANDLINEOPERATION=build
  PBUILDER_OPERATION=build
  PBUILDER_PKGDATADIR=/usr/share/pbuilder
  PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
  PBUILDER_SYSCONFDIR=/etc
  PIPESTATUS=([0]="0")
  POSIXLY_CORRECT=y
  PPID=23349
  PS4='+ '
  PWD=/
  SHELL=/bin/bash
  SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
  SHLVL=3
  SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.yeW9cgkT/pbuilderrc_1Nv2 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.yeW9cgkT/b2 --logfile b2/build.log last-align_1542-1.dsc'
  SUDO_GID=112
  SUDO_UID=107
  SUDO_USER=jenkins
  TERM=unknown
  TZ=/usr/share/zoneinfo/Etc/GMT-14
  UID=0
  USER=root
  _='I: set'
  http_proxy=http://46.16.76.132:3128
I: uname -a
  Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/23349/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: i386
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
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, debhelper
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19788 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 debhelper; however:
  Package debhelper 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:
  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} libarchive-zip-perl{a} libbrotli1{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfreetype6{a} libfribidi0{a} libglib2.0-0t64{a} libgraphite2-3{a} libharfbuzz0b{a} libicu72{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} libreadline8t64{a} libsharpyuv0{a} libsimde-dev{a} libtiff6{a} libtool{a} libuchardet0{a} libunistring5{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxml2{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, 72 newly installed, 0 to remove and 0 not upgraded.
Need to get 34.9 MB of archives. After unpacking 131 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main i386 liblocale-gettext-perl i386 1.07-7+b1 [15.4 kB]
Get: 2 http://deb.debian.org/debian trixie/main i386 libpython3.13-minimal i386 3.13.2-1 [859 kB]
Get: 3 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.4-1 [107 kB]
Get: 4 http://deb.debian.org/debian trixie/main i386 python3.13-minimal i386 3.13.2-1 [2266 kB]
Get: 5 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.13.1-2 [27.0 kB]
Get: 6 http://deb.debian.org/debian trixie/main i386 media-types all 10.1.0 [26.9 kB]
Get: 7 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB]
Get: 8 http://deb.debian.org/debian trixie/main i386 tzdata all 2025a-2 [259 kB]
Get: 9 http://deb.debian.org/debian trixie/main i386 libffi8 i386 3.4.7-1 [21.4 kB]
Get: 10 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-6 [69.4 kB]
Get: 11 http://deb.debian.org/debian trixie/main i386 libreadline8t64 i386 8.2-6 [173 kB]
Get: 12 http://deb.debian.org/debian trixie/main i386 libpython3.13-stdlib i386 3.13.2-1 [1985 kB]
Get: 13 http://deb.debian.org/debian trixie/main i386 python3.13 i386 3.13.2-1 [745 kB]
Get: 14 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.13.1-2 [9952 B]
Get: 15 http://deb.debian.org/debian trixie/main i386 python3 i386 3.13.1-2 [28.0 kB]
Get: 16 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 17 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 18 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 19 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 20 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.23.1-1 [245 kB]
Get: 21 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 22 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-7 [1199 kB]
Get: 23 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.4-4 [96.4 kB]
Get: 24 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 25 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 26 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-5 [301 kB]
Get: 27 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB]
Get: 28 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 29 http://deb.debian.org/debian trixie/main i386 automake all 1:1.17-3 [862 kB]
Get: 30 http://deb.debian.org/debian trixie/main i386 autopoint all 0.23.1-1 [770 kB]
Get: 31 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 32 http://deb.debian.org/debian trixie/main i386 libtool all 2.5.4-3 [539 kB]
Get: 33 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 34 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 35 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 36 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 37 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 38 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 39 http://deb.debian.org/debian trixie/main i386 libunistring5 i386 1.3-1 [458 kB]
Get: 40 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-6 [9582 kB]
Get: 41 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB]
Get: 42 http://deb.debian.org/debian trixie/main i386 gettext i386 0.23.1-1 [1714 kB]
Get: 43 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 44 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 45 http://deb.debian.org/debian trixie/main i386 debhelper all 13.24.1 [920 kB]
Get: 46 http://deb.debian.org/debian trixie/main i386 help2man i386 1.49.3 [198 kB]
Get: 47 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB]
Get: 48 http://deb.debian.org/debian trixie/main i386 libdeflate0 i386 1.23-1+b1 [48.4 kB]
Get: 49 http://deb.debian.org/debian trixie/main i386 libpng16-16t64 i386 1.6.46-4 [292 kB]
Get: 50 http://deb.debian.org/debian trixie/main i386 libfreetype6 i386 2.13.3+dfsg-1 [464 kB]
Get: 51 http://deb.debian.org/debian trixie/main i386 libfribidi0 i386 1.0.16-1 [27.0 kB]
Get: 52 http://deb.debian.org/debian trixie/main i386 libglib2.0-0t64 i386 2.83.3-2 [1581 kB]
Get: 53 http://deb.debian.org/debian trixie/main i386 libgraphite2-3 i386 1.3.14-2+b1 [77.8 kB]
Get: 54 http://deb.debian.org/debian trixie/main i386 libharfbuzz0b i386 10.2.0-1 [504 kB]
Get: 55 http://deb.debian.org/debian trixie/main i386 libimagequant0 i386 2.18.0-1+b2 [36.0 kB]
Get: 56 http://deb.debian.org/debian trixie/main i386 libjbig0 i386 2.1-6.1+b2 [32.2 kB]
Get: 57 http://deb.debian.org/debian trixie/main i386 libjpeg62-turbo i386 1:2.1.5-3+b1 [171 kB]
Get: 58 http://deb.debian.org/debian trixie/main i386 liblcms2-2 i386 2.16-2 [171 kB]
Get: 59 http://deb.debian.org/debian trixie/main i386 liblerc4 i386 4.0.0+ds-5 [191 kB]
Get: 60 http://deb.debian.org/debian trixie/main i386 libopenjp2-7 i386 2.5.3-1 [215 kB]
Get: 61 http://deb.debian.org/debian trixie/main i386 libraqm0 i386 0.10.2-1 [14.6 kB]
Get: 62 http://deb.debian.org/debian trixie/main i386 libsharpyuv0 i386 1.5.0-0.1 [115 kB]
Get: 63 http://deb.debian.org/debian trixie/main i386 libsimde-dev all 0.8.2-2 [467 kB]
Get: 64 http://deb.debian.org/debian trixie/main i386 libwebp7 i386 1.5.0-0.1 [329 kB]
Get: 65 http://deb.debian.org/debian trixie/main i386 libtiff6 i386 4.5.1+git230720-5 [339 kB]
Get: 66 http://deb.debian.org/debian trixie/main i386 libwebpdemux2 i386 1.5.0-0.1 [114 kB]
Get: 67 http://deb.debian.org/debian trixie/main i386 libwebpmux3 i386 1.5.0-0.1 [127 kB]
Get: 68 http://deb.debian.org/debian trixie/main i386 libxau6 i386 1:1.0.11-1 [20.7 kB]
Get: 69 http://deb.debian.org/debian trixie/main i386 libxdmcp6 i386 1:1.1.5-1 [28.2 kB]
Get: 70 http://deb.debian.org/debian trixie/main i386 libxcb1 i386 1.17.0-2+b1 [148 kB]
Get: 71 http://deb.debian.org/debian trixie/main i386 python3-pil i386 11.1.0-5 [535 kB]
Get: 72 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB]
Fetched 34.9 MB in 0s (81.0 MB/s)
Preconfiguring packages ...
Selecting previously unselected package liblocale-gettext-perl.
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(Reading database ... 19788 files and directories currently installed.)
Preparing to unpack .../liblocale-gettext-perl_1.07-7+b1_i386.deb ...
Unpacking liblocale-gettext-perl (1.07-7+b1) ...
Selecting previously unselected package libpython3.13-minimal:i386.
Preparing to unpack .../libpython3.13-minimal_3.13.2-1_i386.deb ...
Unpacking libpython3.13-minimal:i386 (3.13.2-1) ...
Selecting previously unselected package libexpat1:i386.
Preparing to unpack .../libexpat1_2.6.4-1_i386.deb ...
Unpacking libexpat1:i386 (2.6.4-1) ...
Selecting previously unselected package python3.13-minimal.
Preparing to unpack .../python3.13-minimal_3.13.2-1_i386.deb ...
Unpacking python3.13-minimal (3.13.2-1) ...
Setting up libpython3.13-minimal:i386 (3.13.2-1) ...
Setting up libexpat1:i386 (2.6.4-1) ...
Setting up python3.13-minimal (3.13.2-1) ...
Selecting previously unselected package python3-minimal.
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Preparing to unpack .../0-python3-minimal_3.13.1-2_i386.deb ...
Unpacking python3-minimal (3.13.1-2) ...
Selecting previously unselected package media-types.
Preparing to unpack .../1-media-types_10.1.0_all.deb ...
Unpacking media-types (10.1.0) ...
Selecting previously unselected package netbase.
Preparing to unpack .../2-netbase_6.4_all.deb ...
Unpacking netbase (6.4) ...
Selecting previously unselected package tzdata.
Preparing to unpack .../3-tzdata_2025a-2_all.deb ...
Unpacking tzdata (2025a-2) ...
Selecting previously unselected package libffi8:i386.
Preparing to unpack .../4-libffi8_3.4.7-1_i386.deb ...
Unpacking libffi8:i386 (3.4.7-1) ...
Selecting previously unselected package readline-common.
Preparing to unpack .../5-readline-common_8.2-6_all.deb ...
Unpacking readline-common (8.2-6) ...
Selecting previously unselected package libreadline8t64:i386.
Preparing to unpack .../6-libreadline8t64_8.2-6_i386.deb ...
Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
Unpacking libreadline8t64:i386 (8.2-6) ...
Selecting previously unselected package libpython3.13-stdlib:i386.
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Unpacking libpython3.13-stdlib:i386 (3.13.2-1) ...
Selecting previously unselected package python3.13.
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Unpacking python3.13 (3.13.2-1) ...
Selecting previously unselected package libpython3-stdlib:i386.
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Unpacking libpython3-stdlib:i386 (3.13.1-2) ...
Setting up python3-minimal (3.13.1-2) ...
Selecting previously unselected package python3.
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Preparing to unpack .../00-python3_3.13.1-2_i386.deb ...
Unpacking python3 (3.13.1-2) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
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Unpacking libmagic-mgc (1:5.45-3+b1) ...
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Setting up media-types (10.1.0) ...
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Setting up libgraphite2-3:i386 (1.3.14-2+b1) ...
Setting up libsimde-dev (0.8.2-2) ...
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Setting up libxdmcp6:i386 (1:1.1.5-1) ...
Setting up libxcb1:i386 (1.17.0-2+b1) ...
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Setting up liblerc4:i386 (4.0.0+ds-5) ...
Setting up bsdextrautils (2.40.4-4) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.24.1) ...
Setting up libbrotli1:i386 (1.1.0-2+b6) ...
Setting up libmagic1t64:i386 (1:5.45-3+b1) ...
Setting up libdeflate0:i386 (1.23-1+b1) ...
Setting up gettext-base (0.23.1-1) ...
Setting up m4 (1.4.19-5) ...
Setting up file (1:5.45-3+b1) ...
Setting up libjbig0:i386 (2.1-6.1+b2) ...
Setting up libelf1t64:i386 (0.192-4) ...
Setting up tzdata (2025a-2) ...

Current default time zone: 'Etc/UTC'
Local time is now:      Mon Feb 24 23:28:32 UTC 2025.
Universal Time is now:  Mon Feb 24 23:28:32 UTC 2025.
Run 'dpkg-reconfigure tzdata' if you wish to change it.

Setting up autotools-dev (20220109.1) ...
Setting up libjpeg62-turbo:i386 (1:2.1.5-3+b1) ...
Setting up libfribidi0:i386 (1.0.16-1) ...
Setting up libimagequant0:i386 (2.18.0-1+b2) ...
Setting up libunistring5:i386 (1.3-1) ...
Setting up libpng16-16t64:i386 (1.6.46-4) ...
Setting up autopoint (0.23.1-1) ...
Setting up autoconf (2.72-3) ...
Setting up libwebp7:i386 (1.5.0-0.1) ...
Setting up zlib1g-dev:i386 (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up libffi8:i386 (3.4.7-1) ...
Setting up dwz (0.15-1+b1) ...
Setting up sensible-utils (0.0.24) ...
Setting up libtiff6:i386 (4.5.1+git230720-5) ...
Setting up libuchardet0:i386 (0.0.8-1+b2) ...
Setting up libopenjp2-7:i386 (2.5.3-1) ...
Setting up netbase (6.4) ...
Setting up libwebpmux3:i386 (1.5.0-0.1) ...
Setting up readline-common (8.2-6) ...
Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Setting up liblocale-gettext-perl (1.07-7+b1) ...
Setting up automake (1:1.17-3) ...
update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.1-2) ...
Setting up gettext (0.23.1-1) ...
Setting up libtool (2.5.4-3) ...
Setting up libwebpdemux2:i386 (1.5.0-0.1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up help2man (1.49.3) ...
Setting up dh-autoreconf (20) ...
Setting up libglib2.0-0t64:i386 (2.83.3-2) ...
No schema files found: doing nothing.
Setting up libfreetype6:i386 (2.13.3+dfsg-1) ...
Setting up libreadline8t64:i386 (8.2-6) ...
Setting up dh-strip-nondeterminism (1.14.1-2) ...
Setting up groff-base (1.23.0-7) ...
Setting up libharfbuzz0b:i386 (10.2.0-1) ...
Setting up libpython3.13-stdlib:i386 (3.13.2-1) ...
Setting up libpython3-stdlib:i386 (3.13.1-2) ...
Setting up python3.13 (3.13.2-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up python3 (3.13.1-2) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libraqm0:i386 (0.10.2-1) ...
Setting up debhelper (13.24.1) ...
Setting up python3-pil:i386 (11.1.0-5) ...
Processing triggers for libc-bin (2.40-7) ...
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
I: Building the package
I: user script /srv/workspace/pbuilder/23349/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for trixie
I: user script /srv/workspace/pbuilder/23349/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/last-align-1542/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S  > ../last-align_1542-1_source.changes
dpkg-buildpackage: info: source package last-align
dpkg-buildpackage: info: source version 1542-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Charles Plessy <plessy@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
 debian/rules clean
dh  clean
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/last-align-1542'
for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 sse plain; do \
	dh_auto_clean -- SFX=-${SIMD} ; done
	make -j10 clean SFX=-avx2
make[2]: Entering directory '/build/reproducible-path/last-align-1542'
make[3]: Entering directory '/build/reproducible-path/last-align-1542/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-1542/src'
make[2]: Leaving directory '/build/reproducible-path/last-align-1542'
	make -j10 clean SFX=-avx
make[2]: Entering directory '/build/reproducible-path/last-align-1542'
make[3]: Entering directory '/build/reproducible-path/last-align-1542/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-1542/src'
make[2]: Leaving directory '/build/reproducible-path/last-align-1542'
	make -j10 clean SFX=-sse4.1
make[2]: Entering directory '/build/reproducible-path/last-align-1542'
make[3]: Entering directory '/build/reproducible-path/last-align-1542/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-1542/src'
make[2]: Leaving directory '/build/reproducible-path/last-align-1542'
	make -j10 clean SFX=-ssse3
make[2]: Entering directory '/build/reproducible-path/last-align-1542'
make[3]: Entering directory '/build/reproducible-path/last-align-1542/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-1542/src'
make[2]: Leaving directory '/build/reproducible-path/last-align-1542'
	make -j10 clean SFX=-sse3
make[2]: Entering directory '/build/reproducible-path/last-align-1542'
make[3]: Entering directory '/build/reproducible-path/last-align-1542/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-1542/src'
make[2]: Leaving directory '/build/reproducible-path/last-align-1542'
	make -j10 clean SFX=-sse2
make[2]: Entering directory '/build/reproducible-path/last-align-1542'
make[3]: Entering directory '/build/reproducible-path/last-align-1542/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-1542/src'
make[2]: Leaving directory '/build/reproducible-path/last-align-1542'
	make -j10 clean SFX=-sse
make[2]: Entering directory '/build/reproducible-path/last-align-1542'
make[3]: Entering directory '/build/reproducible-path/last-align-1542/src'
rm -f ../bin/lastdb-sse ../bin/lastal-sse ../bin/last-split-sse ../bin/last-merge-batches-sse ../bin/last-pair-probs-sse *.o* */*.o*
make[3]: Leaving directory '/build/reproducible-path/last-align-1542/src'
make[2]: Leaving directory '/build/reproducible-path/last-align-1542'
	make -j10 clean SFX=-plain
make[2]: Entering directory '/build/reproducible-path/last-align-1542'
make[3]: Entering directory '/build/reproducible-path/last-align-1542/src'
rm -f ../bin/lastdb-plain ../bin/lastal-plain ../bin/last-split-plain ../bin/last-merge-batches-plain ../bin/last-pair-probs-plain *.o* */*.o*
make[3]: Leaving directory '/build/reproducible-path/last-align-1542/src'
make[2]: Leaving directory '/build/reproducible-path/last-align-1542'
for i in last-merge-batches last-pair-probs last-split lastal lastdb ; \
do \
   for j in avx avx2 sse2 sse3 sse4.1 ssse3 sse3 sse2 sse ; \
   do \
      rm -f bin/$i-$j ; \
   done ; \
done
make[1]: Leaving directory '/build/reproducible-path/last-align-1542'
   dh_clean
 debian/rules binary
dh  binary
   dh_update_autotools_config
   dh_autoreconf
   dh_auto_configure
   debian/rules override_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/last-align-1542'
mkdir -p /build/reproducible-path/last-align-1542/debian/last-align/usr
mkdir -p /build/reproducible-path/last-align-1542/debian/last-align/usr/lib/last-align
for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 sse; do \
	dh_auto_build -- all SFX=-${SIMD} CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -m${SIMD}" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -m${SIMD}" ; \
	find . -name '*.o' -delete ; \
	find . -name '*.o5' -delete ; \
done
	make -j10 "INSTALL=install --strip-program=true" all SFX=-avx2 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -mavx2" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2"
make[2]: Entering directory '/build/reproducible-path/last-align-1542'
make[3]: Entering directory '/build/reproducible-path/last-align-1542/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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o fileMap.o fileMap.cc
dna_words_finder.cc: In member function ‘void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)’:
dna_words_finder.cc:50:41: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   50 |     baseToCode[lettersToNumbers["ACGT"[i]]] = c;
      |                                 ~~~~~~~~^
dna_words_finder.cc:51:63: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   51 |     if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c;
      |                                                       ~~~~~~~~^
In file included from SubsetSuffixArraySort.cc:6:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
In file included from SubsetSuffixArray.cc:3:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o tantan.o tantan.cc
echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1542) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" | cmp -s version.hh - || echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1542) ' | 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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o lastal.o lastal.cc
In file included from SubsetSuffixArraySearch.cc:3:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o AlignmentPot.o AlignmentPot.cc
In file included from last.hh:11,
                 from lastal.cc:5:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/sls_basic.o alp/sls_basic.cpp
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;
      |              ^~~~~~
In file included from Alignment.hh:10,
                 from AlignmentPot.hh:8,
                 from lastal.cc:13:
In member function ‘size_t cbrc::SegmentPair::end2() const’,
    inlined from ‘void alignGapless1(LastAligner&, cbrc::SegmentPairPot&, const cbrc::MultiSequence&, const SeqData&, const Dispatcher&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, const cbrc::SubsetSuffixArray&, const cbrc::uchar*, unsigned int)’ at lastal.cc:658:21:
SegmentPair.hh:30:41: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized]
   30 |   size_t end2() const { return start2 + size; }  // end in sequence 2
      |                                         ^~~~
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: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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -c -o alp/njn_ioutil.o alp/njn_ioutil.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: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:101:29: note:   by ‘Njn::DynProgProbLim::copy’
  101 |         virtual inline void copy (
      |                             ^~~~
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:101:29: note:   by ‘Njn::DynProgProbLim::copy’
  101 |         virtual inline void copy (
      |                             ^~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -I. -c -o GeneticCode.o GeneticCode.cc
In file included from last.hh:11,
                 from lastdb.cc:6:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int, int)’:
lastdb.cc:356:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual]
  356 |       std::cout.write((char *)m.qualityReader() + b, e - b);
      |                       ^~~~~~~~~~~~~~~~~~~~~~~~~
last-pair-probs.cc: In function ‘Alignment parseMaf(const char* const*, const char* const*, char, double, const std::set<std::__cxx11::basic_string<char> >&)’:
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;
      |                 ^~~~~~~
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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -mavx2 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-merge-batches-avx2 last-merge-batches.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -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-1542/src'
make[2]: Leaving directory '/build/reproducible-path/last-align-1542'
	make -j10 "INSTALL=install --strip-program=true" all SFX=-avx "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -mavx" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx"
make[2]: Entering directory '/build/reproducible-path/last-align-1542'
make[3]: Entering directory '/build/reproducible-path/last-align-1542/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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o TantanMasker.o TantanMasker.cc
In file included from SubsetSuffixArray.cc:3:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
In file included from SubsetSuffixArraySort.cc:6:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o mcf_substitution_matrix_stats.o mcf_substitution_matrix_stats.cc
dna_words_finder.cc: In member function ‘void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)’:
dna_words_finder.cc:50:41: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   50 |     baseToCode[lettersToNumbers["ACGT"[i]]] = c;
      |                                 ~~~~~~~~^
dna_words_finder.cc:51:63: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   51 |     if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c;
      |                                                       ~~~~~~~~^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o tantan.o tantan.cc
echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1542) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" | cmp -s version.hh - || echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1542) ' | 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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o SubsetSuffixArraySearch.o SubsetSuffixArraySearch.cc
In file included from SubsetSuffixArraySearch.cc:3:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o AlignmentPot.o AlignmentPot.cc
In file included from last.hh:11,
                 from lastal.cc:5:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/njn_random.o alp/njn_random.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: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:101:29: note:   by ‘Njn::DynProgProbLim::copy’
  101 |         virtual inline void copy (
      |                             ^~~~
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:101:29: note:   by ‘Njn::DynProgProbLim::copy’
  101 |         virtual inline void copy (
      |                             ^~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -c -o alp/sls_falp_alignment_evaluer.o alp/sls_falp_alignment_evaluer.cpp
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;
      |              ^~~~~~
In file included from Alignment.hh:10,
                 from AlignmentPot.hh:8,
                 from lastal.cc:13:
In member function ‘size_t cbrc::SegmentPair::end2() const’,
    inlined from ‘void alignGapless1(LastAligner&, cbrc::SegmentPairPot&, const cbrc::MultiSequence&, const SeqData&, const Dispatcher&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, const cbrc::SubsetSuffixArray&, const cbrc::uchar*, unsigned int)’ at lastal.cc:658:21:
SegmentPair.hh:30:41: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized]
   30 |   size_t end2() const { return start2 + size; }  // end in sequence 2
      |                                         ^~~~
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: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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -I. -c -o lastdb.o lastdb.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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -mavx -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-merge-batches-avx last-merge-batches.o
In file included from last.hh:11,
                 from lastdb.cc:6:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int, int)’:
lastdb.cc:356:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual]
  356 |       std::cout.write((char *)m.qualityReader() + b, e - b);
      |                       ^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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
last-pair-probs.cc: In function ‘Alignment parseMaf(const char* const*, const char* const*, char, double, const std::set<std::__cxx11::basic_string<char> >&)’:
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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -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-1542/src'
make[2]: Leaving directory '/build/reproducible-path/last-align-1542'
	make -j10 "INSTALL=install --strip-program=true" all SFX=-sse4.1 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -msse4.1" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1"
make[2]: Entering directory '/build/reproducible-path/last-align-1542'
make[3]: Entering directory '/build/reproducible-path/last-align-1542/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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o TantanMasker.o TantanMasker.cc
In file included from SubsetSuffixArraySort.cc:6:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
In file included from SubsetSuffixArray.cc:3:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o fileMap.o fileMap.cc
dna_words_finder.cc: In member function ‘void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)’:
dna_words_finder.cc:50:41: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   50 |     baseToCode[lettersToNumbers["ACGT"[i]]] = c;
      |                                 ~~~~~~~~^
dna_words_finder.cc:51:63: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   51 |     if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c;
      |                                                       ~~~~~~~~^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o tantan.o tantan.cc
echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1542) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" | cmp -s version.hh - || echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1542) ' | 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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o SubsetSuffixArraySearch.o SubsetSuffixArraySearch.cc
In file included from tantan.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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o LastalArguments.o LastalArguments.cc
In file included from SubsetSuffixArraySearch.cc:3:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o Alignment.o Alignment.cc
In file included from last.hh:11,
                 from lastal.cc:5:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o AlignmentWrite.o AlignmentWrite.cc
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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc
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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc
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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o GappedXdropAligner2qual.o GappedXdropAligner2qual.cc
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 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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc
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 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 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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o mcf_gap_costs.o mcf_gap_costs.cc
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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp
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;
      |              ^~~~~~
In file included from Alignment.hh:10:
In member function ‘size_t cbrc::SegmentPair::end2() const’,
    inlined from ‘void alignGapless1(LastAligner&, cbrc::SegmentPairPot&, const cbrc::MultiSequence&, const SeqData&, const Dispatcher&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, const cbrc::SubsetSuffixArray&, const cbrc::uchar*, unsigned int)’ at lastal.cc:658:21:
SegmentPair.hh:30:41: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized]
   30 |   size_t end2() const { return start2 + size; }  // end in sequence 2
      |                                         ^~~~
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: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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -c -o alp/njn_ioutil.o alp/njn_ioutil.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: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:101:29: note:   by ‘Njn::DynProgProbLim::copy’
  101 |         virtual inline void copy (
      |                             ^~~~
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:101:29: note:   by ‘Njn::DynProgProbLim::copy’
  101 |         virtual inline void copy (
      |                             ^~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -I. -c -o lastdb.o lastdb.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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -msse4.1 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-merge-batches-sse4.1 last-merge-batches.o
In file included from last.hh:11,
                 from lastdb.cc:6:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int, int)’:
lastdb.cc:356:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual]
  356 |       std::cout.write((char *)m.qualityReader() + b, e - b);
      |                       ^~~~~~~~~~~~~~~~~~~~~~~~~
last-pair-probs.cc: In function ‘Alignment parseMaf(const char* const*, const char* const*, char, double, const std::set<std::__cxx11::basic_string<char> >&)’:
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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -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-1542/src'
make[2]: Leaving directory '/build/reproducible-path/last-align-1542'
	make -j10 "INSTALL=install --strip-program=true" all SFX=-ssse3 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -mssse3" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3"
make[2]: Entering directory '/build/reproducible-path/last-align-1542'
make[3]: Entering directory '/build/reproducible-path/last-align-1542/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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o TantanMasker.o TantanMasker.cc
In file included from SubsetSuffixArraySort.cc:6:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
In file included from SubsetSuffixArray.cc:3:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o cbrc_linalg.o cbrc_linalg.cc
dna_words_finder.cc: In member function ‘void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)’:
dna_words_finder.cc:50:41: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   50 |     baseToCode[lettersToNumbers["ACGT"[i]]] = c;
      |                                 ~~~~~~~~^
dna_words_finder.cc:51:63: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   51 |     if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c;
      |                                                       ~~~~~~~~^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o tantan.o tantan.cc
echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1542) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" | cmp -s version.hh - || echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1542) ' | 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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o SubsetSuffixArraySearch.o SubsetSuffixArraySearch.cc
In file included from tantan.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 SubsetSuffixArraySearch.cc:3:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o Alignment.o Alignment.cc
In file included from last.hh:11,
                 from lastal.cc:5:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o AlignmentWrite.o AlignmentWrite.cc
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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc
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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc
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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o GappedXdropAligner2qual.o GappedXdropAligner2qual.cc
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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc
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 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 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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o LastEvaluer.o LastEvaluer.cc
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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp
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;
      |              ^~~~~~
In file included from Alignment.hh:10:
In member function ‘size_t cbrc::SegmentPair::end2() const’,
    inlined from ‘void alignGapless1(LastAligner&, cbrc::SegmentPairPot&, const cbrc::MultiSequence&, const SeqData&, const Dispatcher&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, const cbrc::SubsetSuffixArray&, const cbrc::uchar*, unsigned int)’ at lastal.cc:658:21:
SegmentPair.hh:30:41: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized]
   30 |   size_t end2() const { return start2 + size; }  // end in sequence 2
      |                                         ^~~~
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: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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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_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:101:29: note:   by ‘Njn::DynProgProbLim::copy’
  101 |         virtual inline void copy (
      |                             ^~~~
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:101:29: note:   by ‘Njn::DynProgProbLim::copy’
  101 |         virtual inline void copy (
      |                             ^~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -I. -c -o lastdb.o lastdb.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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -mssse3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-merge-batches-ssse3 last-merge-batches.o
In file included from last.hh:11,
                 from lastdb.cc:6:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int, int)’:
lastdb.cc:356:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual]
  356 |       std::cout.write((char *)m.qualityReader() + b, e - b);
      |                       ^~~~~~~~~~~~~~~~~~~~~~~~~
last-pair-probs.cc: In function ‘Alignment parseMaf(const char* const*, const char* const*, char, double, const std::set<std::__cxx11::basic_string<char> >&)’:
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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -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-1542/src'
make[2]: Leaving directory '/build/reproducible-path/last-align-1542'
	make -j10 "INSTALL=install --strip-program=true" all SFX=-sse3 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -msse3" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3"
make[2]: Entering directory '/build/reproducible-path/last-align-1542'
make[3]: Entering directory '/build/reproducible-path/last-align-1542/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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o TantanMasker.o TantanMasker.cc
In file included from SubsetSuffixArraySort.cc:6:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
In file included from SubsetSuffixArray.cc:3:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o cbrc_linalg.o cbrc_linalg.cc
dna_words_finder.cc: In member function ‘void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)’:
dna_words_finder.cc:50:41: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   50 |     baseToCode[lettersToNumbers["ACGT"[i]]] = c;
      |                                 ~~~~~~~~^
dna_words_finder.cc:51:63: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   51 |     if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c;
      |                                                       ~~~~~~~~^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o tantan.o tantan.cc
echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1542) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" | cmp -s version.hh - || echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1542) ' | 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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o SubsetSuffixArraySearch.o SubsetSuffixArraySearch.cc
In file included from tantan.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 SubsetSuffixArraySearch.cc:3:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o Alignment.o Alignment.cc
In file included from last.hh:11,
                 from lastal.cc:5:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o AlignmentWrite.o AlignmentWrite.cc
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() {
      |                                ^
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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc
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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o GappedXdropAligner2qual.o GappedXdropAligner2qual.cc
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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc
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 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 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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o mcf_alignment_path_adder.o mcf_alignment_path_adder.cc
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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/sls_alp.o alp/sls_alp.cpp
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;
      |              ^~~~~~
In file included from Alignment.hh:10:
In member function ‘size_t cbrc::SegmentPair::end2() const’,
    inlined from ‘void alignGapless1(LastAligner&, cbrc::SegmentPairPot&, const cbrc::MultiSequence&, const SeqData&, const Dispatcher&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, const cbrc::SubsetSuffixArray&, const cbrc::uchar*, unsigned int)’ at lastal.cc:658:21:
SegmentPair.hh:30:41: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized]
   30 |   size_t end2() const { return start2 + size; }  // end in sequence 2
      |                                         ^~~~
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: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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -c -o alp/njn_random.o alp/njn_random.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: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:101:29: note:   by ‘Njn::DynProgProbLim::copy’
  101 |         virtual inline void copy (
      |                             ^~~~
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:101:29: note:   by ‘Njn::DynProgProbLim::copy’
  101 |         virtual inline void copy (
      |                             ^~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -I. -c -o lastdb.o lastdb.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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -msse3 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-merge-batches-sse3 last-merge-batches.o
In file included from last.hh:11,
                 from lastdb.cc:6:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int, int)’:
lastdb.cc:356:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual]
  356 |       std::cout.write((char *)m.qualityReader() + b, e - b);
      |                       ^~~~~~~~~~~~~~~~~~~~~~~~~
last-pair-probs.cc: In function ‘Alignment parseMaf(const char* const*, const char* const*, char, double, const std::set<std::__cxx11::basic_string<char> >&)’:
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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -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-1542/src'
make[2]: Leaving directory '/build/reproducible-path/last-align-1542'
	make -j10 "INSTALL=install --strip-program=true" all SFX=-sse2 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -msse2" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2"
make[2]: Entering directory '/build/reproducible-path/last-align-1542'
make[3]: Entering directory '/build/reproducible-path/last-align-1542/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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o TantanMasker.o TantanMasker.cc
In file included from SubsetSuffixArraySort.cc:6:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
In file included from SubsetSuffixArray.cc:3:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o cbrc_linalg.o cbrc_linalg.cc
dna_words_finder.cc: In member function ‘void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)’:
dna_words_finder.cc:50:41: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   50 |     baseToCode[lettersToNumbers["ACGT"[i]]] = c;
      |                                 ~~~~~~~~^
dna_words_finder.cc:51:63: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   51 |     if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c;
      |                                                       ~~~~~~~~^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o tantan.o tantan.cc
echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1542) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" | cmp -s version.hh - || echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1542) ' | 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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o SubsetSuffixArraySearch.o SubsetSuffixArraySearch.cc
In file included from tantan.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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o LastalArguments.o LastalArguments.cc
In file included from SubsetSuffixArraySearch.cc:3:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o Alignment.o Alignment.cc
In file included from last.hh:11,
                 from lastal.cc:5:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o AlignmentPot.o AlignmentPot.cc
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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc
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() {
      |                                ^
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 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 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 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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o LastEvaluer.o LastEvaluer.cc
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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp
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;
      |              ^~~~~~
In file included from Alignment.hh:10:
In member function ‘size_t cbrc::SegmentPair::end2() const’,
    inlined from ‘void alignGapless1(LastAligner&, cbrc::SegmentPairPot&, const cbrc::MultiSequence&, const SeqData&, const Dispatcher&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, const cbrc::SubsetSuffixArray&, const cbrc::uchar*, unsigned int)’ at lastal.cc:658:21:
SegmentPair.hh:30:41: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized]
   30 |   size_t end2() const { return start2 + size; }  // end in sequence 2
      |                                         ^~~~
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: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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -c -o alp/njn_ioutil.o alp/njn_ioutil.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: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:101:29: note:   by ‘Njn::DynProgProbLim::copy’
  101 |         virtual inline void copy (
      |                             ^~~~
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:101:29: note:   by ‘Njn::DynProgProbLim::copy’
  101 |         virtual inline void copy (
      |                             ^~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -I. -c -o lastdb.o lastdb.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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-merge-batches-sse2 last-merge-batches.o
In file included from last.hh:11,
                 from lastdb.cc:6:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int, int)’:
lastdb.cc:356:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual]
  356 |       std::cout.write((char *)m.qualityReader() + b, e - b);
      |                       ^~~~~~~~~~~~~~~~~~~~~~~~~
last-pair-probs.cc: In function ‘Alignment parseMaf(const char* const*, const char* const*, char, double, const std::set<std::__cxx11::basic_string<char> >&)’:
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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -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-1542/src'
make[2]: Leaving directory '/build/reproducible-path/last-align-1542'
	make -j10 "INSTALL=install --strip-program=true" all SFX=-sse "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -msse" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse"
make[2]: Entering directory '/build/reproducible-path/last-align-1542'
make[3]: Entering directory '/build/reproducible-path/last-align-1542/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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -I. -c -o TantanMasker.o TantanMasker.cc
In file included from SubsetSuffixArraySort.cc:6:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
In file included from SubsetSuffixArray.cc:3:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -I. -c -o mcf_substitution_matrix_stats.o mcf_substitution_matrix_stats.cc
dna_words_finder.cc: In member function ‘void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)’:
dna_words_finder.cc:50:41: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   50 |     baseToCode[lettersToNumbers["ACGT"[i]]] = c;
      |                                 ~~~~~~~~^
dna_words_finder.cc:51:63: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   51 |     if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c;
      |                                                       ~~~~~~~~^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -I. -c -o tantan.o tantan.cc
echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1542) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" | cmp -s version.hh - || echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1542) ' | 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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -I. -c -o SubsetSuffixArraySearch.o SubsetSuffixArraySearch.cc
In file included from SubsetSuffixArraySearch.cc:3:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -I. -c -o LastalArguments.o LastalArguments.cc
In file included from tantan.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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -I. -c -o AlignmentPot.o AlignmentPot.cc
In file included from last.hh:11,
                 from lastal.cc:5:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -I. -c -o AlignmentWrite.o AlignmentWrite.cc
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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc
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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc
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 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 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 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 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 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() {
      |                                ^
Alignment.cc: In member function ‘void cbrc::Alignment::extend(std::vector<cbrc::SegmentPair>&, std::vector<char>&, cbrc::Aligners&, bool, bool, mcf::BigSeq, const cbrc::uchar*, size_t, size_t, bool, int, const int (*)[66], int, int, const double* const*, double, int, const mcf::GapCosts&, size_t, const int (*)[66], const cbrc::TwoQualityScoreMatrix&, const cbrc::uchar*, const cbrc::uchar*, const cbrc::Alphabet&, cbrc::AlignmentExtras&, double, int)’:
Alignment.cc:425:33: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized]
  425 |       centroid.addExpectedCounts(start2, isForward, probMat, gap, alph.size,
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  426 |                                  subsCounts, tranCounts);
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~
Alignment.cc:281:11: note: ‘tranCounts’ was declared here
  281 |   double *tranCounts;
      |           ^~~~~~~~~~
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -I. -c -o GreedyXdropAligner.o GreedyXdropAligner.cc
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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp
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;
      |              ^~~~~~
In file included from Alignment.hh:10:
In member function ‘size_t cbrc::SegmentPair::end2() const’,
    inlined from ‘void alignGapless1(LastAligner&, cbrc::SegmentPairPot&, const cbrc::MultiSequence&, const SeqData&, const Dispatcher&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, const cbrc::SubsetSuffixArray&, const cbrc::uchar*, unsigned int)’ at lastal.cc:658:21:
SegmentPair.hh:30:41: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized]
   30 |   size_t end2() const { return start2 + size; }  // end in sequence 2
      |                                         ^~~~
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: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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -c -o alp/njn_random.o alp/njn_random.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: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:101:29: note:   by ‘Njn::DynProgProbLim::copy’
  101 |         virtual inline void copy (
      |                             ^~~~
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:101:29: note:   by ‘Njn::DynProgProbLim::copy’
  101 |         virtual inline void copy (
      |                             ^~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -I. -c -o lastdb.o lastdb.cc
In file included from last.hh:11,
                 from lastdb.cc:6:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -msse -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-merge-batches-sse last-merge-batches.o
lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int, int)’:
lastdb.cc:356:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual]
  356 |       std::cout.write((char *)m.qualityReader() + b, e - b);
      |                       ^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split-sse 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
last-pair-probs.cc: In function ‘Alignment parseMaf(const char* const*, const char* const*, char, double, const std::set<std::__cxx11::basic_string<char> >&)’:
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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-pair-probs-sse 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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastdb-sse 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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastal-sse 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-1542/src'
make[2]: Leaving directory '/build/reproducible-path/last-align-1542'
dh_auto_build -- all SFX=-plain CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3"
	make -j10 "INSTALL=install --strip-program=true" all SFX=-plain "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542'
make[3]: Entering directory '/build/reproducible-path/last-align-1542/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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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
In file included from SubsetSuffixArraySort.cc:6:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
In file included from SubsetSuffixArray.cc:3:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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
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++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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: 1542) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" | cmp -s version.hh - || echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1542) ' | 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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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
In file included from tantan.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 SubsetSuffixArraySearch.cc:3:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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
mcf_simd.hh: In function ‘double mcf::simdHorizontalAddDbl(SimdDbl)’:
mcf_simd.hh:172:5: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi]
  172 |   z = _mm_add_pd(z, _mm256_extractf128_pd(x, 1));
      |     ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o lastal.o lastal.cc
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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
In file included from last.hh:11,
                 from lastal.cc:5:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o GappedXdropAlignerDna.o GappedXdropAlignerDna.cc
In file included from 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() {
      |                                ^
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() {
      |                                ^
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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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
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 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() {
      |                                ^
mcf_simd.hh: In function ‘int mcf::simdHorizontalMax(SimdInt)’:
mcf_simd.hh:156:5: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi]
  156 |   z = _mm_max_epi32(z, _mm256_extracti128_si256(x, 1));
      |     ^
mcf_simd.hh: In function ‘int mcf::simdHorizontalMin1(SimdInt)’:
mcf_simd.hh:164:5: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi]
  164 |   z = _mm_min_epu8(z, _mm256_extracti128_si256(x, 1));
      |     ^
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 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() {
      |                                ^
mcf_simd.hh: In function ‘int mcf::simdHorizontalMax(SimdInt)’:
mcf_simd.hh:156:5: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi]
  156 |   z = _mm_max_epi32(z, _mm256_extracti128_si256(x, 1));
      |     ^
Alignment.cc: In member function ‘void cbrc::Alignment::extend(std::vector<cbrc::SegmentPair>&, std::vector<char>&, cbrc::Aligners&, bool, bool, mcf::BigSeq, const cbrc::uchar*, size_t, size_t, bool, int, const int (*)[66], int, int, const double* const*, double, int, const mcf::GapCosts&, size_t, const int (*)[66], const cbrc::TwoQualityScoreMatrix&, const cbrc::uchar*, const cbrc::uchar*, const cbrc::Alphabet&, cbrc::AlignmentExtras&, double, int)’:
Alignment.cc:425:33: warning: ‘tranCounts’ may be used uninitialized [-Wmaybe-uninitialized]
  425 |       centroid.addExpectedCounts(start2, isForward, probMat, gap, alph.size,
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  426 |                                  subsCounts, tranCounts);
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~
Alignment.cc:281:11: note: ‘tranCounts’ was declared here
  281 |   double *tranCounts;
      |           ^~~~~~~~~~
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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
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() {
      |                                ^
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_alp.o alp/sls_alp.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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
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;
      |              ^~~~~~
In file included from Alignment.hh:10:
In member function ‘size_t cbrc::SegmentPair::end2() const’,
    inlined from ‘void alignGapless1(LastAligner&, cbrc::SegmentPairPot&, const cbrc::MultiSequence&, const SeqData&, const Dispatcher&, cbrc::DiagonalTable&, GaplessAlignmentCounts&, const cbrc::SubsetSuffixArray&, const cbrc::uchar*, unsigned int)’ at lastal.cc:658:21:
SegmentPair.hh:30:41: warning: ‘fwdLen’ may be used uninitialized [-Wmaybe-uninitialized]
   30 |   size_t end2() const { return start2 + size; }  // end in sequence 2
      |                                         ^~~~
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: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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/njn_localmaxstatutil.o alp/njn_localmaxstatutil.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/njn_dynprogproblim.o alp/njn_dynprogproblim.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/njn_ioutil.o alp/njn_ioutil.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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
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:101:29: note:   by ‘Njn::DynProgProbLim::copy’
  101 |         virtual inline void copy (
      |                             ^~~~
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:101:29: note:   by ‘Njn::DynProgProbLim::copy’
  101 |         virtual inline void copy (
      |                             ^~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_falp_alignment_evaluer.o alp/sls_falp_alignment_evaluer.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -I. -c -o split/last-split-main.o split/last-split-main.cc
g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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
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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-merge-batches-plain last-merge-batches.o
In file included from last.hh:11,
                 from lastdb.cc:6:
SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’:
SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow]
   64 |     |    (size_t)c[i*5 + 4] << 32;
      |          ~~~~~~~~~~~~~~~~~~~^~~~~
lastdb.cc: In function ‘void dump1(const std::string&, const cbrc::uchar*, size_t, bool, int, int)’:
lastdb.cc:356:23: warning: cast from type ‘const cbrc::uchar*’ {aka ‘const unsigned char*’} to type ‘char*’ casts away qualifiers [-Wcast-qual]
  356 |       std::cout.write((char *)m.qualityReader() + b, e - b);
      |                       ^~~~~~~~~~~~~~~~~~~~~~~~~
last-pair-probs.cc: In function ‘Alignment parseMaf(const char* const*, const char* const*, char, double, const std::set<std::__cxx11::basic_string<char> >&)’:
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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542=. -fstack-protector-strong -Wformat -Werror=format-security -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-1542/src'
make[2]: Leaving directory '/build/reproducible-path/last-align-1542'
make[1]: Leaving directory '/build/reproducible-path/last-align-1542'
   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-1542'
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-1542/debian/last-align/usr/bin
cd /build/reproducible-path/last-align-1542/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-1542'
   dh_installdocs
   dh_installchangelogs
   dh_installexamples
   debian/rules override_dh_installman
make[1]: Entering directory '/build/reproducible-path/last-align-1542'
dh_installman
help2man --no-info --version-string="1542" \
	 --name='make a dotplot, a.k.a. Oxford Grid, of alignments in LAST tabular format' \
         /build/reproducible-path/last-align-1542/bin/last-dotplot > /build/reproducible-path/last-align-1542/debian/last-align/usr/share/man/man1/last-dotplot.1
help2man --no-info --version-string="1542" \
         --name="genome-scale comparison of biological sequences" \
         --help-option="-h" \
                 /build/reproducible-path/last-align-1542/debian/last-align/usr/bin/lastal > /build/reproducible-path/last-align-1542/debian/last-align/usr/share/man/man1/lastal.1
# help2man output needs manual postprocessing - see debian/mans
#help2man --no-info --version-string="1542" \
#         --name="genome-scale comparison of biological sequences" \
#         --help-option="-h" \
        #         /build/reproducible-path/last-align-1542/debian/last-align/usr/bin/lastdb > /build/reproducible-path/last-align-1542/debian/last-align/usr/share/man/man1/lastdb.1
help2man --no-info --version-string="1542" \
                 --name="Sort MAF-format alignments by sequence name" \
                 /build/reproducible-path/last-align-1542/bin/maf-sort > /build/reproducible-path/last-align-1542/debian/last-align/usr/share/man/man1/maf-sort.1
help2man --no-info --version-string="1542" \
                 --name="changes the order of the sequences in MAF-format alignments" \
                 /build/reproducible-path/last-align-1542/bin/maf-swap > /build/reproducible-path/last-align-1542/debian/last-align/usr/share/man/man1/maf-swap.1
# help2man output needs manual postprocessing - see debian/mans
#help2man --no-info --version-string="1542" \
        #         --name="Add extra column with mapping probabilities" \
        #         /build/reproducible-path/last-align-1542/bin/last-map-probs > /build/reproducible-path/last-align-1542/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="1542" \
        #         --name="Read files of lastal output, merge corresponding batches, and write them." \
        #         /build/reproducible-path/last-align-1542/bin/last-merge-batches > /build/reproducible-path/last-align-1542/debian/last-align/usr/share/man/man1/last-merge-batches.1
#         # These bin were droped
#help2man --no-info --version-string="1542" \
        #         --name="Clean up MAF-format alignments" \
        #         /build/reproducible-path/last-align-1542/bin/last-reduce-alignments > /build/reproducible-path/last-align-1542/debian/last-align/usr/share/man/man1/last-reduce-alignments.1
#help2man --no-info --version-string="1542" \
        #         --name='Remove MAF-format alignments which are "dominated" by others' \
        #         /build/reproducible-path/last-align-1542/bin/last-remove-dominated > /build/reproducible-path/last-align-1542/debian/last-align/usr/share/man/man1/last-remove-dominated.1
help2man --no-info --version-string="1542" \
                 --name='Estimates "split" or "spliced" alignments.' \
                 /build/reproducible-path/last-align-1542/debian/last-align/usr/bin/last-split > /build/reproducible-path/last-align-1542/debian/last-align/usr/share/man/man1/last-split.1
help2man --no-info --version-string="1542" \
                 --name="Join two or more sets of MAF-format multiple alignments" \
                 /build/reproducible-path/last-align-1542/bin/maf-join > /build/reproducible-path/last-align-1542/debian/last-align/usr/share/man/man1/maf-join.1
help2man --no-info --version-string="1542" \
	 --help-option="-h" \
                 /build/reproducible-path/last-align-1542/bin/maf-cut > /build/reproducible-path/last-align-1542/debian/last-align/usr/share/man/man1/maf-cut.1
help2man --no-info --version-string="1542" \
                 --name="Convert MAF-format alignments to tabular format" \
                 /build/reproducible-path/last-align-1542/bin/maf-convert > /build/reproducible-path/last-align-1542/debian/last-align/usr/share/man/man1/maf-convert.1
help2man --no-info --version-string="1542" \
                 --name="Read 2 fastq files, and write them interleaved" \
                 /build/reproducible-path/last-align-1542/bin/fastq-interleave > /build/reproducible-path/last-align-1542/debian/last-align/usr/share/man/man1/fastq-interleave.1
help2man --no-info --version-string="1542" \
                 --name="Read files of lastal output, merge corresponding batches, and write them" \
                 /build/reproducible-path/last-align-1542/debian/last-align/usr/bin/last-merge-batches > /build/reproducible-path/last-align-1542/debian/last-align/usr/share/man/man1/last-merge-batches.1
# help2man output needs manual postprocessing - see debian/mans
#help2man --no-info --version-string="1542" \
        #         --name="Read alignments of paired DNA reads to a genome, and do estimations" \
        #         /build/reproducible-path/last-align-1542/debian/last-align/usr/bin/last-pair-probs > /build/reproducible-path/last-align-1542/debian/last-align/usr/share/man/man1/last-pair-probs.1
help2man --no-info --version-string="1542" \
                 --name="Get alignments that have a segment with score >= threshold, with gentle masking of lowercase letters" \
                 /build/reproducible-path/last-align-1542/bin/last-postmask > /build/reproducible-path/last-align-1542/debian/last-align/usr/share/man/man1/last-postmask.1
help2man --no-info --version-string="1542" \
                 --name="Try to find suitable score parameters for aligning the given sequences" \
                 /build/reproducible-path/last-align-1542/bin/last-train > /build/reproducible-path/last-align-1542/debian/last-align/usr/share/man/man1/last-train.1
help2man --no-info --version-string="1542" \
         --name="Keep the first of identical sequences" \
         --help-option="-h" \
                 /build/reproducible-path/last-align-1542/debian/last-align/usr/bin/fasta-nr > /build/reproducible-path/last-align-1542/debian/last-align/usr/share/man/man1/fasta-nr.1
make[1]: Leaving directory '/build/reproducible-path/last-align-1542'
   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-1542'
dh_gencontrol -- -VBuilt-Using="simde (= 0.8.2-2), "
make[1]: Leaving directory '/build/reproducible-path/last-align-1542'
   dh_md5sums
   dh_builddeb
dpkg-deb: building package 'last-align-dbgsym' in '../last-align-dbgsym_1542-1_i386.deb'.
dpkg-deb: building package 'last-align' in '../last-align_1542-1_i386.deb'.
 dpkg-genbuildinfo --build=binary -O../last-align_1542-1_i386.buildinfo
 dpkg-genchanges --build=binary -O../last-align_1542-1_i386.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: user script /srv/workspace/pbuilder/23349/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/23349/tmp/hooks/B01_cleanup finished
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/23349 and its subdirectories
I: Current time: Tue Feb 25 13:35:47 +14 2025
I: pbuilder-time-stamp: 1740440147